PFRMAT AL 
TARGET t0080 
AUTHOR 4139-4764-1095 
METHOD Secondary structure was predicted with PHD and Predator. 
METHOD We then used threader with weight given to predicted SS. 
METHOD The best scoring alignments were then rethreaded with 
METHOD sequence shuffling. Of the best scoring alignments in the 
METHOD second round, number 2 & 3 had very similar fold. Manual 
METHOD inspection judged hit number 2 to have somewhat better 
METHOD alignment - this is presented below. 
MODEL 1 
PARENT 1pafA 
R  85	V   1 
L  86	N   2 
G  87	T   3 
L  88	I   4 
E  89	I   5 
F  90	Y   6 
F  91	N   7 
D  92	V   8 
Q  93	G   9 
P  94	S  10 
A  95	T  11 
V  96	T  12 
P  97	I  13 
L  98	S  14 
A  99	K  15 
R 100	Y  16 
A 101	A  17 
F 102	T  18 
L 103	F  19 
G 104	L  20 
Q 105	N  21 
V 106	D  22 
L 107	L  23 
V 108	R  24 
R 109	N  25 
R 110	E  26 
L 111	A  27 
P 112	K  28 
N 113	D  29 
G 114	P  30 
T 115	S  31 
E 116	L  32 
L 117	K  33 
R 118	C  34 
G 119	Y  35 
R 120	G  36 
I 121	I  37 
V 122	P  38 
E 123	M  39 
G 139	L  40 
G 140	P  41 
R 141	N  42 
Q 142	T  43 
T 143	N  44 
P 144	T  45 
R 145	N  46 
N 146	P  47 
R 147	K  48 
G 148	Y  49 
M 149	V  50 
F 150	L  51 
M 151	V  52 
K 152	E  53 
P 153	L  54 
G 154	Q  55 
T 155	G  56 
L 156	T  61 
Y 157	I  62 
V 158	T  63 
Y 159	L  64 
I 160	M  65 
I 161	L  66 
Y 162	R  67 
G 163	R  68 
M 164	M  74 
Y 165	G  75 
F 166	Y  76 
C 167	S  77 
M 168	D  78 
N 169	P  79 
I 170	F  80 
S 171	E  81 
G 174	T  82 
D 175	N  83 
G 176	K  84 
A 177	C  85 
C 178	R  86 
V 179	Y  87 
L 180	H  88 
L 181	I  89 
R 182	F  90 
E 185	N  91 
P 186	D  92 
L 187	I  93 
E 188	S  94 
G 189	G  95 
E 191	T  96 
T 192	E  97 
M 193	R  98 
R 194	Q  99 
Q 195	D 100 
L 196	V 101 
R 197	E 102 
S 198	T 103 
T 199	T 104 
L 200	L 105 
R 201	C 106 
K 202	P 107 
G 203	N 108 
T 204	A 109 
A 205	N 110 
S 206	S 111 
R 207	R 112 
V 208	V 113 
L 209	S 114 
K 210	K 115 
D 211	N 116 
R 212	I 117 
E 213	N 118 
L 214	F 119 
C 215	D 120 
S 216	S 121 
G 217	R 122 
P 218	Y 123 
S 219	P 124 
K 220	T 125 
L 221	L 126 
C 222	E 127 
Q 223	S 128 
A 224	K 129 
L 225	A 130 
A 226	G 131 
I 227	V 132 
N 228	K 133 
K 229	S 134 
S 230	Q 139 
F 231	L 140 
D 232	G 141 
Q 233	I 142 
R 234	Q 143 
D 235	I 144 
L 236	L 145 
A 237	D 146 
Q 238	S 147 
D 239	N 148 
E 240	I 149 
A 241	G 150 
V 242	K 151 
W 243	I 152 
L 244	S 153 
E 245	G 154 
R 246	V 155 
G 247	M 156 
P 248	S 157 
L 249	F 158 
P 251	T 159 
S 252	E 160 
E 253	K 161 
P 254	T 162 
A 255	E 163 
V 256	A 164 
V 257	E 165 
A 258	F 166 
A 259	L 167 
A 260	L 168 
R 261	V 169 
V 262	A 170 
G 263	I 171 
V 264	Q 172 
G 265	M 173 
H 266	V 174 
A 267	S 175 
G 268	E 176 
E 269	A 177 
W 270	A 178 
A 271	R 179 
R 272	F 180 
K 273	K 181 
P 274	Y 182 
L 275	I 183 
R 276	E 184 
F 277	N 185 
Y 278	Q 186 
V 279	V 187 
R 280	K 188 
G 281	T 189 
S 282	N 190 
P 283	N 196 
W 284	P 197 
V 285	N 198 
S 286	P 199 
V 287	K 200 
V 288	V 201 
D 289	L 202 
R 290	N 203 
V 291	L 204 
A 292	Q 205 
E 293	E 206 
Q 294	T 207 
D 295	W 208 
T 296	G 209 
Q 297	K 210 
A 298	I 211 
TER 
END 
