Protter output not matching UniProt topology

[Sophie Williams]

Hi,

 

I have recently tried using the interactive web application Protter tool for UniProt identifier (BAMA_ECOLI). Unfortunately the Protter schematic domains do not match up to the UniProt data when the topology settings are kept to automatic or UniProt is selected (I am getting some extracellular loops appearing in the periplasm). Is there any way to fix this?

 

Thank you for your help (and super cool tool)!

 

Thanks,

Sophie