Question: Grouping protein domains into categories?
0
gravatar for exin
8 weeks ago by
exin50
Australia
exin50 wrote:

I want to compare the domain composition of a few of my cell samples.

After mapping peptide sequences on Pfam, I have thousands of domain hits across my dataset. Comparing across my samples hardly makes sense.

Are there any references / databases for domain categories? Similar to the clans/ superfamilies in Pfam but something broader, e.g. kinases, zinc fingers, ankyrins... ?

pfam domain analysis • 121 views
ADD COMMENTlink modified 8 weeks ago by jgreener100 • written 8 weeks ago by exin50
2

To my knowledge, no - I don't think it gets much broader than "Zinc-finger containing protein" if you're specifically interested in the domains themselves.

The next level up would be pathway ontologies through Kegg/GO etc, but its not entirely the same thing.

ADD REPLYlink written 8 weeks ago by jrj.healey13k

Thank you!!!
So no way to categorise them other than manually going through the domain names? - Currently they're like zf-C3HC4, zf-C2H2, zf-RING2....

ADD REPLYlink written 8 weeks ago by exin50

AFAIK, no; but I won’t claim to be an expert here.

If your dataset is reasonably well organised/curated you may be able to get some of the way with assorted regex magic, but that’s rarely the case with annotations.

ADD REPLYlink written 8 weeks ago by jrj.healey13k
1
gravatar for jgreener
8 weeks ago by
jgreener100
United Kingdom
jgreener100 wrote:

There are a few resources for organising protein domains:

  • CATH sorts domains by structure into class, architecture, topology and homologous superfamily.
  • ECOD sorts domains by evolutionary relationship into architecture, possible homology, homology, topology and family level.
  • SCOP and its later incarnations, SCOP2 and SCOPe, also sort domains by structure.

I would recommend the first ECOD paper as a good read for how to organise protein domains and how these resources relate to each other.

Hopefully one of those resources will help you make sense of your domains.

ADD COMMENTlink written 8 weeks ago by jgreener100

Great!! Thank you for these!!

ADD REPLYlink written 8 weeks ago by exin50
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