Tue, 06/26/2012 - 00:30
#2
Just out of curiosity...
What's going on with the sequence at the N-terminus? (Is it an added polyhistidine tag, or was it a part of the "natural" sequence?)
Tue, 06/26/2012 - 00:48
#3
Exactly, it's most likely a his tag
In fact, the RosettaServer only modeled this sequence:
SSGRENLYFQGAGPLLTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLL
EKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDV
LSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSL
Although we can't be 100% sure since the CASP10 organizers did not give us any additional information about it. We'll have to see what all the servers did with the first 7 residues.
Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=137
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Here is the sequence logo predicted by the SAM server.
H = helix
E = sheet
C = loop (or coil)
The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.
For example, the Leucines at residues 27, 31, 34, 60-61, 73, 82-84, 91-95, 101, 105, 116, 123, 130 & 140 are highly predicted to be in a helix. However, the Leucines at residues 14, 22-23, 150 & 152 are predicted to be anything.
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Link to template PDBs:
http://www.pdb.org/pdb/explore/explore.do?structureId=1gqe
http://www.pdb.org/pdb/explore/explore.do?structureId=1ls4
http://www.pdb.org/pdb/explore/explore.do?structureId=3tul
http://www.pdb.org/pdb/explore/explore.do?structureId=3k29
http://www.pdb.org/pdb/explore/explore.do?structureId=1ya9
http://www.pdb.org/pdb/explore/explore.do?structureId=3lg7