
PFRMAT AL
TARGET T0092
AUTHOR 3670-4530-6947
METHOD Overview
METHOD 
METHOD Fold recognition for this target was performed using the SAM-T99 and
METHOD SAM-T2K methods (which are similar to SAM_T98 [3]) using SAM version
METHOD 3.1 [1], a refinement of the methods developed by this group for CASP3
METHOD [7]).  These methods attempt to find and multiply align a set of
METHOD homologs to a given sequence, then create an HMM from that multiple
METHOD alignment.
METHOD 
METHOD First, a set of sequence weights is determined from the alignment.  Next, 
METHOD Modelfromalign is used to build the model from the alignment and the 
METHOD sequence weights.  Finally, hmmscore performs a local, all-paths scoring 
METHOD of the sequences, using a reversed-sequence normalization feature.
METHOD 
METHOD The weighting method, detailed in publications [3,4], uses Dirichlet
METHOD mixtures [6] to regularize the counts and an entropy method to set the
METHOD final weights.
METHOD 
METHOD We are currently using SAM-T2K to generate the HMM from the target
METHOD sequence, but are still using the library of SAM-T99 template HMMs,
METHOD since the SAM-T2K method is not yet fully stable.
METHOD 
METHOD Alignment generation
METHOD 
METHOD The initial step uses WU-BLASTP to search NRP to get nested sets of
METHOD possible homologs---from a set of very similar sequences to a set of
METHOD possibly related sequences.
METHOD 
METHOD The method then uses multiple iterations of a selection, training, and 
METHOD alignment procedure.  Each iteration involves an initial alignment, a set 
METHOD of search sequences, a threshold value, and a transition regularizer. 
METHOD 
METHOD The first iteration uses a single sequence (or seed alignment) as the
METHOD initial alignment and the most similar sequences found by BLASTP are
METHOD used as the search set.  The threshold is set very strictly, so that
METHOD only good matches to the sequence are considered.  
METHOD 
METHOD On subsequent iterations the input alignment is the output from the
METHOD previous iteration, the search set is a larger set of possible
METHOD homologs found by BLASTP, and the thresholds are gradually loosened.
METHOD 
METHOD The HMM used for scoring and aligning sequences is built from a
METHOD multiple alignment using the w0.5 script, which aims to get an average
METHOD of 0.5 bits of information per column of the alignment.
METHOD 
METHOD All PDB protein sequences (including, unfortunately, theoretical
METHOD models) are scored with the HMM built from the target alignment, and
METHOD all the template HMMs in our SAM-T99 library (about 3760) are used to
METHOD score the target sequence.
METHOD 
METHOD High-scoring hits in either direction are examined by hand, as are
METHOD other potential targets found by public servers (see the CAFASP
METHOD experiment) or by functional considerations.
METHOD 
METHOD The final alignment is selected from among the various alignments
METHOD obtained by varying whether the template model or the target model is
METHOD used for the alignment, whether local or global alignment is chosen,
METHOD and various other parameters.  In some cases parts of different
METHOD alignments are combined.
METHOD 
METHOD 
METHOD References
METHOD [1] R. Hughey and A. Krogh, CABIOS 12(2): 95-107, 1996.
METHOD     http://www.cse.ucsc.edu/research/compbio/sam.html.  
METHOD [2] K. Karplus, K. Sjolander, C. Barrett, M. Cline, D. Haussler, R.
METHOD     Hughey, L. Holm, and C. Sander, Proteins: Structure, Function, and 
METHOD     Genetics, Suppl. 1, 134-9, 1997.
METHOD [3] K. Karplus, C. Barrett, and R. Hughey, Technical Report UCSC-CRL-98-06,
METHOD     Department of Computer Engineering, Univ. of California, Santa Cruz, 1998.
METHOD [4] J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard,
METHOD     and C. Chothia, http://cyrah.med.harvard.edu/~jong/assess_final.html, 1998.
METHOD [5] S. Henikoff and J. C. Henikoff, JMB, vol 243, pp 574-578, Nov 1994.
METHOD [6] K. Sjolander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S.
METHOD    Mian, and D. Haussler, CABIOS 12(4):327-345, 1996.
METHOD [7] Karplus, K; Barrett, C; Cline, M; Diekhans, M; Grate, L; Hughey, R. 
METHOD     Predicting protein structure using only sequence information.
METHOD     Proteins, 1999, Suppl 3:121-5.
METHOD 
METHOD 
METHOD The top-scoring hit with the target model and the template model is
METHOD 1xvaA (Glycine N-Methyltransferase).
