REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0077AL019_1_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : UCSC-COMPBIO 
REMARK  ---------------------------------------------------------- 
TARGET T0077  
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 an alignemnt that aligns 1tif to the first half of   
METHOD T0077 and 1mit to the second half.    
METHOD   
METHOD 1tif was our second best model library hit when score summing was  
METHOD used.  With a score of -5.9, 1tif falls in the range where we expect a  
METHOD false positive with 85% likelihood.  We were encourages by this hit  
METHOD because of the residue conservation and the fact that it is a ribosome  
METHOD binding factor.  
METHOD   
METHOD Since 1tif only aligns the first half of T0077, we performed a target  
METHOD search for the remaining sequence.  We chose 1mit because it  
METHOD had an okay score with the FSSP model (-6.2), seemed to have decent residue  
METHOD conservation, and could plausibly form a compact structure with 1tif.  
METHOD   
METHOD Our confidence in both predictions is not terribly strong, but we feel  
METHOD more certain about 1tif than 1mit.MODEL 1  
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1tif 
ATOM      1  N   GLU     8       9.092  -1.981  13.524  1.00  0.00              
ATOM      2  CA  GLU     8      10.331  -2.095  12.753  1.00  0.00              
ATOM      3  C   GLU     8      11.405  -1.035  13.030  1.00  0.00              
ATOM      4  O   GLU     8      12.519  -1.147  12.522  1.00  0.00              
ATOM      5  N   SER     9      11.069   0.010  13.782  1.00  0.00              
ATOM      6  CA  SER     9      12.045   1.052  14.104  1.00  0.00              
ATOM      7  C   SER     9      13.049   0.532  15.132  1.00  0.00              
ATOM      8  O   SER     9      14.136   1.096  15.297  1.00  0.00              
ATOM      9  N   ILE    10      12.652  -0.511  15.858  1.00  0.00              
ATOM     10  CA  ILE    10      13.488  -1.113  16.890  1.00  0.00              
ATOM     11  C   ILE    10      14.675  -1.823  16.249  1.00  0.00              
ATOM     12  O   ILE    10      14.509  -2.586  15.302  1.00  0.00              
ATOM     13  N   ASN    11      15.869  -1.560  16.770  1.00  0.00              
ATOM     14  CA  ASN    11      17.084  -2.162  16.235  1.00  0.00              
ATOM     15  C   ASN    11      17.664  -3.299  17.087  1.00  0.00              
ATOM     16  O   ASN    11      18.520  -4.052  16.615  1.00  0.00              
ATOM     17  N   GLN    12      17.207  -3.424  18.331  1.00  0.00              
ATOM     18  CA  GLN    12      17.696  -4.468  19.235  1.00  0.00              
ATOM     19  C   GLN    12      17.508  -5.885  18.692  1.00  0.00              
ATOM     20  O   GLN    12      16.438  -6.227  18.184  1.00  0.00              
ATOM     21  N   LYS    13      18.549  -6.708  18.817  1.00  0.00              
ATOM     22  CA  LYS    13      18.506  -8.095  18.352  1.00  0.00              
ATOM     23  C   LYS    13      17.556  -8.920  19.221  1.00  0.00              
ATOM     24  O   LYS    13      16.812  -9.771  18.718  1.00  0.00              
ATOM     25  N   LEU    14      17.641  -8.712  20.529  1.00  0.00              
ATOM     26  CA  LEU    14      16.792  -9.402  21.487  1.00  0.00              
ATOM     27  C   LEU    14      16.241  -8.397  22.479  1.00  0.00              
ATOM     28  O   LEU    14      16.898  -7.399  22.796  1.00  0.00              
ATOM     29  N   ALA    15      15.030  -8.661  22.957  1.00  0.00              
ATOM     30  CA  ALA    15      14.358  -7.779  23.905  1.00  0.00              
ATOM     31  C   ALA    15      13.650  -8.606  24.978  1.00  0.00              
ATOM     32  O   ALA    15      13.428  -9.805  24.794  1.00  0.00              
ATOM     33  N   LEU    16      13.358  -7.989  26.117  1.00  0.00              
ATOM     34  CA  LEU    16      12.609  -8.662  27.170  1.00  0.00              
ATOM     35  C   LEU    16      11.182  -8.209  26.865  1.00  0.00              
ATOM     36  O   LEU    16      10.912  -7.007  26.789  1.00  0.00              
