PFRMAT AL 
TARGET T0063 
AUTHOR 2234-4819-7150 
REMARK In this case, similarity of function between elongation factor TU (pdb hit) and 
REMARK translation initiation factor 5A (query) made case for this hit. 
REMARK Only segments of query sequence that aligned with PDB sequence are given (N-terminal 90 aa). 
METHOD Identification of PDB sequences related by evolution to the target 
METHOD (query) sequence is performed by a seried of BLAST searches performed 
METHOD locally.  The first search is performed with the CASP3 sequence 
METHOD against the non-redundant protein database ("nr").  The hits from this 
METHOD sequence are then used as query sequences against a database of 
METHOD sequences related to sequences in the PDB.  (This database has been 
METHOD compiled by running BLAST on a set of non-redundant sequences from the 
METHOD PDB.  Approximately 1/3 of nr sequences are present in this database.) 
METHOD The hits from this search of PDB-related sequences are then used as 
METHOD query sequences against the PDB.  A link is thus established between 
METHOD the original query sequence and some sequene in the PDB via 0,1, or 2 
METHOD GenBank sequences.  Depending on the the E-values in each search, the 
METHOD link can be considered significant or random.  Biological similarity 
METHOD and secondary structure comparisons (prediction for the query, 
METHOD experimental in terms of the PDB structure) serve to identify the most 
METHOD probable hits.  The alignments between the query and first nr 
METHOD sequence, between the first and second nr sequence, and the second nr 
METHOD sequence and the pdb sequence imply an alignment between the query and 
METHOD PDB sequence.  The alignment has been adjusted manually to maximize 
METHOD sequence identity and/or to increase correspondence between predicted 
METHOD and experimental secondary structures. 
METHOD 
MODEL  1 
PARENT 1eft 
M   1    I 231 
V   2    T 232 
L   3    G 233 
K   4    R 234 
W   5    G 235 
V   6    T 236 
M   7    V 237 
S   8    A 238 
T   9    T 239 
K  10    G 240 
Y  11    R 241 
V  12    I 242 
E  13    E 243 
A  14    R 244 
G  15    G 245 
E  16    K 246 
L  17    V 247 
K  18    K 248 
E  19    V 249 
G  20    G 250 
S  21    D 251 
Y  22    E 252 
V  23    V 253 
V  24    E 254 
I  25    I 255 
D  26    V 256 
G  27    G 257 
E  28    L 258 
K  39    A 259 
T  40    P 260 
G  41    T 262 
K  42    R 263 
K  47    K 264 
A  48    T 265 
R  49    V 266 
I  50    V 267 
V  51    T 268 
A  52    G 269 
V  53    V 270 
G  54    E 271 
V  55    M 272 
F  56    H 273 
D  57    R 274 
G  58    K 275 
G  59    T 276 
K  60    L 277 
R  61    Q 278 
T  62    E 279 
L  63    G 280 
S  64    I 281 
L  65    A 282 
P  66    G 283 
V  67    D 284 
D  68    N 285 
A  69    V 286 
Q  70    G 287 
V  71    L 288 
E  72    L 289 
V  73    L 290 
P  74    R 291 
I  75    G 292 
I  76    V 293 
E  77    S 294 
K  78    R 295 
F  79    E 296 
T  80    R 300 
A  81    G 301 
Q  82    Q 302 
I  83    V 303 
L  84    L 304 
S  85    A 305 
V  86    K 306 
S  87    P 307 
G  88    G 308 
D  89    S 309 
V  90    I 310 
TER 
END 
