REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0053AL019_1_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : UCSC-COMPBIO 
REMARK  ---------------------------------------------------------- 
TARGET T0053  
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 Although our best hit for T0053 was 1djxB at about -27 nats (where we  
METHOD expect almost no false positives), we chose to submit the bulk of  
METHOD T0053 aligned to 1fvkA based on clustering of histidine residues,  
METHOD compactness of structure, and the conserved identical residue pattern.  
METHOD 1fvkA received a sum score of about -6 nats, where we expect about  
METHOD half of the hits to be false positives.  
METHOD   
METHOD We performed another search for the piece of T0053 that did not  
METHOD align to 1fvkA and settled with 1ash mainly because of the observed  
METHOD residue identity.  1ash received a summed score of -5.8, again in  
METHOD the range where the likelihood of a false positive is about 50%.  
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1ash 
ATOM      1  N   ILE    22      11.738 -18.807   0.784  1.00  0.00              
ATOM      2  CA  ILE    22      10.809 -17.733   0.546  1.00  0.00              
ATOM      3  C   ILE    22      10.091 -17.461   1.823  1.00  0.00              
ATOM      4  O   ILE    22       9.895 -16.278   2.131  1.00  0.00              
ATOM      5  N   VAL    23       9.750 -18.459   2.638  1.00  0.00              
ATOM      6  CA  VAL    23       9.147 -18.189   3.934  1.00  0.00              
ATOM      7  C   VAL    23      10.093 -17.362   4.803  1.00  0.00              
ATOM      8  O   VAL    23       9.633 -16.373   5.396  1.00  0.00              
ATOM      9  N   ALA    24      11.394 -17.648   4.899  1.00  0.00              
ATOM     10  CA  ALA    24      12.289 -16.815   5.710  1.00  0.00              
ATOM     11  C   ALA    24      12.369 -15.345   5.275  1.00  0.00              
ATOM     12  O   ALA    24      12.392 -14.510   6.162  1.00  0.00              
ATOM     13  N   CYS    25      12.266 -14.958   4.012  1.00  0.00              
ATOM     14  CA  CYS    25      12.196 -13.560   3.612  1.00  0.00              
ATOM     15  C   CYS    25      10.869 -12.964   4.017  1.00  0.00              
ATOM     16  O   CYS    25      10.835 -11.822   4.458  1.00  0.00              
ATOM     17  N   GLU    26       9.772 -13.703   3.929  1.00  0.00              
ATOM     18  CA  GLU    26       8.534 -13.169   4.370  1.00  0.00              
ATOM     19  C   GLU    26       8.575 -12.992   5.867  1.00  0.00              
ATOM     20  O   GLU    26       8.026 -12.012   6.360  1.00  0.00              
ATOM     21  N   ARG    27       9.196 -13.876   6.643  1.00  0.00              
ATOM     22  CA  ARG    27       9.246 -13.705   8.089  1.00  0.00              
ATOM     23  C   ARG    27      10.172 -12.540   8.444  1.00  0.00              
ATOM     24  O   ARG    27       9.856 -11.763   9.361  1.00  0.00              
ATOM     25  N   LEU    29      11.301 -12.298   7.753  1.00  0.00              
ATOM     26  CA  LEU    29      12.184 -11.207   8.175  1.00  0.00              
ATOM     27  C   LEU    29      11.543  -9.887   7.931  1.00  0.00              
ATOM     28  O   LEU    29      11.727  -9.009   8.751  1.00  0.00              
ATOM     29  N   ALA    30      10.736  -9.624   6.918  1.00  0.00              
ATOM     30  CA  ALA    30      10.157  -8.296   6.896  1.00  0.00              
ATOM     31  C   ALA    30       8.850  -8.170   7.687  1.00  0.00              
ATOM     32  O   ALA    30       8.521  -7.052   8.055  1.00  0.00              
ATOM     33  N   ALA    31       8.094  -9.214   8.049  1.00  0.00              
ATOM     34  CA  ALA    31       6.949  -9.074   8.956  1.00  0.00              
