PFRMAT AL 
TARGET T0081 
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 have submitted 3chy as the template for T0081.  With a score of 
METHOD -4.250, it was one of our top FSSP alignments.  While we have not 
METHOD calibrated these FSSP models, we estimate by analogy to our target98 
METHOD models that this structure is a false positive with roughly a 60% 
METHOD likelihood. 
METHOD  
METHOD We had a number of hits in this range (where we expect most to 
METHOD be false positives), but found that the known active site residues 
METHOD of T0081 only clustered nicely near the active site of 3chy.  Active 
METHOD site residues were taken from 
METHOD  
METHOD  Saadat D, et al.  
METHOD  Identification of catalytic bases in the active site of 
METHOD    Escherichia coli methylglyoxal synthase: cloning, expression, and 
METHOD    functional characterization of conserved aspartic acid residues.  
METHOD  Biochemistry. 1998 Jul 14; 37(28): 10074-10086.  
METHOD  
METHOD Our main competing structure for 3chy was 1auoA.  It displayed  
METHOD encouraging residue conservation in the core and clustered some of the 
METHOD active site residues fairly well.  Noting that 3chy and 1auoA are both 
METHOD composed of a central beta sheet sandwiched between alpha helices, we 
METHOD felt encouraged that we had the correct fold.  Since the 3chy alignment 
METHOD was the least disruptive and only single model predictions are being 
METHOD allowed for this CASP, we chose to 3chy over 1auoA. 
MODEL 1 
PARENT 3chy 
P 9 A 2 
A 10 D 3 
R 11 K 4 
K 12 E 5 
H 13 L 6 
I 14 K 7 
A 15 F 8 
L 16 L 9 
V 17 V 10 
A 18 V 11 
H 19 D 12 
D 20 D 13 
H 21 F 14 
K 23 S 15 
Q 24 T 16 
M 25 M 17 
L 26 R 18 
M 27 R 19 
S 28 I 20 
W 29 V 21 
V 30 R 22 
E 31 N 23 
R 32 L 24 
H 33 L 25 
Q 34 K 26 
P 35 E 27 
L 36 L 28 
L 37 G 29 
E 38 F 30 
Q 39 N 31 
G 66 N 32 
P 67 V 33 
M 68 E 34 
G 69 E 35 
G 70 A 36 
D 71 E 37 
Q 72 D 38 
Q 73 G 39 
V 74 V 40 
G 75 D 41 
A 76 A 42 
L 77 L 43 
I 78 N 44 
S 79 K 45 
E 80 L 46 
G 81 G 49 
K 82 G 50 
I 83 Y 51 
D 84 G 52 
V 85 F 53 
L 86 V 54 
I 87 I 55 
F 88 S 56 
F 89 D 57 
W 90 W 58 
D 91 N 59 
D 99 M 60 
P 100 P 61 
D 101 N 62 
V 102 M 63 
K 103 D 64 
A 104 G 65 
L 105 L 66 
L 106 E 67 
R 107 L 68 
L 108 L 69 
A 109 K 70 
T 110 T 71 
V 111 I 72 
W 112 S 79 
N 113 A 80 
I 114 L 81 
P 115 P 82 
V 116 V 83 
A 117 L 84 
T 118 M 85 
N 119 V 86 
V 120 T 87 
A 121 A 88 
T 122 E 89 
A 123 A 90 
D 124 K 91 
F 125 K 92 
I 126 E 93 
I 127 N 94 
Q 128 I 95 
S 129 I 96 
P 130 G 102 
H 131 A 103 
F 132 S 104 
N 133 G 105 
D 134 Y 106 
A 135 V 107 
V 136 V 108 
D 137 K 109 
P 141 P 110 
D 142 F 111 
Y 143 T 112 
Q 144 A 113 
R 145 A 114 
Y 146 T 115 
L 147 L 116 
A 148 E 117 
D 149 E 118 
R 150 K 119 
L 151 L 120 
K 152 N 121 
TER 
END 