ATOM     37  N   VAL    17      10.281  -9.167  26.690  1.00  0.00              
ATOM     38  CA  VAL    17       8.906  -8.873  26.314  1.00  0.00              
ATOM     39  C   VAL    17       7.855  -8.964  27.414  1.00  0.00              
ATOM     40  O   VAL    17       7.810  -9.940  28.158  1.00  0.00              
ATOM     41  N   ILE    18       7.018  -7.930  27.512  1.00  0.00              
ATOM     42  CA  ILE    18       5.917  -7.879  28.479  1.00  0.00              
ATOM     43  C   ILE    18       4.667  -7.679  27.615  1.00  0.00              
ATOM     44  O   ILE    18       4.633  -6.772  26.769  1.00  0.00              
ATOM     45  N   LYS    19       3.653  -8.525  27.786  1.00  0.00              
ATOM     46  CA  LYS    19       2.459  -8.384  26.959  1.00  0.00              
ATOM     47  C   LYS    19       1.493  -7.314  27.459  1.00  0.00              
ATOM     48  O   LYS    19       1.710  -6.727  28.516  1.00  0.00              
ATOM     49  N   SER    20       0.393  -7.125  26.736  1.00  0.00              
ATOM     50  CA  SER    20      -0.592  -6.098  27.073  1.00  0.00              
ATOM     51  C   SER    20      -1.226  -6.198  28.464  1.00  0.00              
ATOM     52  O   SER    20      -1.735  -5.205  28.983  1.00  0.00              
ATOM     53  N   GLY    21      -1.155  -7.377  29.080  1.00  0.00              
ATOM     54  CA  GLY    21      -1.728  -7.583  30.411  1.00  0.00              
ATOM     55  C   GLY    21      -0.710  -7.646  31.555  1.00  0.00              
ATOM     56  O   GLY    21      -1.081  -7.848  32.715  1.00  0.00              
ATOM     57  N   LYS    22       0.569  -7.471  31.235  1.00  0.00              
ATOM     58  CA  LYS    22       1.591  -7.505  32.266  1.00  0.00              
ATOM     59  C   LYS    22       2.310  -8.833  32.413  1.00  0.00              
ATOM     60  O   LYS    22       3.135  -8.999  33.311  1.00  0.00              
ATOM     61  N   TYR    23       1.999  -9.782  31.538  1.00  0.00              
ATOM     62  CA  TYR    23       2.632 -11.098  31.566  1.00  0.00              
ATOM     63  C   TYR    23       4.062 -10.954  31.044  1.00  0.00              
ATOM     64  O   TYR    23       4.280 -10.383  29.972  1.00  0.00              
ATOM     65  N   THR    24       5.029 -11.423  31.831  1.00  0.00              
ATOM     66  CA  THR    24       6.443 -11.356  31.465  1.00  0.00              
ATOM     67  C   THR    24       6.760 -12.542  30.557  1.00  0.00              
ATOM     68  O   THR    24       6.913 -13.672  31.029  1.00  0.00              
ATOM     69  N   LEU    25       6.844 -12.283  29.257  1.00  0.00              
ATOM     70  CA  LEU    25       7.113 -13.322  28.267  1.00  0.00              
ATOM     71  C   LEU    25       8.575 -13.766  28.152  1.00  0.00              
ATOM     72  O   LEU    25       8.874 -14.757  27.480  1.00  0.00              
ATOM     73  N   GLY    26       9.475 -13.056  28.824  1.00  0.00              
ATOM     74  CA  GLY    26      10.879 -13.419  28.782  1.00  0.00              
ATOM     75  C   GLY    26      11.646 -12.786  27.640  1.00  0.00              
ATOM     76  O   GLY    26      11.147 -11.889  26.956  1.00  0.00              
ATOM     77  N   TYR    27      12.876 -13.249  27.446  1.00  0.00              
ATOM     78  CA  TYR    27      13.738 -12.724  26.398  1.00  0.00              
ATOM     79  C   TYR    27      13.373 -13.364  25.071  1.00  0.00              
ATOM     80  O   TYR    27      13.340 -14.589  24.950  1.00  0.00              
ATOM     81  N   LYS    28      13.082 -12.526  24.084  1.00  0.00              
ATOM     82  CA  LYS    28      12.699 -12.984  22.758  1.00  0.00              
ATOM     83  C   LYS    28      13.506 -12.261  21.691  1.00  0.00              
ATOM     84  O   LYS    28      13.979 -11.144  21.906  1.00  0.00              
ATOM     85  N   SER    29      13.662 -12.901  20.538  1.00  0.00              
ATOM     86  CA  SER    29      14.349 -12.263  19.429  1.00  0.00              
