Exercises BEM2

Reconstructing the anomalous domain order in BEM2

1. Get the sequence of the yeast signaling protein BEM2, a RasGEF / CDC25HD domain containing protein, from here. Put it in SMART (this can also be done at PFAM but for this question we want to use some of the functionality of SMART). It should contain a RasGEFN domain. Click around. why is "RasGEFN" called RasGEFN? Is this also true for BEM2? So why is it anomalous?
2. Click on the RasGEF domain, then click on the identifier after "SMART ACC:". Then click on the first number in the line "There are x RasGEF domains in y proteins in SMART's a database". On the resulting page, click on the button that says "Display proteins". Browse the results. Is the defining property of RasGEFN indeed apparent? What else do you notice about RasGEF containing proteins?
3. Get the sequence of the BEM2 ortholog from the early branching / primitive fungus Rhizopus oryzae: RO3G_03905.fasta (obtained from here). Put the sequence of RO3G_03905 in Conserved Domain Database search and change the expect value to 10. Look at the position in the sequence of the significant but also the insigificant hits. how do we now infer that the anomalous domain organisation of yeast BEM2 came into existence? (i.e. sketch a reconstruction of what happened, and specifically how the Rhizopus sequence would suggest a different mutation as inferred from yeast BEM2). Finally consider if/how your proposed scenario fits with the "proteome evolutionary operators which were introduced in the lecture"