Question

Find Proteins Containing A Specific Domain?

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14.5 years ago

Rajarshi Guha ▴ 880

Hi, could somebody point me to a database that will allow me to identify proteins that contain a specific domain (say the PX domain)? I've looked at SMARTS and it seems to do the trick, but I can't see an easy way to download the results.

protein database • 6.9k views

ADD COMMENT • link updated 14.5 years ago by Neilfws 49k • written 14.5 years ago by Rajarshi Guha ▴ 880

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Thanks for the pointers everybody. Uniprot seems quite handy and good to see that I'll be able to do this via Bioconductor and BioMart

ADD REPLY • link 14.5 years ago by Rajarshi Guha ▴ 880

score 6 · Answer 1 · 2010-06-08

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14.5 years ago

Khader Shameer 18k

I would recommend Pfam or Interpro than SMART for protein domain related analysis.

My personal favorite is Pfam : Here is link to the Pfam page for PX domain Pfam reports that 2400 proteins have PX domains. You can download the sequences here

ADD COMMENT • link 14.5 years ago by Khader Shameer 18k

score 4 · Answer 2 · 2010-06-08

4

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14.5 years ago

Andrew Su 4.9k

I'd use BioMart. For example, once you determine that PX domain has an interpro ID of IPR001683, it's pretty easy to set up the query. You can see how I set it up using this link: http://bit.ly/aM1Ypw

ADD COMMENT • link 14.5 years ago by Andrew Su 4.9k

score 2 · Answer 3 · 2010-06-08

Hi,

It seems that swissprot can be of help here. I did a quick search using 'cytochrome c' and followed the link in the 'domain' section down there to EMBL-EBI and here is what I get:

Domain results

The page provides me with a list of other proteins containing this domain.

Does this help you? What else could you need?

Cheers

score 2 · Answer 4 · 2010-06-09

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14.5 years ago

Neilfws 49k

All of the suggestions so far are good. My suggestion is to use UniProt.

Simply type "PX" in the query field at the top of the page. On the results page, you'll see a link that begins: "Restrict term "px" to domain (235)...". Click this and you'll see how to formulate this query in the search form - "domain:px".

The "Download" link, top right of page, offers download in multiple formats: sequences, ID list, XML, delimited, spreadsheet and so on.

ADD COMMENT • link 14.5 years ago by Neilfws 49k

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Neil : AFAIK, Pfam is using sequence from Uniprot running hmmpfam on sequence and assign domains to sequence. But here it's only 235 domains reported in Uniprot, but 2400 (from full sequence in Pfam) domains reported in Pfam. Any idea why such a huge difference between them ?

ADD REPLY • link 14.5 years ago by Khader Shameer 18k

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None at all! A more stringent filter at UniProt perhaps? Will have to look into that.

ADD REPLY • link 14.5 years ago by Neilfws 49k

score 1 · Answer 5 · 2010-06-08

At the NCBI searching for PX with eutilities returns 118 records:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=cdd&term=PX

from one of those ID (e.g. 154983 ) you can retrieve all the related proteins with ELink:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=cdd&db=protein&id=154983

here, the first protein is http://www.ncbi.nlm.nih.gov/protein/241260146