Functional Annotation Of Domains...

Question

[pixie@bioinfo]

We are trying to assign function to a domain of unknown function (DUF). We have already assigned folds to it.

I have checked some databases which gives domain specific interaction information of proteins. Unfortunately, I didn't find info regarding my domain.

I searched in String database by pasting the domain sequence to get some interaction...but it is showing the interaction info of the entire protein rather than the specific domain..

It will be great if I could get some ideas regarding what else can we do for functional annotation of domain.

Answer 1

[Khader Shameer]

If you have a Pfam / Interpro ID for your domain, you may use DOMINE to identify potential interactions of your domain. Please note that DOMINE is database that provide interaction information at the level of domain-domain interactions.

Another option is to use remote homology detection approaches like CASCADE-PSI-BLAST or indirect sequence search method based approach like Prediction of Unassigned REgions (PURE).

Disclaimer: I am one of the author of PURE.

[pixie@bioinfo]

thanks so much...hope we can proceed with these tools...

[pixie@bioinfo]

Yes, I do have a Pfam id...thanks so much...hope we can proceed with these tools..

[pixie@bioinfo]

Yes, I do have a Pfam id...thanks so much...hope I can proceed with these tools.

[pixie@bioinfo]

One query regarding PURE...my domain sequence length is 53 residues...so will it be better if I give the entire protein sequence?

[pixie@bioinfo]

One query regarding PURE...my domain sequence length is 53 residues...so will it be better if I give the entire protein sequence?

I gave the domain sequence (53 residues) and the results were mailed to me. When I clicked the urls, its giving "Not Found" error..is it a server issue?

[Khader Shameer]

You may try with full 53 residues. I will ask my lab members to check the Not Found error and update you.

[pixie@bioinfo]

thanx...kindly let me know when its wrking..

[Khader Shameer]

Sorry about the issues with PURE server. It seems the server is recently upgraded with new hardware and some of the soft-links are broken. Will fix this soon and update you.

[Khader Shameer]

Sanchari: Not sure if this is useful at this point. But I thought to share it with you. PURE server is up and running now, you may try your query.

Answer 2

[Larry_Parnell]

I like the domain interaction approach you're taking. I would also use genetics to help in annotation of this DUF. Without knowing the source species you're studying, I cannot be specific. In general, one can check if GWAS SNPs map to the protein or the DUF, or if a QTL for any trait maps to this sequence.

Is the DUF found in other species? If so, check out genetics results in those organisms as described above.

In addition, use mRNA expression data to get an idea of where this gene - and its potential protein-protein interactors are co-expressed. This is a standard way to add legitimacy to your claim of interaction from.

[pixie@bioinfo]

The duf that we are interested in ...is found across species including human....really thanx a lot for these ideas...exploring the genetic aspects might give some hopes..

Answer 3

[Treylathe]

Would SMART help? http://smart.embl.de/

Perhaps the sequence SMART would give you the possible domain and description of function and interactions of the domain.

[pixie@bioinfo]

we have already checked out smart ...but no luck :(......but thanks for ur suggestions..

Answer 4

[Daniel]

if you have the SCOP id(s) of your protein, you can try Scop2go. Scop2go is a database of gene ontology functional annotations at the structural domain level:

http://pdg.cnb.uam.es/scop2go/