Hello, Shikha,

The best way to process such large amount of sequences would be using the Workflow Designer. Do the following:
1. Click "Run or create workflow" on the Start Page.
2. Find "Search sequences with profile HMM" on the samples tab at the left side of the page and double click on it.
3. On the "Input sequence(s)" page set all sequences you want to process searching at (about 4k, as I have understood).
4. Click "Next" and set HMM profiles and, optionally, some additional parameters.
5. Click Run.

Is this what you was looking for?

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.