ATOM     87  C   SER    29      13.367 -11.179  18.983  1.00  0.00              
ATOM     88  O   SER    29      12.158 -11.306  19.214  1.00  0.00              
ATOM     89  N   THR    30      13.871 -10.111  18.377  1.00  0.00              
ATOM     90  CA  THR    30      13.006  -9.041  17.897  1.00  0.00              
ATOM     91  C   THR    30      11.968  -9.609  16.926  1.00  0.00              
ATOM     92  O   THR    30      10.804  -9.212  16.950  1.00  0.00              
ATOM     93  N   VAL    31      12.399 -10.543  16.081  1.00  0.00              
ATOM     94  CA  VAL    31      11.523 -11.188  15.103  1.00  0.00              
ATOM     95  C   VAL    31      10.314 -11.871  15.763  1.00  0.00              
ATOM     96  O   VAL    31       9.174 -11.677  15.334  1.00  0.00              
ATOM     97  N   LYS    32      10.566 -12.673  16.796  1.00  0.00              
ATOM     98  CA  LYS    32       9.481 -13.366  17.488  1.00  0.00              
ATOM     99  C   LYS    32       8.578 -12.372  18.218  1.00  0.00              
ATOM    100  O   LYS    32       7.357 -12.542  18.251  1.00  0.00              
ATOM    101  N   SER    33       9.177 -11.328  18.786  1.00  0.00              
ATOM    102  CA  SER    33       8.417 -10.303  19.499  1.00  0.00              
ATOM    103  C   SER    33       7.460  -9.614  18.528  1.00  0.00              
ATOM    104  O   SER    33       6.299  -9.357  18.862  1.00  0.00              
ATOM    105  N   LEU    34       7.947  -9.343  17.319  1.00  0.00              
ATOM    106  CA  LEU    34       7.147  -8.706  16.278  1.00  0.00              
ATOM    107  C   LEU    34       6.001  -9.628  15.832  1.00  0.00              
ATOM    108  O   LEU    34       4.905  -9.163  15.505  1.00  0.00              
ATOM    109  N   ARG    35       6.260 -10.931  15.816  1.00  0.00              
ATOM    110  CA  ARG    35       5.232 -11.901  15.439  1.00  0.00              
ATOM    111  C   ARG    35       4.110 -11.930  16.473  1.00  0.00              
ATOM    112  O   ARG    35       2.930 -11.935  16.115  1.00  0.00              
ATOM    113  N   GLN    36       0.146 -11.004  15.763  1.00  0.00              
ATOM    114  CA  GLN    36      -0.978 -11.920  15.922  1.00  0.00              
ATOM    115  C   GLN    36      -2.051 -11.346  16.839  1.00  0.00              
ATOM    116  O   GLN    36      -3.224 -11.704  16.727  1.00  0.00              
ATOM    117  N   GLY    37      -1.654 -10.424  17.712  1.00  0.00              
ATOM    118  CA  GLY    37      -2.582  -9.787  18.635  1.00  0.00              
ATOM    119  C   GLY    37      -3.102  -8.455  18.116  1.00  0.00              
ATOM    120  O   GLY    37      -3.866  -7.776  18.803  1.00  0.00              
ATOM    121  N   LYS    38      -2.680  -8.088  16.909  1.00  0.00              
ATOM    122  CA  LYS    38      -3.085  -6.834  16.282  1.00  0.00              
ATOM    123  C   LYS    38      -2.738  -5.637  17.162  1.00  0.00              
ATOM    124  O   LYS    38      -3.534  -4.704  17.323  1.00  0.00              
ATOM    125  N   SER    39      -1.548  -5.694  17.751  1.00  0.00              
ATOM    126  CA  SER    39      -1.034  -4.648  18.623  1.00  0.00              
ATOM    127  C   SER    39       0.360  -4.242  18.128  1.00  0.00              
ATOM    128  O   SER    39       0.879  -4.811  17.160  1.00  0.00              
ATOM    129  N   LYS    40       0.964  -3.269  18.799  1.00  0.00              
ATOM    130  CA  LYS    40       2.289  -2.786  18.425  1.00  0.00              
ATOM    131  C   LYS    40       3.324  -3.260  19.434  1.00  0.00              
ATOM    132  O   LYS    40       2.991  -3.565  20.579  1.00  0.00              
ATOM    133  N   LEU    41       4.575  -3.319  18.992  1.00  0.00              
ATOM    134  CA  LEU    41       5.698  -3.694  19.845  1.00  0.00              
ATOM    135  C   LEU    41       6.319  -2.335  20.172  1.00  0.00              
ATOM    136  O   LEU    41       6.819  -1.652  19.282  1.00  0.00              
ATOM    137  N   ILE    42       6.249  -1.928  21.432  1.00  0.00              
