how to search the proline-rich domain from protein sequence

Question

[xiaozhan063]

Hi, everyone.

From a new protein sequence, there was no information to certify the structure of this protein. The first step is describing the properties of this protein. How can I search the pro-rich region (from the sequence, there is a region contain high rate of proline), and how can I certify the specific region (the range) in this protein?

Answer 1

[Denise CS]

You may want to try InterProScan, a software package that allows sequences to be scanned against InterPro's signatures.

[xiaozhan063]

Thanks for your answer! I have tried interproscan before, with the options all selected, and the results showed the aspect of domains and some signatures, there was no predict repeat in my sequence, but from the SMART software, have showed low complexity regions on some acid rich region. How can I certify the specific region(the range)with these acid rich in this protein?

[Denise CS]

SMART is a member of InterPro, so the discrepancy in the results might be due to different versions of the softwares (there can be a lag) or perhaps due to different search algorithms that were used. Not sure if there is anyone here from InterPro who could comment but at any rate I'd suggest you to contact them directly.