Question: protein classification based on functional regions
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gravatar for ar19yf60
2.2 years ago by
ar19yf6010
ar19yf6010 wrote:

Is anything out there in terms of classifying proteins based on functional regions?

For example, suppose you have 2 very similar sequences A and B, perhaps in the same protein family, and an unknown sequence C. To determine which of A and B the unknown protein C is, you could look beyond the overall alignment to the functional regions.

ADD COMMENTlink modified 2.2 years ago by Jean-Karim Heriche17k • written 2.2 years ago by ar19yf6010
0
gravatar for Jean-Karim Heriche
2.2 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche17k wrote:

PFAM, InterPro and CATH

ADD COMMENTlink written 2.2 years ago by Jean-Karim Heriche17k

Hi Jean-Karim,

It looks like PFAM and Interpro both classify proteins into families making use of functional regions, without distinguishing between proteins within the same family. CATH displays families as well as the found domains.

I'm looking for a greater level of specificity achieved by using protein attributes. For example, uniprot has a 'sites' section which lists feature keys (like active sites, element binding sites, etc) in addition to their sequence positions.

Can you not differentiate between proteins of the same family by looking at conservation across these sequence positions? I'm looking for a tool which has done this.

I'm a student looking for a way to contribute in the area of annotation, your opinion is greatly appreciated.

Thanks

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by ar19yf6010

I am not sure I get which level of specificity you need. If UniProt has the info you need, why not use it ? UniProt integrates information from Interpro and PFAM among others. If you want to distinguish between members of a protein family such as differentiating between paralogs, you may need to do a phylogenetic analysis.

ADD REPLYlink written 2.2 years ago by Jean-Karim Heriche17k
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