PFRMAT AL 
TARGET t0043 
AUTHOR 4139-4764-1095 
METHOD 1) Secondary structure was predicted with PHD and Predator. 
METHOD 2) We used a hidden markov model that predicts SCOP 
METHOD    classification based on sequence and secondary structure. 
METHOD 3) THREADER:  
METHOD    Many of the good scorers were in the same SCOP class as the 
METHOD    best results from the HMM. We picked out these and repeated 
METHOD    the threading with sequence shuffling. 
METHOD    Of the structures with good score in both methods, 1sbp and 
METHOD    1lfa were manually judged to be the best when relying on the 
METHOD    PHD secondary structure (there was no clear consensus with 
METHOD    Predator). Since large parts of 1sbp are missing in the  
METHOD    final alignment, the alignments to the two domains are 
METHOD    only our second and third models, respectively. 
METHOD    The final alignments are in principle taken from the HMM, 
METHOD    with some minor manual tweaks. 
MODEL 3 
PARENT 1sbp 
T   1	I   3 
V   2	Q   4 
A   3	L   5 
Y   4	L   6 
I   5	N   7 
A   6	V   8 
I   7	S   9 
G   8	Y  10 
S   9	D  11 
N  10	P  12 
L  11	T  13 
A  12	R  14 
S  13	E  15 
P  14	L  16 
L  15	Y  17 
E  16	E  18 
Q  17	Q  19 
V  18	Y  20 
N  19	N  21 
A  20	K  22 
A  21	A  23 
L  22	F  24 
K  23	S  25 
A  24	A  26 
L  25	H  27 
G  26	W  28 
D  27	K  29 
I  28	Q  30 
P  29	E  31 
E  30	T  32 
S  31	G  33 
H  32	D  34 
I  33	N  35 
L  34	V  36 
T  35	V  37 
V  36	I  38 
S  37	D  39 
S  38	Q  40 
F  39	S  41 
Y  40	H  42 
R  41	G  43 
T  42	G  44 
P  43	G  46 
P  44	K  47 
L  45	Q  48 
G  46	A  49 
P  47	T  50 
Q  48	S  51 
D  49	V  52 
Q  50	I  53 
P  51	N  54 
D  52	G  55 
Y  53	I  56 
L  54	E  57 
N  55	A  58 
A  56	D  59 
A  57	T  60 
V  58	V  61 
A  59	T  62 
L  60	L  63 
E  61	A  64 
T  62	L  65 
S  63	A  66 
L  64	Y  67 
A  65	D  68 
P  66	V  69 
E  67	N  70 
E  68	A  71 
L  69	I  72 
L  70	A  73 
N  71	E  74 
H  72	R  75 
R  92	G  76 
T  93	R  77 
L  94	I  78 
D  95	D  79 
L  96	K  80 
D  97	N  81 
I  98	W  82 
M  99	I  83 
L 100	K  84 
F 101	R  85 
G 102	L  86 
N 103	P  87 
E 104	D  88 
V 105	D  89 
I 106	S  90 
N 107	A  91 
T 108	P  92 
E 109	Y  93 
N 120	T  94 
R 121	E 220 
G 122	P 221 
F 123	T 222 
M 124	V 223 
L 125	S 224 
W 126	V 225 
P 127	V 226 
F 129	D 227 
E 130	K 228 
I 131	V 229 
A 132	V 230 
P 133	E 231 
E 134	K 232 
L 135	K 233 
V 136	D 234 
F 137	T 235 
G 140	K 236 
E 141	A 237 
M 142	V 238 
L 143	A 239 
R 144	E 240 
Q 145	A 241 
I 146	Y 242 
L 147	L 243 
H 148	K 244 
T 149	Y 245 
R 150	L 246 
A 151	Y 247 
F 152	S 248 
D 153	P 249 
K 154	E 250 
L 155	G 251 
N 156	Q 252 
K 157	E 253 
W 158	I 254 
TER 
END 