ATOM     35  C   ALA    31       7.461  -8.873  10.383  1.00  0.00              
ATOM     36  O   ALA    31       6.766  -8.326  11.224  1.00  0.00              
ATOM     37  N   SER    32       8.675  -9.273  10.764  1.00  0.00              
ATOM     38  CA  SER    32       9.226  -9.023  12.088  1.00  0.00              
ATOM     39  C   SER    32      10.126  -7.794  12.149  1.00  0.00              
ATOM     40  O   SER    32      10.670  -7.513  13.203  1.00  0.00              
ATOM     41  N   CYS    33      10.254  -6.995  11.109  1.00  0.00              
ATOM     42  CA  CYS    33      11.132  -5.876  11.099  1.00  0.00              
ATOM     43  C   CYS    33      10.745  -4.794  12.082  1.00  0.00              
ATOM     44  O   CYS    33      11.600  -4.137  12.701  1.00  0.00              
ATOM     45  N   PRO    34       9.452  -4.579  12.308  1.00  0.00              
ATOM     46  CA  PRO    34       9.092  -3.511  13.220  1.00  0.00              
ATOM     47  C   PRO    34       9.360  -3.869  14.680  1.00  0.00              
ATOM     48  O   PRO    34       9.230  -2.998  15.517  1.00  0.00              
ATOM     49  N   ASP    35       9.750  -5.079  15.083  1.00  0.00              
ATOM     50  CA  ASP    35      10.131  -5.413  16.451  1.00  0.00              
ATOM     51  C   ASP    35      11.546  -5.946  16.260  1.00  0.00              
ATOM     52  O   ASP    35      11.813  -7.114  15.937  1.00  0.00              
ATOM     53  N   ARG    36      12.495  -5.065  16.475  1.00  0.00              
ATOM     54  CA  ARG    36      13.854  -5.446  16.277  1.00  0.00              
ATOM     55  C   ARG    36      14.347  -6.579  17.138  1.00  0.00              
ATOM     56  O   ARG    36      15.270  -7.258  16.678  1.00  0.00              
ATOM     57  N   ASP    37      13.795  -6.854  18.327  1.00  0.00              
ATOM     58  CA  ASP    37      14.274  -7.955  19.147  1.00  0.00              
ATOM     59  C   ASP    37      13.913  -9.291  18.527  1.00  0.00              
ATOM     60  O   ASP    37      14.749 -10.204  18.460  1.00  0.00              
ATOM     61  N   LEU    38      12.703  -9.378  17.960  1.00  0.00              
ATOM     62  CA  LEU    38      12.324 -10.580  17.225  1.00  0.00              
ATOM     63  C   LEU    38      13.096 -10.719  15.934  1.00  0.00              
ATOM     64  O   LEU    38      13.536 -11.839  15.614  1.00  0.00              
ATOM     65  N   PHE    39      13.262  -9.614  15.198  1.00  0.00              
ATOM     66  CA  PHE    39      13.984  -9.606  13.925  1.00  0.00              
ATOM     67  C   PHE    39      15.402 -10.132  14.109  1.00  0.00              
ATOM     68  O   PHE    39      15.833 -11.038  13.385  1.00  0.00              
ATOM     69  N   ARG    40      16.120  -9.625  15.128  1.00  0.00              
ATOM     70  CA  ARG    40      17.505 -10.013  15.361  1.00  0.00              
ATOM     71  C   ARG    40      17.569 -11.403  15.815  1.00  0.00              
ATOM     72  O   ARG    40      18.447 -12.115  15.359  1.00  0.00              
ATOM     73  N   ALA    41      16.729 -11.827  16.749  1.00  0.00              
ATOM     74  CA  ALA    41      16.687 -13.216  17.140  1.00  0.00              
ATOM     75  C   ALA    41      16.443 -14.232  16.001  1.00  0.00              
ATOM     76  O   ALA    41      17.061 -15.295  15.910  1.00  0.00              
ATOM     77  N   PHE    42      15.532 -13.902  15.104  1.00  0.00              
ATOM     78  CA  PHE    42      15.267 -14.717  13.928  1.00  0.00              
ATOM     79  C   PHE    42      16.465 -14.776  12.971  1.00  0.00              
ATOM     80  O   PHE    42      16.791 -15.856  12.484  1.00  0.00              
ATOM     81  N   THR    43      17.149 -13.678  12.674  1.00  0.00              
