PFRMAT AL 
TARGET T0067 
AUTHOR 9070-5088-8627 
REMARK  
REMARK Prediction date: Monday June 22, 1998 
REMARK Group name: UCSC-compbio 
REMARK Authors: Christian Barrett, Melissa Cline, Mark Diekens, Leslie Grate, 
REMARK 	 Kevin Karplus, David Haussler and Richard Hughey 
REMARK University of California, Santa Cruz 
REMARK  
METHOD Overview 
METHOD  
METHOD Fold recognition was performed using the Target98 (SAM-T98) method 
METHOD [3] using SAM version 2.1.1 [1], a refinement of the methods developed 
METHOD by this group for CASP2 [2].  This method attempts to find and multiply  
METHOD align a set of homologs to a given sequence, then create an HMM from that  
METHOD multiple 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 upcoming publications [3,4], 
METHOD combines the Henikoffs' scheme [5], Dirichlet mixtures [6], and an 
METHOD entropy method to set the final weights. 
METHOD  
METHOD Alignment generation 
METHOD  
METHOD The initial step uses BLASTP to search NRP twice: once to produce a set 
METHOD of very close homologs, and once to produce a set of possible homologs. 
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 close homologs found by BLASTP are used as the  
METHOD search set.  The threshold is set very strictly, so that only good matches  
METHOD to the sequence are considered.  This iteration uses a transition regularizer  
METHOD that was designed to match the gap costs used by BLASTP. 
METHOD  
METHOD On subsequent iterations the input alignment is the output from the 
METHOD previous iteration, the search set is the larger set of possible 
METHOD homologs found by BLASTP, and the thresholds are gradually loosened. 
METHOD The second through second-from-last iteration use a ``long-match'' 
METHOD transition regularizer, and the final iteration uses a transition regularizer  
METHOD trained on FSSP alignments. 
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  
METHOD  
METHOD We found no close homologs with wu-blast or double-blast, and the top 
METHOD score with our method (summing both ways) was only -6.04, in a range 
METHOD where over three-quarters of the hits are false positives in our tests. 
METHOD  
METHOD We finally chose the top-scoring hit with the target model, 1rhi2, 
METHOD because we got a moderate number of conserved residues with few gaps 
METHOD or inserts.  We did a little hand-tweaking to improve the alignment. 
METHOD  
METHOD A paper by Schoentgen, Seddiqi, Bucquoy, et al. suggested 3pgk as a 
METHOD template, but we could find no support using our methods for this 
METHOD claim, and the alignment looked little better than a random one. 
METHOD One interesting point is that their predicted ATP-binding site 
METHOD (KGTGLHRYVWLYE) has similar structure in both 3pgk and 1rhi2, though 
METHOD the 3pgk alignment required a large insertion in the site, while the 
METHOD 1rhi2 alignment does not. 
MODEL 1 
PARENT 1rhi_2 
M 1 Q 111 
P 2 C 112 
V 3 N 113 
D 4 A 114 
L 5 T 115 
S 6 K 116 
K 7 F 117 
W 8 H 118 
S 9 S 119 
G 10 G 120 
P 11 C 121 
L 12 L 122 
S 13 L 123 
L 14 V 124 
Q 15 V 125 
E 16 V 126 
V 17 I 127 
D 18 P 128 
E 19 E 129 
Q 20 H 130 
Q 22 Q 131 
H 23 L 132 
P 24 A 133 
L 25 S 134 
H 26 H 135 
V 27 E 136 
V 34 P 149 
D 35 G 150 
E 36 D 151 
L 37 R 152 
G 38 G 153 
K 39 I 154 
V 40 D 155 
L 41 L 156 
T 42 D 157 
P 43 T 158 
T 44 V 159 
Q 45 E 160 
V 46 V 161 
K 47 A 162 
N 48 G 163 
R 49 G 164 
P 50 P 165 
T 51 T 166 
S 52 S 167 
I 53 D 168 
S 54 A 169 
W 55 I 170 
D 56 Y 171 
G 57 N 172 
L 58 M 173 
D 59 D 174 
S 60 G 175 
G 61 T 176 
K 62 L 177 
L 63 L 178 
Y 64 G 179 
T 65 N 180 
L 66 L 181 
V 67 L 182 
L 68 I 183 
T 69 F 184 
H 86 P 185 
F 87 H 186 
L 88 Q 187 
V 89 F 188 
V 90 I 189 
N 91 N 190 
M 92 M 191 
K 93 R 192 
G 94 T 193 
N 95 N 194 
D 96 N 195 
S 99 T 196 
G 100 A 197 
T 101 T 198 
V 102 I 199 
L 103 V 200 
S 104 V 201 
D 105 P 202 
Y 106 Y 203 
V 107 I 204 
G 108 N 205 
S 109 S 206 
G 110 V 207 
P 111 P 208 
P 112 I 209 
K 113 D 210 
G 114 S 211 
T 115 M 212 
G 116 T 213 
L 117 R 214 
H 118 H 215 
R 119 N 216 
Y 120 N 217 
V 121 V 218 
W 122 S 219 
L 123 L 220 
V 124 M 221 
Y 125 V 222 
E 126 V 223 
Q 127 P 224 
D 128 I 225 
R 129 A 226 
P 130 P 227 
L 131 L 228 
K 132 N 229 
TER 
END 
