 
PFRMAT AL 
TARGET T0079 
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, but our 
METHOD method got a fairly strong hit for 1neq (score -9.7, which is the 
METHOD range where only about 25% of the hits are false positives).  Most of 
METHOD the other hits were also to DNA-binding proteins, so we had reasonable 
METHOD confidence in there being a helix-turn-helix domain. 
METHOD  
METHOD We aligned the first half of T0079 to 1neq, and then treated the 
METHOD second half as a separate target.  Somewhat surprisingly, we again had 
METHOD a fairly strong hit on DNA-binding proteins (1san at -8.03, in a range 
METHOD where about 60% of the hits are false positives).  The two 
METHOD domains seem to be too close to bind DNA simultaneously. 
METHOD  
METHOD We hand-edited the alignments to make the domain boundary match up and 
METHOD to improve the alignment to 1san.  We have considerably more 
METHOD confidence in the 1neq alignment than the 1san alignment. 
MODEL 1 
PARENT 1san 
R 63 R 10 
K 64 Y 11 
M 65 Q 12 
T 66 T 13 
E 67 L 14 
I 68 E 15 
A 69 L 16 
Q 70 E 17 
K 71 K 18 
L 72 E 19 
K 73 F 20 
E 74 H 21 
S 75 F 22 
N 76 N 23 
P 78 R 24 
I 79 Y 25 
L 80 L 26 
Y 81 T 27 
L 82 R 28 
A 83 R 29 
E 84 R 30 
R 85 R 31 
Y 86 I 32 
G 87 E 33 
F 88 I 34 
E 89 A 35 
S 90 H 36 
Q 91 L 38 
Q 92 S 39 
T 93 L 40 
L 94 T 41 
T 95 E 42 
R 96 R 43 
T 97 Q 44 
F 98 I 45 
K 99 K 46 
N 100 I 47 
Y 101 W 48 
F 102 F 49 
D 103 Q 50 
V 104 N 51 
P 105 R 52 
P 106 R 53 
H 107 M 54 
K 108 K 55 
Y 109 W 56 
R 110 K 57 
M 111 K 58 
T 112 E 59 
N 113 N 60 
M 114 K 61 
Q 115 T 62 
G 116 G 64 
E 117 E 65 
S 118 P 66 
R 119 G 67 
TER 
END 
