PFRMAT SS 
TARGET T0063 
AUTHOR 5529-3140-9255 
REMARK Prediction team BENNER-COHEN has two group leaders, 
REMARK but we will consistently use Steven Benner's predictor 
REMARK number to avoid confusion concerning a second team 
REMARK connected with Fred Cohen (called Cohen, Fred). 
REMARK (Fred Cohen's number as a group leader is 6140-7890-6093). 
REMARK Prediction team members: D.L.Gerloff, G.Cannarozzi, 
REMARK M.Joachimiak, F.E.Cohen & S.A.Benner. 
METHOD 
METHOD Secondary structure was predicted semi-automatically, 
METHOD based on Surface-Interior-Active-Site-Parse Assignments 
METHOD using transparent prediction methods as recently reviewed 
METHOD in Chem.Rev. 97:2725-2843. Individual predictions were 
METHOD made for three different subalignments of the IF-5A 
METHOD superfamily, with each subalignment containing proteins 
METHOD from species of one of the three primary kingdoms of  
METHOD life, prokaryotes, eukaryotes, and archae. The master 
METHOD alignment was aligned using PileUp (GCG) and minor modi- 
METHOD fications made manually.  
METHOD 
METHOD We present here a consensus prediction for the core  
METHOD elements in three kingdoms over the N-terminal part, 
METHOD and of only the archae and eukaryotes in the second 
METHOD part. In particular, the predicted helix around po- 
METHOD sitions 57-63 in the target sequence, is not found 
METHOD in the individual prediction for the archae structure; 
METHOD it may even be missing altogether. 
METHOD 
METHOD The alignment, the individual predictions, structural  
METHOD divergence within the superfamily in the C-terminal 
METHOD part, and the impact of the increasing sequence data 
METHOD bases for a secondary prediction like this one, are 
METHOD discussed in a manuscript submitted to BBRC before 
METHOD the deadline for T0063. (Gerloff, Joachmiak, Cohen, 
METHOD Cannarozzi, Chamberlin and Benner. Structure prediction 
METHOD in a post-genomic environment. A secondary and tertiary 
METHOD structural model for the initiation factor 5A (IF-5A) 
METHOD family.) Abstract and the tertiary structure models 
METHOD supported by this secondary structure prediction to 
METHOD follow as a threading alignment submission. 
METHOD      
MODEL 1 
M    C     1.0 
V    C     1.0 
L    C     1.0 
K    C     1.0 
W    C     1.0 
V    C     1.0 
M    C     1.0 
S    C     1.0 
T    C     1.0 
K    E     0.7 
Y    E     0.7 
V    E     1.0 
E    E     1.0 
A    E     1.0 
G    E     1.0 
E    E     1.0 
L    E     1.0 
K    E     0.7 
E    C     1.0 
G    C     1.0 
S    E     0.5 
Y    E     1.0 
V    E     1.0 
V    E     1.0 
I    E     0.7 
D    E     0.7 
G    C     1.0 
E    C     1.0 
P    C     1.0 
C    E     0.7 
R    E     0.7 
V    E     1.0 
V    E     1.0 
E    E     1.0 
I    E     1.0 
E    E     1.0 
K    E     1.0 
S    C     1.0 
K    C     1.0 
T    C     1.0 
G    C     1.0 
K    C     1.0 
H    C     1.0 
G    C     1.0 
S    C     1.0 
A    E     0.7 
K    E     0.7 
A    E     1.0 
R    E     1.0 
I    E     1.0 
V    E     1.0 
A    E     1.0 
V    C     0.5 
G    C     1.0 
V    C     0.7 
F    C     0.7 
D    C     0.7 
G    C     0.5 
G    H     0.6 
K    H     0.6 
R    H     0.8 
T    H     0.8 
L    H     0.6 
S    H     0.6 
L    C     1.0 
P    C     1.0 
V    C     0.7 
D    E     0.7 
A    E     0.7 
Q    E     1.0 
V    E     1.0 
E    E     1.0 
V    E     1.0 
P    E     0.7 
I    E     0.7 
I    E     0.7 
E    C     1.0 
K    C     1.0 
F    C     1.0 
T    C     1.0 
A    E     1.0 
Q    E     1.0 
I    E     1.0 
L    E     1.0 
S    E     1.0 
V    E     0.7 
S    E     0.7 
G    C     1.0 
D    C     1.0 
V    C     1.0 
I    E     1.0 
Q    E     1.0 
L    E     1.0 
M    E     1.0 
D    E     0.7 
M    E     0.6 
R    C     0.7 
D    C     1.0 
Y    C     1.0 
K    C     1.0 
T    C     1.0 
I    E     0.8 
E    E     0.8 
V    E     0.8 
P    C     1.0 
M    C     1.0 
K    C     1.0 
Y    C     1.0 
V    C     1.0 
E    H     0.7 
E    H     0.7 
E    H     1.0 
A    H     1.0 
K    H     1.0 
G    H     1.0 
R    H     1.0 
L    H     1.0 
A    H     1.0 
P    C     1.0 
G    C     1.0 
A    C     1.0 
E    C     1.0 
V    E     0.8 
E    E     0.8 
V    E     0.8 
W    C     1.0 
Q    C     1.0 
I    C     1.0 
L    C     1.0 
D    C     1.0 
R    C     1.0 
Y    C     1.0 
K    C     1.0 
I    E     0.8 
I    E     0.8 
R    E     0.8 
V    E     0.8 
K    E     0.8 
END 
