Changes between Version 32 and Version 33 of HIVspikes

Timestamp:

Oct 16, 2009, 8:16:32 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -162 +162 @@
 For example, open gp120 family sequence alignment from PFAM (PF00516seed.slx, attached).  1gc1 does not automatically associate, but use Multalign Viewer "Structure... Associations," associate chain G with best match.  Unfortunately that takes a while to compare against 24 sequences (1-2 seconds each?), so other alternatives are just to tell it to associate with the ENV-HV1B1 sequence, or open a session with the alignment already associated. There is also a tree (PF00516seed.nhx) that could be loaded
 
-(This part also works with the HIV gp120 norecomb protein alignment, which more evenly samples multiple HIV1 clades but lacks the HIV2 and SIV present in the PFAM alignment -- actually the conservation coloring as done below looks better/more obvious with the norecomb set.  "best-matching" would take too long with the 38 sequences in the norecomb set, but you could just tell it to associate with Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455)
+(This part also works with the HIV1 gp120 norecomb protein alignment, attached along with tree, which more evenly samples multiple HIV1 clades but lacks the HIV2 and SIV present in the PFAM alignment -- actually the conservation coloring as done below looks better/more obvious with the norecomb set.  "best-matching" would take too long with the 38 sequences in the norecomb set, but you could just tell it to associate with Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455)
+
+(Yet another attached alignment and tree, 50 diverse sequences from Consurf, could be used for this part.  Advantage is that it automatically associates with 1gc1 and includes its exact sequence, disadvantage is that the sequence names are not as informative as in the PFAM or norecomb alignments mentioned above.)
 
 To create this crystallizable gp120 core construct, the variable loops were replaced with shorter sequences. V1 and V2 were each replaced with Gly-Ala-Gly (GAG).  The red outline below shows residues that are not in the structure, and the solid red shows where GAG is present instead of the residue types in the sequence alignment.