PFRMAT AL 
TARGET T0085 
AUTHOR 7169-6295-1599 
METHOD T0085, its related sequences and their multiple alignment were threaded on 
METHOD the structural library composed of PDB rel.83 by several method we have 
METHOD developed, however the results are not significant in a straight-forward way.  
METHOD We thought the four HEM binding motifs (CXXCH) were crucial. Sequence 
METHOD similarity search against the structural known proteins, the group of the 
METHOD cytochrome c3 (2cdv etc.), the group of the cytochrome c553 (1dvh etc.) and 
METHOD hydroxyalamine oxidoreductase (1fgj) are searched as they have the heme 
METHOD binding motifs. 
METHOD Among them, the length between motifs are suitable in 1fgj only, thus we 
METHOD consider it may be plausible candidate for the compatible structure. Next, 
METHOD we consider the heme ligands. 
METHOD One of the residues of heme ligand is contained in the motif (His) and it is 
METHOD shared by the target and 1fgj. In 1fgj, another ligand binding site is also  
METHOD His. In the alignment of the target and 1fgj, the two His and two Tyr are  
METHOD at the corresponding positions. Tyr residue seems suitable to the heme 
METHOD ligand. At last, we perform the inverse folding search using 1fgj structure 
METHOD against the target sequence and the sequence database constructed from PDB 
METHOD rel. 83. The target sequence appears at the high ranking position (2nd 
METHOD position). These results strongly support that T0085 takes the same  
METHOD as 1fgj. 
METHOD  
MODEL 1 
PARENT 1fgj_A 
A 1 S 69 
D 2 P 70 
A 3 K 71 
P 4 E 72 
F 5 V 73 
E 6 A 74 
G 7 E 75 
R 8 R 76 
K 9 K 77 
K 10 D 78 
C 11 C 79 
S 12 V 80 
S 13 E 81 
C 14 C 82 
H 15 H 83 
K 16 S 84 
A 17 D 85 
Q 18 E 86 
A 19 T 87 
Q 20 R 92 
S 21 A 93 
W 22 W 94 
K 23 K 95 
D 24 R 96 
T 25 S 97 
A 26 T 98 
H 27 H 99 
A 28 A 100 
K 29 N 101 
M 31 L 102 
E 32 D 103 
S 33 K 104 
L 34 I 105 
K 35 R 106 
N 37 N 107 
V 38 L 108 
K 39 K 109 
K 40 S 110 
E 41 D 111 
A 42 D 112 
K 43 P 113 
Q 44 K 117 
K 45 K 118 
A 46 G 119 
K 47 K 120 
L 48 L 121 
D 49 E 122 
P 50 E 123 
A 51 V 124 
K 52 K 137 
D 53 E 138 
Y 54 T 139 
T 55 L 140 
Q 56 K 141 
D 57 E 142 
K 58 V 143 
D 59 G 144 
C 60 C 145 
V 61 I 146 
G 62 D 147 
C 63 C 148 
H 64 H 149 
V 65 V 150 
D 66 D 151 
G 67 N 153 
F 68 K 154 
G 69 K 155 
Q 70 D 156 
K 71 K 157 
G 72 A 158 
G 73 D 159 
Y 74 H 160 
T 75 T 161 
I 76 K 162 
E 77 D 163 
S 78 I 164 
P 79 R 165 
K 80 M 166 
P 81 P 167 
T 84 T 168 
G 85 A 169 
V 86 D 170 
G 87 T 171 
C 88 C 172 
E 89 G 173 
S 90 T 174 
C 91 C 175 
H 92 H 176 
G 93 G 195 
P 94 Q 196 
G 95 W 197 
R 96 P 198 
N 97 A 199 
F 98 G 200 
R 99 R 201 
G 100 P 202 
D 101 S 203 
H 102 H 204 
R 103 A 205 
K 104 L 206 
S 105 D 207 
G 106 Y 208 
Q 107 T 209 
A 108 A 210 
F 109 I 212 
E 110 E 213 
K 111 T 214 
S 112 T 215 
G 113 V 216 
K 114 W 217 
K 115 A 218 
T 116 T 219 
P 117 P 221 
R 118 Q 222 
K 119 R 223 
D 120 E 224 
L 121 V 225 
A 122 A 226 
K 123 E 227 
K 124 G 228 
G 125 C 229 
Q 126 T 230 
D 127 M 231 
F 128 C 232 
H 129 H 233 
F 130 T 234 
E 131 N 235 
E 132 Q 236 
R 133 K 238 
C 134 C 239 
S 135 D 240 
A 136 N 241 
C 137 C 242 
H 138 H 243 
L 139 T 244 
N 140 R 245 
Y 141 H 246 
E 142 E 247 
G 143 F 248 
S 144 S 249 
P 145 A 250 
W 146 A 251 
K 147 E 252 
G 148 S 253 
A 149 R 254 
K 150 K 255 
P 158 P 256 
E 159 E 257 
V 160 A 258 
D 161 C 259 
A 162 A 260 
K 163 T 261 
Y 164 C 262 
T 165 H 263 
F 166 S 264 
K 167 G 265 
F 168 V 266 
D 169 D 267 
E 170 H 268 
M 171 N 269 
V 172 N 270 
K 173 W 271 
E 174 E 272 
V 175 A 273 
K 176 Y 274 
A 177 T 275 
M 178 M 276 
H 179 S 277 
E 180 K 278 
H 181 H 279 
Y 182 G 280 
K 183 K 281 
L 184 L 282 
E 185 A 283 
G 186 E 284 
V 187 M 285 
P 192 N 286 
K 193 R 287 
F 194 D 288 
K 195 K 289 
F 196 W 290 
H 197 N 291 
D 198 W 292 
E 199 E 293 
F 200 V 294 
Q 201 R 295 
A 202 L 296 
S 203 K 297 
A 204 D 298 
K 205 A 299 
P 206 F 300 
A 207 S 301 
K 208 K 302 
K 209 G 303 
G 210 G 304 
K 211 Q 305 
TER 
END 