ATOM    138  CA  ILE    42       6.765  -0.625  21.833  1.00  0.00              
ATOM    139  C   ILE    42       7.996  -0.715  22.734  1.00  0.00              
ATOM    140  O   ILE    42       7.984  -1.408  23.751  1.00  0.00              
ATOM    141  N   ILE    43       9.054  -0.002  22.359  1.00  0.00              
ATOM    142  CA  ILE    43      10.282   0.000  23.141  1.00  0.00              
ATOM    143  C   ILE    43      10.101   0.961  24.319  1.00  0.00              
ATOM    144  O   ILE    43      10.341   2.159  24.198  1.00  0.00              
ATOM    145  N   ILE    44       9.661   0.434  25.456  1.00  0.00              
ATOM    146  CA  ILE    44       9.420   1.263  26.633  1.00  0.00              
ATOM    147  C   ILE    44      10.640   1.536  27.506  1.00  0.00              
ATOM    148  O   ILE    44      10.643   2.499  28.269  1.00  0.00              
ATOM    149  N   ALA    45      11.659   0.689  27.412  1.00  0.00              
ATOM    150  CA  ALA    45      12.878   0.877  28.196  1.00  0.00              
ATOM    151  C   ALA    45      14.074   0.582  27.296  1.00  0.00              
ATOM    152  O   ALA    45      14.689  -0.482  27.385  1.00  0.00              
ATOM    153  N   ALA    46      14.447   1.554  26.448  1.00  0.00              
ATOM    154  CA  ALA    46      15.559   1.455  25.499  1.00  0.00              
ATOM    155  C   ALA    46      16.902   1.117  26.112  1.00  0.00              
ATOM    156  O   ALA    46      17.686   0.379  25.518  1.00  0.00              
ATOM    157  N   ASN    47      17.163   1.641  27.304  1.00  0.00              
ATOM    158  CA  ASN    47      18.446   1.417  27.954  1.00  0.00              
ATOM    159  C   ASN    47      18.524   0.277  28.965  1.00  0.00              
ATOM    160  O   ASN    47      19.545   0.114  29.635  1.00  0.00              
ATOM    161  N   THR    48      17.459  -0.512  29.073  1.00  0.00              
ATOM    162  CA  THR    48      17.453  -1.646  29.991  1.00  0.00              
ATOM    163  C   THR    48      18.251  -2.766  29.334  1.00  0.00              
ATOM    164  O   THR    48      18.507  -2.723  28.127  1.00  0.00              
ATOM    165  N   PRO    49      16.908  -4.532  26.270  1.00  0.00              
ATOM    166  CA  PRO    49      15.849  -3.519  26.132  1.00  0.00              
ATOM    167  C   PRO    49      14.456  -4.112  26.352  1.00  0.00              
ATOM    168  O   PRO    49      14.167  -5.215  25.894  1.00  0.00              
ATOM    169  N   VAL    50      13.604  -3.380  27.066  1.00  0.00              
ATOM    170  CA  VAL    50      12.253  -3.858  27.360  1.00  0.00              
ATOM    171  C   VAL    50      11.202  -3.339  26.387  1.00  0.00              
ATOM    172  O   VAL    50      11.133  -2.140  26.101  1.00  0.00              
ATOM    173  N   LEU    51      10.402  -4.264  25.871  1.00  0.00              
ATOM    174  CA  LEU    51       9.327  -3.943  24.943  1.00  0.00              
ATOM    175  C   LEU    51       7.999  -4.354  25.556  1.00  0.00              
ATOM    176  O   LEU    51       7.903  -5.379  26.236  1.00  0.00              
ATOM    177  N   ARG    52       6.974  -3.553  25.306  1.00  0.00              
ATOM    178  CA  ARG    52       5.645  -3.838  25.813  1.00  0.00              
ATOM    179  C   ARG    52       4.704  -3.940  24.623  1.00  0.00              
ATOM    180  O   ARG    52       4.827  -3.176  23.656  1.00  0.00              
ATOM    181  N   LYS    53       3.808  -4.918  24.666  1.00  0.00              
ATOM    182  CA  LYS    53       2.837  -5.090  23.592  1.00  0.00              
ATOM    183  C   LYS    53       1.635  -4.239  23.978  1.00  0.00              
ATOM    184  O   LYS    53       1.072  -4.416  25.059  1.00  0.00              
ATOM    185  N   SER    54       1.268  -3.301  23.111  1.00  0.00              
ATOM    186  CA  SER    54       0.147  -2.407  23.383  1.00  0.00              
ATOM    187  C   SER    54      -0.266  -1.681  22.119  1.00  0.00              
ATOM    188  O   SER    54       0.438  -1.721  21.112  1.00  0.00              
END