ATOM     82  CA  THR    43      18.382 -13.674  11.905  1.00  0.00              
ATOM     83  C   THR    43      19.451 -14.562  12.557  1.00  0.00              
ATOM     84  O   THR    43      20.122 -15.353  11.881  1.00  0.00              
ATOM     85  N   SER    44      19.638 -14.552  13.877  1.00  0.00              
ATOM     86  CA  SER    44      20.614 -15.432  14.529  1.00  0.00              
ATOM     87  C   SER    44      20.221 -16.883  14.312  1.00  0.00              
ATOM     88  O   SER    44      21.058 -17.742  14.012  1.00  0.00              
ATOM     89  N   GLY    45      18.935 -17.193  14.398  1.00  0.00              
ATOM     90  CA  GLY    45      18.478 -18.554  14.186  1.00  0.00              
ATOM     91  C   GLY    45      18.680 -18.971  12.753  1.00  0.00              
ATOM     92  O   GLY    45      19.114 -20.097  12.536  1.00  0.00              
ATOM     93  N   MET    46      18.498 -18.091  11.775  1.00  0.00              
ATOM     94  CA  MET    46      18.811 -18.380  10.384  1.00  0.00              
ATOM     95  C   MET    46      20.266 -18.729  10.307  1.00  0.00              
ATOM     96  O   MET    46      20.606 -19.661   9.586  1.00  0.00              
ATOM     97  N   ILE    47      21.157 -18.042  11.035  1.00  0.00              
ATOM     98  CA  ILE    47      22.581 -18.358  10.978  1.00  0.00              
ATOM     99  C   ILE    47      22.826 -19.706  11.597  1.00  0.00              
ATOM    100  O   ILE    47      23.527 -20.546  11.041  1.00  0.00              
ATOM    101  N   ILE    48      22.168 -19.970  12.703  1.00  0.00              
ATOM    102  CA  ILE    48      22.351 -21.194  13.433  1.00  0.00              
ATOM    103  C   ILE    48      21.895 -22.398  12.627  1.00  0.00              
ATOM    104  O   ILE    48      22.514 -23.467  12.677  1.00  0.00              
ATOM    105  N   ARG    49      20.839 -22.231  11.834  1.00  0.00              
ATOM    106  CA  ARG    49      20.304 -23.298  11.007  1.00  0.00              
ATOM    107  C   ARG    49      21.191 -23.615   9.828  1.00  0.00              
ATOM    108  O   ARG    49      21.076 -24.691   9.266  1.00  0.00              
ATOM    109  N   LYS    50      22.071 -22.740   9.391  1.00  0.00              
ATOM    110  CA  LYS    50      22.966 -23.123   8.329  1.00  0.00              
ATOM    111  C   LYS    50      24.150 -23.773   9.004  1.00  0.00              
ATOM    112  O   LYS    50      24.650 -24.810   8.584  1.00  0.00              
ATOM    113  N   LEU    51      24.622 -23.176  10.079  1.00  0.00              
ATOM    114  CA  LEU    51      25.718 -23.739  10.827  1.00  0.00              
ATOM    115  C   LEU    51      25.461 -25.153  11.349  1.00  0.00              
ATOM    116  O   LEU    51      26.342 -25.985  11.492  1.00  0.00              
ATOM    117  N   ARG    52      24.204 -25.470  11.566  1.00  0.00              
ATOM    118  CA  ARG    52      23.661 -26.762  12.030  1.00  0.00              
ATOM    119  C   ARG    52      24.193 -27.859  11.128  1.00  0.00              
ATOM    120  O   ARG    52      24.723 -28.891  11.577  1.00  0.00              
ATOM    121  N   ASP    55      24.036 -27.566   9.846  1.00  0.00              
ATOM    122  CA  ASP    55      24.370 -28.432   8.743  1.00  0.00              
ATOM    123  C   ASP    55      25.667 -27.996   8.057  1.00  0.00              
ATOM    124  O   ASP    55      25.891 -28.263   6.874  1.00  0.00              
ATOM    125  N   GLY    56      26.534 -27.247   8.726  1.00  0.00              
ATOM    126  CA  GLY    56      27.846 -26.825   8.209  1.00  0.00              
ATOM    127  C   GLY    56      27.869 -26.095   6.880  1.00  0.00              
ATOM    128  O   GLY    56      28.825 -26.168   6.098  1.00  0.00              
ATOM    129  N   ILE    57      26.817 -25.324   6.630  1.00  0.00              
