Determine identify of protein domains in a fusion protein

Question

[elkington]

I have a list of fusion proteins that contain domains similar to known enzymes; however, other portions of the fusion proteins are not similar to other known domains. I've used BLAST, HMMs, IPRscan, and NCBI Conserved Domain Search.

Does anyone have any ideas to try to find domains with some similarity to portions of the fusion proteins?

Answer 1

[Jean-Karim Heriche]

Have you tried Pfam ? You can input a sequence and get matching Pfam domains. There is also a batch search mode.