Changes between Version 30 and Version 31 of HIVspikes

Timestamp:

Oct 16, 2009, 4:44:12 PM (17 years ago)

Author:

meng

Comment:

--

HIVspikes

@@ -156 +156 @@
 Alternatively, instead of finding the pattern on the sequence, just select it on the structures directly with main menu Select... Sequence, PROSITE Pattern, which is then reflected in the green selection region on the sequences. Another possibility here is calculating percent ID (in Multalign Viewer menu, Tools... Percent Identity).
 
-== Conservation alternative (Elaine) ==
-
-A sequence alignment allows assessment of conservation and includes the loops that are missing from the crystal structures.
+== Sequence alignment of related proteins (Elaine) ==
+
+A sequence alignment allows assessment of conservation and includes full-length sequences with the loops that are missing from the crystal structures.
 
 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
@@ -164 +164 @@
 (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 coloring 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)
 
-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 alignment file.
+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.
 
 [[Image(pfam-alignment.png)]]