
PFRMAT ABF1
TARGET T0005
AUTHOR 6792-8330-8583 D.Gerloff & F.Cohen, UCSF, gerloff@cgl.ucsf.edu
REMARK Secondary structure was predicted according to Benner & Gerloff and
REMARK later refined based on a preferred low-resolution tertiary structure model
REMARK for 2 separate parts (domains) of the target protein (res. 3-126 and 147-248).
REMARK Probabilities for the three-state secondary structure prediction reflect
REMARK (a) center or ending positions in a predicted sec.str. element,
REMARK (b) possible sec.str. alternatives, and (c) correlation or contradiction
REMARK of the prediction with the preferred 3D-models.
REMARK In short, our secondary structure prediction revealed a segregation of
REMARK 3 or 4 strand-helix units (alpha/buried-beta) framed by indels, followed by
REMARK probably 4 amphiphilic strands (i.e. exposed to solvent on one side of the
REMARK sheet), then a major deletion in the non-fibrinogen sequences in the alignment
REMARK (with experimental data indicating a fibrinogen domain boundary in this part),
REMARK and finally 6 possible, amphiphilic strands until res. 249 (alignment quality
REMARK is insufficient for the very C-terminus of gamma-fibrinogen). Further
REMARK implications for secondary structure packing and domain boundaries were
REMARK derived from various sources besides the multiple sequence alignment,
REMARK including biochemical literature data (exp. & theoretical, most significant
REMARK papers by R.F. Doolittle), manual (subjective, non-exhaustive) combinatorial
REMARK assembly, SCOP browsing, and (weak) sequence similarity between the putative
REMARK 2nd domain of the target protein and chymotrypsinogen. Low resolution models
REMARK (backbone only) were built using SYBYL (Tripos) and are submitted jointly in
REMARK 3.1. format to allow verification of the 2.1. prediction (assigned manually
REMARK from the models). The template core structures used in the models are 7acn 
REMARK (aconitase, C-term domain) for domain 1 (3 -126) and 3gct (chymotrypsinogen, 
REMARK 1st beta-barrel) for domain 2 (147-248). Part of the Ca-binding site (173-178)
REMARK was locally modelled to resemble one of the calmodulin loops. An alternative
REMARK model for the 2nd domain could be built using an OB-fold as template. However, 
REMARK we strongly favor the chymotrypsin-like topology submitted here. Possible 
REMARK contacts between domains 1 and 2 were not predicted (probability 0.00 in 2.1).
BEGDAT 1.1 1 1.0
SS 269
V C 0.00
Q C 0.00
I E 0.40
H E 0.40
D E 0.40
I C 0.40
T C 0.40
G C 0.80
K H 0.80
D H 0.80
C H 0.80
Q H 0.80
D H 0.80
I H 0.80
A H 0.80
N H 0.80
K H 0.80
G H 0.70
A H 0.70
