REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0077AL019_1_2 
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: 1mit 
ATOM      1  N   ASN    74       1.861   0.699   6.432  1.00  0.00              
ATOM      2  CA  ASN    74       3.093   1.468   6.118  1.00  0.00              
ATOM      3  C   ASN    74       4.246   0.987   6.998  1.00  0.00              
ATOM      4  O   ASN    74       4.322   1.379   8.145  1.00  0.00              
ATOM      5  N   ASN    75       5.100   0.164   6.453  1.00  0.00              
ATOM      6  CA  ASN    75       6.243  -0.338   7.260  1.00  0.00              
ATOM      7  C   ASN    75       7.553  -0.064   6.526  1.00  0.00              
ATOM      8  O   ASN    75       7.559  -0.030   5.311  1.00  0.00              
ATOM      9  N   GLU    76       8.614   0.126   7.261  1.00  0.00              
ATOM     10  CA  GLU    76       9.915   0.395   6.598  1.00  0.00              
ATOM     11  C   GLU    76      10.369  -0.866   5.870  1.00  0.00              
ATOM     12  O   GLU    76      10.316  -1.929   6.451  1.00  0.00              
ATOM     13  N   LEU    77      10.797  -0.729   4.646  1.00  0.00              
ATOM     14  CA  LEU    77      11.249  -1.930   3.894  1.00  0.00              
ATOM     15  C   LEU    77      12.111  -2.822   4.787  1.00  0.00              
ATOM     16  O   LEU    77      13.298  -2.585   4.893  1.00  0.00              
ATOM     17  N   GLY    78      11.509  -3.809   5.399  1.00  0.00              
ATOM     18  CA  GLY    78      12.305  -4.710   6.282  1.00  0.00              
ATOM     19  C   GLY    78      11.502  -5.044   7.543  1.00  0.00              
ATOM     20  O   GLY    78      11.841  -5.986   8.230  1.00  0.00              
ATOM     21  N   THR    79      10.479  -4.281   7.812  1.00  0.00              
ATOM     22  CA  THR    79       9.662  -4.555   9.022  1.00  0.00              
ATOM     23  C   THR    79       9.252  -6.026   9.049  1.00  0.00              
ATOM     24  O   THR    79       8.493  -6.457   8.203  1.00  0.00              
ATOM     25  N   ALA    80       9.764  -6.743  10.013  1.00  0.00              
ATOM     26  CA  ALA    80       9.464  -8.173  10.171  1.00  0.00              
ATOM     27  C   ALA    80       7.956  -8.388  10.294  1.00  0.00              
ATOM     28  O   ALA    80       7.426  -8.286  11.383  1.00  0.00              
ATOM     29  N   VAL    81       7.312  -8.675   9.196  1.00  0.00              
ATOM     30  CA  VAL    81       5.843  -8.896   9.246  1.00  0.00              
ATOM     31  C   VAL    81       5.521 -10.338   8.860  1.00  0.00              
ATOM     32  O   VAL    81       6.425 -11.144   8.764  1.00  0.00              
ATOM     33  N   GLY    82       4.265 -10.625   8.653  1.00  0.00              
ATOM     34  CA  GLY    82       3.887 -12.012   8.274  1.00  0.00              
ATOM     35  C   GLY    82       4.441 -12.340   6.890  1.00  0.00              
ATOM     36  O   GLY    82       5.069 -11.494   6.284  1.00  0.00              
ATOM     37  N   LYS    83       4.200 -13.536   6.427  1.00  0.00              
ATOM     38  CA  LYS    83       4.712 -13.915   5.084  1.00  0.00              
ATOM     39  C   LYS    83       3.566 -13.951   4.076  1.00  0.00              
ATOM     40  O   LYS    83       3.759 -13.562   2.942  1.00  0.00              
ATOM     41  N   LEU    84       2.420 -14.409   4.502  1.00  0.00              
ATOM     42  CA  LEU    84       1.265 -14.469   3.566  1.00  0.00              
ATOM     43  C   LEU    84       0.690 -13.071   3.352  1.00  0.00              
ATOM     44  O   LEU    84       0.539 -12.335   4.307  1.00  0.00              
ATOM     45  N   PHE    85       0.388 -12.742   2.125  1.00  0.00              
ATOM     46  CA  PHE    85      -0.177 -11.395   1.846  1.00  0.00              
ATOM     47  C   PHE    85      -1.680 -11.504   1.596  1.00  0.00              
ATOM     48  O   PHE    85      -2.127 -12.520   1.105  1.00  0.00              
ATOM     49  N   ARG    86      -2.412 -10.476   1.932  1.00  0.00              
ATOM     50  CA  ARG    86      -3.882 -10.527   1.711  1.00  0.00              
ATOM     51  C   ARG    86      -4.302  -9.448   0.714  1.00  0.00              
ATOM     52  O   ARG    86      -3.850  -8.326   0.825  1.00  0.00              
ATOM     53  N   VAL    87      -5.143  -9.805  -0.219  1.00  0.00              
