Matching to non-LBD components of MCPs

[tslaird]

Hello,

I was attempting to use this database to characterize the ligand binding domains of several MCPs. When running them through with hmmscan, the matches I retrieved were not to the LBD of the MCPs but rather to other segments. I encountered this specifically with clusters 2554 and 2893. I was confused because these sequences (2553 and 2893) have the canonical "MCP signal domain". Do these represent intracellular LBDs?

Thanks,

-Tyler-

[csanchis]

Hi, sorry for the delay.
I'm revising the issue, could you please send me the output of the hmmscan analysis? And if it is okay, could you send me your sequences too?
email: c.sanchisl@upm.es

Thank you very much
Claudia