K H 0.70
Q C 0.70
S C 0.80
G C 0.70
L E 0.80
Y E 0.80
F E 0.80
I E 0.80
K E 0.80
P C 0.80
L C 0.80
K C 0.80
A C 0.60
N H 0.60
Q H 0.60
Q H 0.70
F H 0.70
L H 0.70
V H 0.70
Y H 0.70
C H 0.70
E H 0.70
I H 0.70
D H 0.60
G C 1.00
S C 1.00
G C 1.00
N C 1.00
G C 1.00
W E 0.80
T E 0.90
V E 0.90
F E 0.90
Q E 0.90
K E 0.90
R C 0.70
L C 0.70
D C 0.90
G C 0.50
S H 0.90
V H 1.00
D H 1.00
F H 1.00
K H 1.00
K H 1.00
N H 1.00
W H 1.00
I H 1.00
Q H 1.00
Y H 1.00
K H 1.00
E H 1.00
G H 1.00
F H 0.70
G C 0.60
H C 0.60
L C 0.60
S C 1.00
P C 1.00
T C 1.00
G C 1.00
T C 1.00
T E 0.60
E E 0.60
F E 0.70
W E 0.70
L E 0.70
G C 0.80
N C 0.70
E H 0.60
K H 0.80
I H 0.80
H H 0.80
L H 0.80
I H 0.80
S H 0.80
T H 0.80
Q H 0.80
S H 0.60
A C 1.00
I C 1.00
P C 1.00
Y E 0.60
A E 0.70
L E 0.90
R E 0.90
V E 0.90
E E 0.90
L E 0.90
E E 0.70
D C 0.80
W C 0.80
N C 1.00
G C 0.60
R E 0.60
T E 0.90
S E 0.90
T E 0.90
A E 0.90
D E 0.60
Y C 0.70
A C 0.80
M C 0.60
F E 0.90
K E 0.90
V E 0.90
G E 0.80
P C 1.00
E C 1.00
A C 1.00
D C 1.00
K E 1.00
Y E 1.00
R E 1.00
L E 1.00
T E 1.00
Y E 1.00
A E 1.00
Y E 0.70
F E 0.70
A E 0.70
G C 1.00
G C 1.00
D C 1.00
A C 1.00
G C 1.00
D C 1.00
A C 0.50
F C 0.50
D C 0.50
G H 0.50
F H 0.50
D H 0.50
F H 0.50
G H 0.50
D H 0.50
D C 1.00
P C 1.00
S C 1.00
D C 0.40
K C 0.40
F C 0.40
F C 0.40
T C 0.40
S C 0.40
H C 0.40
N C 1.00
G C 1.00
M E 0.80
Q E 0.80
F E 0.80
S E 0.80
T E 0.80
W C 1.00
D C 1.00
N C 1.00
D C 1.00
N C 1.00
D C 1.00
K C 1.00
F C 0.90
E C 0.90
G C 0.90
N C 0.90
C E 0.50
A E 0.70
E E 0.70
Q E 0.70
D E 0.70
G C 1.00
S C 1.00
G C 1.00
W E 0.60
W E 0.90
M E 0.90
N E 0.90
K E 0.50
C C 0.70
H C 0.70
A C 0.70
G C 0.70
H C 0.70
L C 0.70
N C 1.00
G C 1.00
V E 0.70
Y E 0.70
Y E 0.70
Q E 0.70
G C 1.00
G C 1.00
T C 0.60
Y C 0.60
S C 0.60
K C 0.60
A C 0.60
S C 0.60
T C 0.60
P C 1.00
N C 0.60
G C 0.40
Y C 0.40
D C 0.40
N E 0.50
G E 0.80
I E 1.00
I E 1.00
W E 1.00
A E 1.00
T E 1.00
W E 1.00
K C 0.40
T C 1.00
R C 1.00
W C 0.60
Y E 1.00
S E 1.00
M E 1.00
K E 0.70
K E 0.70
T E 1.00
T E 1.00
M E 1.00
K E 1.00
I E 1.00
I E 1.00
P C 1.00
F C 1.00
N C 1.00
R C 1.00
L C 0.00
T C 0.00
I C 0.00
G C 0.00
E C 0.00
G C 0.00
Q C 0.00
Q C 0.00
H C 0.00
H C 0.00
L C 0.00
G C 0.00
G C 0.00
A C 0.00
K C 0.00
Q C 0.00
A C 0.00
G C 0.00
D C 0.00
V C 0.00
ENDDAT 1.1
BEGDAT 2.1 1 0.8 1
134
1 2  OT 0.80 0 0 0.00
1 3  KK 0.80 0 0 0.00
1 8  -- 0.40 0 0 0.00
1 9  -- 0.40 0 0 0.00
1 12 -- 0.00 0 0 0.00
1 13 -- 0.00 0 0 0.00
1 14 -- 0.00 0 0 0.00
1 15 -- 0.00 0 0 0.00
1 16 -- 0.00 0 0 0.00
1 17 -- 0.00 0 0 0.00
1 18 -- 0.00 0 0 0.00
1 19 -- 0.00 0 0 0.00
2 3  OT 1.00 0 0 0.00
2 4  PD 1.00 0 0 0.00
2 12 -- 0.00 0 0 0.00
2 13 -- 0.00 0 0 0.00
