PFRMAT AL 
TARGET T0083 
AUTHOR 9070-5088-8627 
REMARK  
REMARK Prediction date: 4 Sept 1998 
REMARK Group name: UCSC-compbio 
REMARK Authors: Christian Barrett, Melissa Cline, Mark Diekhans, 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 got fairly strong hits for repressor-like DNA-binding domains, 
METHOD especially 1lmb3 and 1lliA (-20, which is in the range where only 
METHOD about 6% of the hits were false positives in our tests).  Despite the 
METHOD strong scores, we are not convinced that this prediction is correct, 
METHOD since there is no reason to believe that T0083 (cyanase) binds DNA. 
METHOD  
METHOD We looked for other possible alignments, and got reasonable-looking 
METHOD alignments to annexin i (1ain) and to glutathione s-transferase a4-4 
METHOD (1gukA).  The annexin alignment has no more functional justification 
METHOD than the repressor one, but the glutathione transferase is a metabolic 
METHOD enzyme.  
METHOD  
METHOD All our alignments cover only the helices near the beginning of the 
METHOD alignment, and they all pack the helices differently.  We expect some 
METHOD beta strands towards the end of the sequence (since CD spectroscopy 
METHOD reportedly indicates both alpha and beta structure). 
METHOD  
METHOD We regard it as quite likely that T0083 is a new fold, but are 
METHOD submitting the 1lmb3, 1ain, and 1gukA alignments as remote 
METHOD possibilities. 
METHOD  
MODEL 2 
PARENT 1guk_A 
I 18 L 123 
L 19 I 124 
L 20 L 125 
S 21 S 126 
K 22 R 127 
A 23 A 128 
K 24 K 129 
K 25 T 130 
D 26 R 131 
L 27 P 134 
S 28 V 135 
F 29 F 136 
A 30 E 137 
E 31 K 138 
I 32 I 139 
A 33 L 140 
D 34 K 141 
G 35 D 142 
T 36 H 143 
G 37 G 144 
A 45 E 145 
A 46 A 146 
L 47 F 147 
L 48 L 148 
G 49 V 149 
Q 50 G 150 
Q 51 N 151 
A 52 Q 152 
L 53 L 153 
P 54 S 154 
A 55 W 155 
D 56 A 156 
A 57 D 157 
A 58 I 158 
R 59 Q 159 
L 60 L 160 
V 61 L 161 
G 62 E 162 
A 63 A 163 
K 64 I 164 
L 65 L 165 
D 66 M 166 
L 67 V 167 
D 68 E 168 
E 69 E 169 
D 70 L 170 
S 71 S 171 
I 72 A 172 
L 73 P 173 
L 74 V 174 
L 75 L 175 
Q 76 S 176 
M 77 D 177 
I 78 F 178 
P 79 P 179 
L 80 L 180 
R 81 L 181 
G 82 Q 182 
C 83 A 183 
I 84 F 184 
D 85 K 185 
D 86 T 186 
R 87 R 187 
I 88 I 188 
P 89 S 189 
T 90 N 190 
D 91 I 191 
P 92 P 192 
T 93 T 193 
M 94 I 194 
Y 95 K 195 
R 96 K 196 
F 97 F 197 
Y 98 L 198 
TER 
END 
