beta_helix's picture
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Additional info about this CASP target

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

infjamc's picture
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Joined: 02/20/2009
Groups: Contenders
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?)

beta_helix's picture
User offline. Last seen 13 hours 57 min ago. Offline
Joined: 05/09/2008
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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.

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