Structure-based alignments and sequence correlators

 
"structure-based" means that in regions where the structures 
superimpose, each residue is aligned with its closest mate 
in the superimposed structure. 

Scrolling down below this alignment you will find a "sequence correlator"
for answering questions like "what residue in yeast corresponds to
P124 of Rb capsulatus?". It is a vertical sequence alignment with 
residue number as well as type for each residue. In the case of yeast
where appropriate two numberings are given, one with the presequence 
as in Hunte's structures, and one counting from the first residue of 
the mature protein. 
excerpt of cyt b:
      Bos chick Sacchce Rb.s Parac Rb.capsul
 120  S106  S107  S105  S120  S120  S120  
 121  Y107  Y108  Y106  Y121  Y121  Y121  
 122  T108  L109  R107  K122  K122  K122  
 123  --    --    S108  A123  A123  A123  
 124  --    --    P109  P124  P124  P124  
 125  F109  Y110  R110  R125  R125  R125  
 126  L110  K111  V111  E126  E126  E126  

Cyt. bc1 subunits:

Iron-Sulfur Protein

Cytochrome c1

Cytochrome c1, Helices marked (byt Rb.caps seq wrong)

Cytochrome b

Cytochrome b/b6-IV

Core1&2, MPPa&b

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Links:

Structural Biology Division Home Page

LBNL Physical Biosciences Division

U.C. Berkeley
Return to LBNL homepage.

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Ernest Orlando Lawrence Berkeley National Laboratory
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