Basic Information
The sequence files for each individual subunit are provided as text files under Subunit sequences. Notice that there are several instances of the same fungus with different subunits (a,b, or c). You should be careful to collect the right one. If you have a question about which is the right one, let me know.
In the alignment, you should be able to find S. cereviseae CDC50, Analysis of its sequence by a program call MPex (combined with editing by me) gave:
Number of translocon TM (transmembrane) predicted segments: 2
TM1 (N-terminal) is at 45-67 (23 aa) : VLPLLIFVACIFTPIGIGLIVSA
TM2 (C terminal) is at 334-356 (22aa) : SLGVLYLIVAGLCALFGIIFLV
The sequence from your protein that you submit will be a combination of the amino acids that come before the sequence in your protein corresponding to TM1, a linker consisting of the amino acids AGAGAGA, and the amino acids that come after the sequence in your protein corresponding to TM2. You can see an example of such a combined sequence below (the one I submitted for P. tritici-repentens). Your constructed sequences should be submitted on the following server page:
http://zhanglab.ccmb.med.umich.edu/QUARK/
On submission, you will get a message more or less like this:
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Your submitted sequence is Ptritici Cdc50 (150 residues):
MSRTQQGDTADSITSQDPARDEPKKAKSRRPPNTAFRQQRLKAWQPILTPKTAGAGAGAH
LIKPRSVYLTLKYHHTADMATGNSVITPTSPGITTSPVRLRPLVERAAHEYDHCLERLAY
LVSSFLSLFLKCSLDSQYCMYITSLRRPGV
After your job Q10126 is finished, the result will be sent to plwilliamson@amherst.edu.
The complete predictions will be available on the following webpage for job Q10126:
http://zhanglab.ccmb.med.umich.edu/QUARK/output/Q10126/
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When the job is completed, you will be notified by an email which will also contain a link to the predicted model(s) and other information, and has attached a PDB file of the preferred model.