Conservation, Evolutionary: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,122 edits
→INTREPID: polishing
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,122 edits
Line 123: Line 123:
==Limiting ConSurf Analysis to Proteins of a Single Function==
==Limiting ConSurf Analysis to Proteins of a Single Function==


As explained [[#ConSurf-DB Often Obscures Some Functional Sites|above]], the ConSurf-DB ''Evolutionary Conservation'' scene available in Proteopedia often includes proteins with multiple functions. However, the best way to find all functional sites by conservation analysis is to limit the analysis to proteins with a single function. A procedure for doing this follows. In June, 2009, the ConSurf development team is working on a new version that, once released, will greatly simplify this procedure.
As explained [[#ConSurf-DB Often Obscures Some Functional Sites|above]], the ConSurf-DB ''Evolutionary Conservation'' scene available in Proteopedia often includes proteins with multiple functions. However, the best way to find all functional sites by conservation analysis is to limit the analysis to proteins with a single function. A procedure for doing this follows. In June, 2009, the ConSurf development team is working on a new version that, once released, will enable selection of arbitrary sequences from the PSI-BLAST list.


#Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB).
#Go to [http://consurf.tau.ac.il consurf.tau.ac.il], the ConSurf Server (distinct from ConSurf-DB).
Line 130: Line 130:
#Submit the job.
#Submit the job.
#When the job is completed, under ''Running Messages'', note the number of unique sequences used in the calculation.
#When the job is completed, under ''Running Messages'', note the number of unique sequences used in the calculation.
#Under ''Final Results'', ''Sequences'', click on ''PSI-BLAST output''.
#Under ''Final Results'', ''Sequences'', click on ''Unique Sequences Used''.
#Block the entire list of ''Sequences producing significant alignments'', copy, and paste it into a text editor that enables you to number the lines. See [[#Examining Functions of Proteins in ConSurf-DB's MSA|above]] for instructions on how to number lines. The total number of sequences should be almost identical to the number of unique sequences used in the calculation (noted earlier).
#Looking down the list of sequences from the top, find where the function of the protein first differs from that of the query protein of interest. Note the number of the last sequence with the same function as the query protein. We'll call this the '''max with same function''' number.
#Looking down the list of sequences from the top, find where the function of the protein first differs from that of the query protein of interest. Note the number one line above this first function-different sequence; that is, note the number of the last sequence with the same function as the query protein. We'll call this the '''max with same function''' number.
#Re-run your ConSurf job making only one change. Set the ''Max. Number of Homologues'' to the "max with same function" that you determined in the previous step.
#Re-run your ConSurf job making only one change. Set the ''Max. Number of Homologues'' to the "max with same function" that you determined in the previous step.


Retrieved from "https://proteopedia.org/Conservation,_Evolutionary"