how to get protein motif sequence from pfam database?

Question

[Haifeng]

Hi, I downloaded a Pfam database, and in the database, there are different protein domain information. However, how could I know which part is a protein motif from this database? Thanks.

[Haifeng]

Hi, Natasha,

Thank you very much for your reply. It's very helpful for me. Really appreciate.

I thought these sequences are the domain information in a PFam family, is that right?

[natasha.sernova]

Dear Haifeng,

See this post.

A: Find Proteins Containing A Specific Domain?

Domain and motif in PFAM are different.

A: Motif Extraction Using R Package?

You can isolate motifs and domains separately:

A: How To Judge If A Pfam Domain Is A Repeat And The Functional Similarities Of A S

[Haifeng]

Hi, Natasha,

Thank you very much.

should I see the Pfam database with the tag "#=GF TP Motif"? With this tag are motifs, and others are not? Is that right? Thanks.

Best, Haifeng

[GenoMax]

Please use ADD REPLY button when responding to existing posts. Don't use SUBMIT ANSWER unless you are providing a new answer to the original question.

Answer 1

[natasha.sernova]

I was searching PFAM with keyword ‘motif’

The result was the following, I've got a table.

http://pfam.xfam.org/search/keyword?query=motif

The table columns are : accession, ..., Pfam, Seq_info, pdb, GO, Interpro.

How to find a motif-sequence you wanted to have:

Press on accession link – PF-link in the first column

Then press on Alignment link in the first column of a new table.

(You will have the same output from the Secuence button in the upper menu).

Then you will be able to download a FASTA format file containing the full-length sequences for all

sequences in the full alignment - see the bottom line of the page. You will have fasta-file

for all species in PFam with this particular chosen motif in archive.

[Haifeng]

Hi, Natasha,

Thank you very much for your reply. It's very helpful for me. Really appreciate.

I thought these sequences are the domain information in a PFam family, is that right?