Question: PFAM domains for all protein Isoforms from same protein
0
gravatar for Michi
3.6 years ago by
Michi930
Barcelona
Michi930 wrote:

Hi

Is it possible to get PFAM domain mapping for different isoforms of the same protein?

At Uniprot for example they report all positional data relative to their canonical isoform

At PFAM, I found this proteome-file: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam27.0/proteomes/9606.tsv.gz. This file nevertheless seems to link the Uniprot identifiers - without specifying any isoform

So I am a bit stuck and don't know how to proceed. Or maybe I misunderstood something(s)?

Thanks for any additional info/help

 

 

 

ADD COMMENTlink modified 3.6 years ago by cdsouthan1.8k • written 3.6 years ago by Michi930
0
gravatar for cdsouthan
3.6 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

Not from UniProt because I don't think the isoforms are run through Pfam.  Runinig each of them them yourself would be hard work and  I'm not sure how useful that would be.  Isoforms with a missing exon (i.e. most of them) would just gap the global allignments that are compiled from the cannonical (all exon) forms
 

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by cdsouthan1.8k

So what would you do if you'd like to map the domains from the canonical transcript to the isoforms?

ADD REPLYlink written 3.6 years ago by Michi930

If you could expand on the biological question you are trying to answer I might be able to help more.  On a a coorditnates basis sure- you can map domain markup across to residue positions in isoforms but this is not bilogically valid. If you delete a sizable exon chunk out of a Pfam domain (or any other InterPro signature in fact)  that part of the protein is probably not going to fold properly - regardless of domain boundaries.

ADD REPLYlink written 3.6 years ago by cdsouthan1.8k
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