
PFRMAT SS
TARGET T0105
AUTHOR 1020-4390-8741
REMARK Prediction team GERLOFF consists of the following
REMARK team members: Dietlind L. Gerloff (1),
REMARK Cairan Duffy (1), Zeti A. M. Hussein (1),
REMARK Melanie H. McCarthy-Troke (1), 
REMARK Siu-wai Leung (2), Gina M. Cannarozzi (3).
REMARK (1): ICMB Biocomputing Research Unit & 
REMARK (2): Division of Informatics, University of Edinburgh;
REMARK (3): Computational Biochemistry Research Group, ETH Zurich
REMARK Contact email is Dietlind.Gerloff@ed.ac.uk
REMARK
REMARK Prediction for T0105 was by: DLG, MHMT.
METHOD
METHOD This secondary structure prediction accompanies a TS submission
METHOD made earlier; it serves to clarify our coordinate model which is
METHOD of medium-to-poor quality in places.
METHOD 
METHOD Our prediction for T0105 is an ab initio assembly of predicted
METHOD secondary structure elements (see separate SS entry) based primarily
METHOD on function predictions: a putative cluster of Cys residues (Zn-
METHOD binding?) in all homologues but drawn from different locations
METHOD in the sequence; DNA-binding via a recognition helix, and predicted
METHOD amphiphilic or internal character of the beta strands. The result is
METHOD a strongly twisted, half open and concave barrel structure which can
METHOD be viewed almost as a cyclic permutated SH3-barrel. This is our favorite
METHOD model; it was predicted through a combinatorial analysis (mostly
METHOD manually with physical models) and there would have been others that
METHOD might be plausible. Modelling the structure from scratch was attempted
METHOD by combining pieces from other proteins using SYBYL. We are not very
METHOD happy with the coordinate representation of this topology prediction
METHOD but we hope that the intended topology is apparent..
METHOD
METHOD Additional sequences to those provided by the non-redundant data
METHOD base were gathered in the literature (eg. TIBS review by T.Gibson).
METHOD
REMARK This is a separate secondary structure prediction for a TS model.
REMARK
MODEL 1
D C 1.00
E C 1.00
N C 1.00
I E 1.00
N E 1.00
F E 0.90
K E 0.90
Q E 0.70
S C 1.00
E C 1.00
L C 1.00
P E 1.00
V E 1.00
T E 1.00
C E 1.00
G C 1.00
E C 1.00
V E 0.70
K E 0.90
G E 0.90
T E 0.90
L E 0.90
Y E 0.90
K C 1.00
E C 1.00
R C 1.00
F C 1.00
K C 0.80
Q C 0.80
G E 0.70
T E 0.70
S E 0.70
K C 0.70
K C 0.70
C E 0.90
I E 0.90
Q E 0.90
S E 0.90
E E 0.70
D C 1.00
K C 1.00
K E 0.90
W E 0.90
F E 0.90
T C 1.00
P C 1.00
R C 1.00
E E 0.90
F E 0.90
E E 0.90
I E 0.90
E E 0.70
G C 1.00
D C 1.00
R C 1.00
G C 0 90
A C 0.90
S C 0.90
K H 1.00
N H 1.00
W H 1.00
K H 1.00
L H 1.00
S H 1.00
I H 1.00
R H 1.00
C H 1.00
G C 1.00
G C 0.70
Y C 0.70
T H 1.00
L H 1.00
K H 1.00
V H 1.00
L H 1.00
M H 1.00
E H 1.00
N C 1.00
K C 1.00
F C 0.70
L C 0.70
P C 1.00
E C 1.00
P C 1.00
P C 1.00
S C 1.00
T C 1.00
R C 1.00
K C 0.70
K C 0.70
V E 0.70
T E 0.70
I E 0.70
K C 0.70
END

