
PFRMAT AL
TARGET T0088
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 We did not get any good two-way hits with our simple HMMs for this
METHOD target (i.e., template to target and target to template).
METHOD 
METHOD The sequences in our t2k alignment were adhesins, lectins, and adhesin
METHOD precursors.  The adhesins and lectins in PDB seem to be
METHOD beta-sandwiches, and our secondary structure prediction is for a fair
METHOD amount of beta-strand residues in t88.  Research on GafD revealed that
METHOD the protein is a fimbrial lectin (or adhesin), similar in fuction to
METHOD concanavalin A and other plant lectins.  (Saarela, et.al Infection and
METHOD Immunity Jul '96 2857-2860 Saarela et. al Journal of Bacteriology, Mar
METHOD 1995 1477-1484.)
METHOD 
METHOD There are 86 PDB files for concanavalin A, and 366 chains in SCOP for
METHOD the lectin domain 2.28.1, but we did not get a good alignment to any
METHOD of these, much as we would have liked to.
METHOD 
METHOD We chose 1wkt and 1qtsA from our best scoring alignments.
METHOD Both alignments we are submitting have been lightly hand-edited.
METHOD 
METHOD The 1wkt alignment gets excellent conservation on the beta sandwich,
METHOD and got high scoring alignments with both target and template models
METHOD (with essentially the same alignment).  Two predicted strands are in
METHOD an insertion, but these are on the edge of the beta sandwich, and
METHOD could extend the sandwich or make it into a barrel.
METHOD 
METHOD The 1qtsA alignment has 20 identical residues and aligns a nice beta
METHOD sandwich.  It was based on a 2track HMM using both amino acids and
METHOD predicted secondary structure.
MODEL 2
PARENT 1qts_A
G 6 G 692
S 7 S 693
T 8 P 694
E 9 G 695
N 10 I 696
D 11 R 697
V 12 L 698
G 13 G 699
P 14 S 700
S 15 S 701
Q 16 E 702
G 17 D 703
S 18 N 704
Y 19 F 705
S 20 A 706
S 21 R 707
T 22 F 708
H 23 V 709
A 24 C 710
M 25 K 711
D 26 N 712
N 27 N 713
L 28 G 714
P 29 V 715
F 30 L 716
V 31 F 717
Y 32 E 718
N 33 N 719
T 34 Q 720
G 35 L 721
Y 36 L 722
N 37 Q 723
I 38 I 724
G 39 G 725
Y 40 L 726
Q 41 K 727
N 44 S 728
V 45 E 729
W 46 F 730
R 47 R 731
I 48 Q 732
S 49 N 733
G 50 L 734
G 51 G 735
F 52 R 736
C 53 M 737
V 54 F 738
G 55 I 739
L 56 F 740
D 57 Y 741
G 58 G 742
K 59 N 743
V 60 K 744
D 61 T 745
L 62 S 746
P 63 T 747
V 64 Q 748
V 65 F 749
G 66 L 750
S 67 N 751
L 68 F 752
D 69 T 753
G 70 P 754
Q 71 T 755
S 72 L 756
I 73 I 757
Y 74 C 758
G 75 A 759
L 76 D 760
T 77 D 761
E 78 L 762
E 79 Q 763
V 80 T 764
G 81 N 765
L 82 L 766
L 83 N 767
I 84 L 768
W 85 Q 769
M 86 T 770
G 87 K 771
D 88 P 772
T 89 V 773
N 90 D 774
G 94 P 775
T 95 T 776
A 96 V 777
M 97 D 778
S 98 G 779
G 99 G 780
N 100 A 781
S 101 Q 782
W 102 V 783
E 103 Q 784
N 104 Q 785
V 105 V 786
F 106 V 787
S 107 N 788
G 108 I 789
W 109 E 790
C 110 C 791
V 111 I 792
G 112 S 793
N 113 D 794
Y 114 F 795
V 115 T 796
S 116 E 797
T 117 A 798
Q 118 P 799
G 119 V 800
L 120 L 801
S 121 N 802
V 122 I 803
H 123 Q 804
V 124 F 811
R 125 Q 812
P 126 N 813
V 127 V 814
I 128 S 815
L 129 V 816
K 130 K 817
R 131 L 818
N 132 P 819
S 133 I 820
TER
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