How Can I Determine Whether Two Proteins Have The Same Multi Domain Architecture?

Question

[Doug]

How can I determine whether two proteins have the same multi domain architecture? For example, if I do a BLAST search for proteins with high alignment scores, what can I do with the resulting list of proteins to determine which of them have, and which of them do not have, the same multi domain architecture?

[Michael Schubert]

Have you tried searching for the domains (InterPro, NCBI CDD) and then just compare if they have the same?

Answer 1

[Mary]

Use SMART. You can pull up your protein's domains with the "sequence analysis" part, and lists of those that look similar "Display orthology and other data: Display all proteins with similar domain ORGANISATION or COMPOSITION". You can also blast this vs other proteins in SMART.

There's also a place you can see MSAs of the proteins that have a domain your protein shares "Family Alignment".

And you can use one of the other sides of the main page to choose the domains you want to see in lists "architecture analysis".

It's not exactly what you describe, but if you want lists of similar domain structure in proteins this can do it.

http://smart.embl.de/

[Larry_Parnell]

Sometimes what is also important in this analysis is the size of the inter-domain region(s), as well as the size of the COOH- and NH3-tails.

Answer 2

[Hari]

You can use SMART or even PFAM,here is an example query http://pfam.sanger.ac.uk//family/PF00621#tabview=tab1 if you click on domain organisation it will give you the domain combinations for a particular protein.

Answer 3

[Larry_Parnell]

I like the above answers, both +1. The approach can be called “Pfam strings,” where the order and spacing of protein domains is used to classify proteins and describe function. See Geer et al. 2002 Genome Res 12:1619 and my comment under Mary's response.