PFRMAT AL 
TARGET T0062 
AUTHOR 5827-4749-3439 
METHOD This alignment has not been edited in any way from the 
METHOD automatic hmm-produced alignment. 
METHOD 
METHOD As usual, we employed a two-pronged approach:  
METHOD (1) We scored the target and BLAST-identified homologs 
METHOD against all the HMMs and threading models in our libraries, and (2) we  
METHOD constructed an HMM for the target and homologs  
METHOD (using UCSC's HMM software), and  
METHOD scored PDB. This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD The HMM analysis showed a very strong preference for members 
METHOD of a SCOP fold -- the structure chosen as the model for this 
METHOD target, d2cnd_2, had the highest score against the target HMM 
METHOD (NLL-NULL score of -25) for any sequence in a non-redundant  
METHOD set of PDB structures. 
METHOD  
METHOD Interestingly, another SCOP superfamily also gave high 
METHOD scores to this target, but none of the alignments were 
METHOD convincing, leading us to choose d2cnd_2. 
METHOD For the record, these domains were d1doi, d1frd, and d2pia_3. 
METHOD 
METHOD The alignment submitted was created by aligning the target and structure  
METHOD to an HMM constructed for a subfamily of the domain d2cnd_2, 
METHOD using Sjolander's Bayesian evolutionary tree estimation, 
METHOD and subfamily HMM construction software. 
MODEL 1 
PARENT 2cnd 
E    101    N    135 
E    102    A    136 
R    103    R    137 
P    104    R    138 
M    105    L    139 
I    106    A    140 
L    107    M    141 
I    108    I    142 
A    109    C    143 
G    110    G    144 
G    111    G    145 
T    112    S    146 
G    113    G    147 
F    114    I    148 
S    115    T    149 
Y    116    P    150 
A    117    M    151 
R    118    Y    152 
S    119    Q    153 
I    120    I    154 
L    121    I    155 
L    122    Q    156 
T    123    A    157 
A    124    V    158 
L    125    L    159 
A    126    D    161 
R    127    P    163 
N    128    E    164 
P    129    D    165 
N    130    H    166 
R    131    T    167 
D    132    E    168 
I    133    M    169 
T    134    H    170 
I    135    L    171 
Y    136    V    172 
W    137    Y    173 
G    138    A    174 
G    139    N    175 
R    140    R    176 
E    141    T    177 
E    142    E    178 
Q    143    D    179 
H    144    D    180 
L    145    I    181 
Y    146    L    182 
D    147    L    183 
L    148    R    184 
C    149    D    185 
E    150    E    186 
L    151    L    187 
E    152    D    188 
A    153    R    189 
L    154    W    190 
S    155    A    191 
L    156    A    192 
K    157    E    193 
H    158    Y    194 
P    159    P    195 
G    160    R    197 
L    161    L    198 
Q    162    K    199 
V    163    V    200 
V    164    W    201 
P    165    Y    202 
V    166    V    203 
V    167    I    204 
E    168    K    208 
Q    169    R    209 
P    170    P    210 
E    171    E    211 
A    172    E    212 
G    173    G    213 
W    174    W    214 
R    175    K    215 
G    176    Y    216 
R    177    S    217 
T    178    V    218 
G    179    G    219 
T    180    F    220 
V    181    V    221 
L    182    T    222 
T    183    E    223 
A    184    A    224 
V    185    V    225 
L    186    L    226 
Q    187    R    227 
D    188    E    228 
H    189    H    229 
G    190    V    230 
T    191    P    231 
L    192    G    233 
A    193    G    234 
E    194    D    235 
H    195    T    237 
D    196    L    238 
I    197    A    239 
Y    198    L    240 
I    199    A    241 
A    200    C    242 
G    201    G    243 
R    202    P    244 
F    203    P    245 
E    204    P    246 
M    205    M    247 
A    206    I    248 
K    207    Q    249 
I    208    A    251 
A    209    I    252 
R    210    S    253 
D    211    P    254 
L    212    N    255 
F    213    L    256 
S    215    E    257 
E    216    K    258 
R    217    M    259 
N    218    K    260 
A    219    Y    261 
R    220    D    262 
E    221    M    263 
D    222    A    264 
R    223    N    265 
L    224    S    266 
F    225    F    267 
G    226    V    268 
D    227    V    269 
TER 
END 