METHOD 
METHOD Evidence supporting 1xvaA appears in the abstract for 
METHOD "Hypothetical Proteins from Haemophilus Influenzae: Two New Structures
METHOD Implying Methyltransferase Function" by Kap Lim, Hong Zhang,  Alexandra 
METHOD Tempczyk, Nicklas Bonander, John Toedt, Andrew J. Howard, Edward Eisenstein, 
METHOD and Osnat Herzberg  (from Center for Advanced Research in Biotechnology).
METHOD This abstract was listed on the American Crystallographic Association 
METHOD website.  The abstract describes our target (HI0319) as a "core 
METHOD methyltransferase fold of a central beta-sheet surrounded by alpha-helices 
METHOD on both faces."
METHOD 
METHOD The best alignment of 1xvaA and the target, based on agreement with our 
METHOD secondary structure predictor, was a global alignment from an HMM 
METHOD built from the FSSP multiple alignments.  We hand-edited this alignment
METHOD to force the two final strands since they were originally matched with
METHOD the other domain.  Two of these hand-edits look good and we are submitting
METHOD them both.  However, neither of these alignments match our secondary 
METHOD structure prediction for the two final strands.
METHOD 
METHOD 
MODEL 2
PARENT 1xva_A
G 15 P 18
D 16 D 19
F 17 Q 20
I 18 Y 21
F 19 A 22
D 20 D 23
E 21 G 24
N 22 E 25
V 23 A 26
A 24 A 27
E 25 R 28
V 26 V 29
F 27 W 30
P 28 Q 31
D 29 L 32
M 30 Y 33
I 31 I 34
Q 32 G 35
R 33 D 36
S 34 T 37
V 35 R 38
P 36 S 39
G 37 R 40
Y 38 T 41
S 39 A 42
N 40 E 43
I 41 Y 44
I 42 K 45
T 43 A 46
A 44 W 47
I 45 L 48
G 46 L 49
M 47 G 50
L 48 L 51
A 49 L 52
E 50 R 53
R 51 Q 54
F 52 H 55
D 56 C 57
S 57 H 58
N 58 R 59
V 59 V 60
Y 60 L 61
D 61 D 62
L 62 V 63
G 63 A 64
C 64 C 65
S 65 G 66
R 66 T 67
G 67 G 68
A 68 V 69
A 69 D 70
T 70 S 71
L 71 I 72
S 72 M 73
A 73 L 74
R 74 V 75
R 75 E 76
N 76 E 77
N 81 G 78
V 82 F 79
K 83 S 80
I 84 V 81
I 85 T 82
G 86 S 83
I 87 V 84
D 88 D 85
N 89 A 86
S 90 S 87
Q 91 D 88
P 92 K 89
M 93 M 90
V 94 L 91
E 95 K 92
R 96 Y 93
C 97 A 94
R 98 L 95
Q 99 K 96
H 100 E 97
I 101 R 98
A 102 W 99
A 103 N 100
Y 104 R 101
H 105 R 102
S 106 K 103
E 107 E 104
I 108 P 105
P 109 K 109
V 110 W 110
E 111 V 111
I 112 I 112
L 113 E 113
C 114 E 114
N 115 A 115
H 119 D 123
V 120 V 124
E 121 P 125
I 122 A 126
K 123 D 128
N 124 G 129
A 125 F 130
S 126 D 131
M 127 A 132
V 128 V 133
I 129 I 134
L 130 C 135
N 131 L 136
F 132 G 137
T 133 S 139
L 134 F 140
Q 135 A 141
F 136 H 142
L 137 L 143
P 138 P 144
P 139 D 145
E 140 S 151
D 141 E 152
R 142 H 153
I 143 R 154
A 144 L 155
L 145 A 156
L 146 L 157
T 147 K 158
K 148 N 159
I 149 I 160
Y 150 A 161
E 151 S 162
G 152 M 163
L 153 V 164
N 154 R 165
P 155 P 166
N 156 G 167
G 157 G 168
V 158 L 169
L 159 L 170
V 160 V 171
L 161 I 172
S 162 D 173
E 163 H 174
K 164 R 175
F 165 A 248
R 166 S 249
F 167 F 250
E 168 T 251
D 169 E 252
T 170 L 253
K 171 V 254
I 172 Q 255
N 173 E 256
H 174 A 257
L 175 F 258
L 176 G 259
I 177 G 260
D 178 R 261
L 179 C 262
H 180 Q 263
H 181 H 264
Q 182 S 265
F 183 V 266
K 184 L 267
R 185 G 268
A 186 D 269
N 187 F 270
G 188 K 271
Y 189 P 272
S 190 C 282
E 191 Y 283
L 192 F 284
E 193 I 285
V 194 H 286
S 195 V 287
Q 196 L 288
K 197 K 289
R 198 K 290
T 199 T 291
A 200 G 292
TER
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