2 14 -- 0.00 0 0 0.00
2 15 -- 0.00 0 0 0.00
2 16 -- 0.00 0 0 0.00
2 17 -- 0.00 0 0 0.00
2 18 -- 0.00 0 0 0.00
2 19 -- 0.00 0 0 0.00
3 4  OT 1.00 0 0 0.00
3 5  KK 1.00 0 0 0.00
3 8  -- 0.40 0 0 0.00
3 9  RD 1.00 0 0 0.00
3 10 LS 1.00 0 0 0.00
3 11 RD 1.00 0 0 0.00
3 12 -- 0.00 0 0 0.00
3 13 -- 0.00 0 0 0.00
3 14 -- 0.00 0 0 0.00
3 15 -- 0.00 0 0 0.00
3 16 -- 0.00 0 0 0.00
3 17 -- 0.00 0 0 0.00
3 18 -- 0.00 0 0 0.00
3 19 -- 0.00 0 0 0.00
4 5  OT 1.00 0 0 0.00
4 6  PE 0.70 0 0 0.00
4 12 -- 0.00 0 0 0.00
4 13 -- 0.00 0 0 0.00
4 14 -- 0.00 0 0 0.00
4 15 -- 0.00 0 0 0.00
4 16 -- 0.00 0 0 0.00
4 17 -- 0.00 0 0 0.00
4 18 -- 0.00 0 0 0.00
4 19 -- 0.00 0 0 0.00
5 6  OT 1.00 0 0 0.00
5 7  KK 1.00 0 0 0.00
5 8  -- 0.40 0 0 0.00
5 9  RD 1.00 0 0 0.00
5 10 LS 1.00 0 0 0.00
5 11 RD 1.00 0 0 0.00
5 12 -- 0.00 0 0 0.00
5 13 -- 0.00 0 0 0.00
5 14 -- 0.00 0 0 0.00
5 15 -- 0.00 0 0 0.00
5 16 -- 0.00 0 0 0.00
5 17 -- 0.00 0 0 0.00
5 18 -- 0.00 0 0 0.00
5 19 -- 0.00 0 0 0.00
6 7  OT 1.00 0 0 0.00
6 12 -- 0.00 0 0 0.00
6 13 -- 0.00 0 0 0.00
6 14 -- 0.00 0 0 0.00
6 15 -- 0.00 0 0 0.00
6 16 -- 0.00 0 0 0.00
6 17 -- 0.00 0 0 0.00
6 18 -- 0.00 0 0 0.00
6 19 -- 0.00 0 0 0.00
7 8  -- 0.40 0 0 0.00
7 9  RD 1.00 0 0 0.00
7 10 LS 1.00 0 0 0.00
7 11 RD 1.00 0 0 0.00
7 12 -- 0.00 0 0 0.00
7 13 -- 0.00 0 0 0.00
7 14 -- 0.00 0 0 0.00
7 15 -- 0.00 0 0 0.00
7 16 -- 0.00 0 0 0.00
7 17 -- 0.00 0 0 0.00
7 18 -- 0.00 0 0 0.00
7 19 -- 0.00 0 0 0.00
8 11 OS 0.50 0 0 0.00
8 12 -- 0.00 0 0 0.00
8 13 -- 0.00 0 0 0.00
8 14 -- 0.00 0 0 0.00
8 15 -- 0.00 0 0 0.00
8 16 -- 0.00 0 0 0.00
8 17 -- 0.00 0 0 0.00
8 18 -- 0.00 0 0 0.00
8 19 -- 0.00 0 0 0.00
9 10 HH 1.00 0 0 0.00
9 12 -- 0.00 0 0 0.00
9 13 -- 0.00 0 0 0.00
9 14 -- 0.00 0 0 0.00
9 15 -- 0.00 0 0 0.00
9 16 -- 0.00 0 0 0.00
9 17 -- 0.00 0 0 0.00
9 18 -- 0.00 0 0 0.00
9 19 -- 0.00 0 0 0.00
10 11 HH 0.00 0 0 0.00
10 12 -- 0.00 0 0 0.00
10 13 -- 0.00 0 0 0.00
10 14 -- 0.00 0 0 0.00
10 15 -- 0.00 0 0 0.00
10 16 -- 0.00 0 0 0.00
10 17 -- 0.00 0 0 0.00
10 18 -- 0.00 0 0 0.00
10 19 -- 0.00 0 0 0.00
11 12 -- 0.00 0 0 0.00
11 13 -- 0.00 0 0 0.00
11 14 -- 0.00 0 0 0.00
11 15 -- 0.00 0 0 0.00
11 16 -- 0.00 0 0 0.00
11 17 -- 0.00 0 0 0.00
11 18 -- 0.00 0 0 0.00
11 19 -- 0.00 0 0 0.00
12 13 -- 0.00 0 0 0.00
12 14 -- 0.00 0 0 0.00
12 15 -- 0.00 0 0 0.00
12 16 -- 0.00 0 0 0.00
12 17 -- 0.00 0 0 0.00
12 18 -- 0.00 0 0 0.00
12 19 -- 0.00 0 0 0.00
13 15 LE 0.70 0 0 0.00
14 15 HH 1.00 0 0 0.00
14 16 LS 1.00 0 0 0.00
14 17 HH 1.00 0 0 0.00
14 19 -- 0.40 0 0 0.00
15 16 HH 1.00 0 0 0.00
15 17 LS 1.00 0 0 0.00
16 17 RD 1.00 0 0 0.00
16 19 HH 1.00 0 0 0.00
17 19 RD 1.00 0 0 0.00
18 19 HH 1.00 0 0 0.00
ENDDAT 2.1
END