ATOM    130  CA  ILE    57      26.805 -24.465   5.466  1.00  0.00              
ATOM    131  C   ILE    57      27.475 -23.234   6.079  1.00  0.00              
ATOM    132  O   ILE    57      26.834 -22.413   6.729  1.00  0.00              
ATOM    133  N   ASP    58      28.787 -23.101   6.043  1.00  0.00              
ATOM    134  CA  ASP    58      29.432 -21.907   6.586  1.00  0.00              
ATOM    135  C   ASP    58      29.668 -21.032   5.392  1.00  0.00              
ATOM    136  O   ASP    58      30.123 -21.508   4.343  1.00  0.00              
ATOM    137  N   ILE    59      29.362 -19.744   5.535  1.00  0.00              
ATOM    138  CA  ILE    59      29.434 -18.768   4.446  1.00  0.00              
ATOM    139  C   ILE    59      30.116 -17.479   4.867  1.00  0.00              
ATOM    140  O   ILE    59      29.748 -16.986   5.942  1.00  0.00              
ATOM    141  N   THR    61      31.081 -16.907   4.093  1.00  0.00              
ATOM    142  CA  THR    61      31.667 -15.588   4.348  1.00  0.00              
ATOM    143  C   THR    61      30.581 -14.524   4.457  1.00  0.00              
ATOM    144  O   THR    61      29.574 -14.534   3.736  1.00  0.00              
ATOM    145  N   PRO    62      30.737 -13.566   5.359  1.00  0.00              
ATOM    146  CA  PRO    62      29.670 -12.652   5.685  1.00  0.00              
ATOM    147  C   PRO    62      29.294 -11.854   4.425  1.00  0.00              
ATOM    148  O   PRO    62      28.157 -11.443   4.314  1.00  0.00              
ATOM    149  N   LEU    63      25.941 -13.074   2.432  1.00  0.00              
ATOM    150  CA  LEU    63      24.655 -12.655   2.958  1.00  0.00              
ATOM    151  C   LEU    63      24.325 -11.302   2.367  1.00  0.00              
ATOM    152  O   LEU    63      23.161 -11.155   1.992  1.00  0.00              
ATOM    153  N   GLN    64      25.273 -10.357   2.182  1.00  0.00              
ATOM    154  CA  GLN    64      25.046  -9.096   1.463  1.00  0.00              
ATOM    155  C   GLN    64      24.718  -9.473   0.026  1.00  0.00              
ATOM    156  O   GLN    64      23.734  -8.958  -0.494  1.00  0.00              
ATOM    157  N   ALA    65      25.423 -10.373  -0.671  1.00  0.00              
ATOM    158  CA  ALA    65      25.082 -10.633  -2.061  1.00  0.00              
ATOM    159  C   ALA    65      23.677 -11.133  -2.251  1.00  0.00              
ATOM    160  O   ALA    65      23.020 -10.797  -3.238  1.00  0.00              
ATOM    161  N   LEU    66      23.183 -11.833  -1.247  1.00  0.00              
ATOM    162  CA  LEU    66      21.860 -12.378  -1.298  1.00  0.00              
ATOM    163  C   LEU    66      20.877 -11.269  -1.556  1.00  0.00              
ATOM    164  O   LEU    66      20.098 -11.427  -2.491  1.00  0.00              
ATOM    165  N   GLN    67      20.884 -10.141  -0.845  1.00  0.00              
ATOM    166  CA  GLN    67      19.833  -9.164  -1.062  1.00  0.00              
ATOM    167  C   GLN    67      19.940  -8.533  -2.411  1.00  0.00              
ATOM    168  O   GLN    67      18.883  -8.154  -2.933  1.00  0.00              
ATOM    169  N   LYS    68      21.113  -8.481  -3.060  1.00  0.00              
ATOM    170  CA  LYS    68      21.160  -8.059  -4.485  1.00  0.00              
ATOM    171  C   LYS    68      20.417  -9.110  -5.350  1.00  0.00              
ATOM    172  O   LYS    68      19.590  -8.791  -6.215  1.00  0.00              
ATOM    173  N   LEU    69      20.626 -10.391  -5.074  1.00  0.00              
ATOM    174  CA  LEU    69      19.948 -11.475  -5.766  1.00  0.00              
ATOM    175  C   LEU    69      18.463 -11.518  -5.547  1.00  0.00              
ATOM    176  O   LEU    69      17.741 -11.910  -6.459  1.00  0.00              
END