ATOM     54  CA  VAL    87      -5.592  -8.803  -1.222  1.00  0.00              
ATOM     55  C   VAL    87      -6.371  -7.688  -0.532  1.00  0.00              
ATOM     56  O   VAL    87      -6.727  -6.722  -1.179  1.00  0.00              
ATOM     57  N   GLY    88      -6.616  -7.837   0.740  1.00  0.00              
ATOM     58  CA  GLY    88      -7.370  -6.784   1.463  1.00  0.00              
ATOM     59  C   GLY    88      -6.412  -5.982   2.333  1.00  0.00              
ATOM     60  O   GLY    88      -6.831  -5.439   3.336  1.00  0.00              
ATOM     61  N   VAL    89      -5.168  -5.927   1.941  1.00  0.00              
ATOM     62  CA  VAL    89      -4.191  -5.160   2.751  1.00  0.00              
ATOM     63  C   VAL    89      -3.049  -4.645   1.882  1.00  0.00              
ATOM     64  O   VAL    89      -2.139  -5.399   1.598  1.00  0.00              
ATOM     65  N   VAL    90      -3.107  -3.405   1.481  1.00  0.00              
ATOM     66  CA  VAL    90      -2.004  -2.882   0.640  1.00  0.00              
ATOM     67  C   VAL    90      -0.846  -2.545   1.570  1.00  0.00              
ATOM     68  O   VAL    90      -0.888  -1.531   2.238  1.00  0.00              
ATOM     69  N   SER    91       0.145  -3.393   1.588  1.00  0.00              
ATOM     70  CA  SER    91       1.311  -3.146   2.474  1.00  0.00              
ATOM     71  C   SER    91       2.262  -2.122   1.860  1.00  0.00              
ATOM     72  O   SER    91       3.051  -2.475   1.006  1.00  0.00              
ATOM     73  N   ILE    92       2.165  -0.900   2.304  1.00  0.00              
ATOM     74  CA  ILE    92       3.059   0.152   1.758  1.00  0.00              
ATOM     75  C   ILE    92       4.343   0.172   2.580  1.00  0.00              
ATOM     76  O   ILE    92       4.277  -0.010   3.780  1.00  0.00              
ATOM     77  N   LEU    93       5.462   0.387   1.947  1.00  0.00              
ATOM     78  CA  LEU    93       6.727   0.410   2.725  1.00  0.00              
ATOM     79  C   LEU    93       7.545   1.649   2.388  1.00  0.00              
ATOM     80  O   LEU    93       7.281   2.287   1.389  1.00  0.00              
ATOM     81  N   GLU    94       8.500   1.958   3.222  1.00  0.00              
ATOM     82  CA  GLU    94       9.343   3.153   2.963  1.00  0.00              
ATOM     83  C   GLU    94      10.798   2.721   2.797  1.00  0.00              
ATOM     84  O   GLU    94      11.311   2.023   3.648  1.00  0.00              
ATOM     85  N   ALA    95      11.420   3.133   1.727  1.00  0.00              
ATOM     86  CA  ALA    95      12.837   2.740   1.518  1.00  0.00              
ATOM     87  C   ALA    95      13.761   3.702   2.263  1.00  0.00              
ATOM     88  O   ALA    95      13.537   4.897   2.219  1.00  0.00              
ATOM     89  N   GLY    96      14.756   3.164   2.917  1.00  0.00              
ATOM     90  CA  GLY    96      15.702   4.033   3.669  1.00  0.00              
ATOM     91  C   GLY    96      16.070   5.258   2.837  1.00  0.00              
ATOM     92  O   GLY    96      16.451   6.265   3.400  1.00  0.00              
ATOM     93  N   ASP    99      15.952   5.153   1.542  1.00  0.00              
ATOM     94  CA  ASP    99      16.298   6.317   0.685  1.00  0.00              
ATOM     95  C   ASP    99      15.474   7.531   1.108  1.00  0.00              
ATOM     96  O   ASP    99      15.685   8.606   0.583  1.00  0.00              
ATOM     97  N   ILE   100      14.570   7.336   2.031  1.00  0.00              
ATOM     98  CA  ILE   100      13.732   8.478   2.488  1.00  0.00              
ATOM     99  C   ILE   100      12.516   8.610   1.571  1.00  0.00              
ATOM    100  O   ILE   100      12.095   9.717   1.298  1.00  0.00              
ATOM    101  N   LEU   101      11.987   7.503   1.124  1.00  0.00              
ATOM    102  CA  LEU   101      10.803   7.578   0.228  1.00  0.00              
ATOM    103  C   LEU   101       9.776   6.517   0.615  1.00  0.00              
ATOM    104  O   LEU   101      10.069   5.676   1.442  1.00  0.00              
ATOM    105  N   THR   102       8.617   6.581   0.018  1.00  0.00              
ATOM    106  CA  THR   102       7.569   5.580   0.346  1.00  0.00              
ATOM    107  C   THR   102       7.409   4.596  -0.810  1.00  0.00              
ATOM    108  O   THR   102       6.836   4.952  -1.820  1.00  0.00              
ATOM    109  N   THR   103       7.912   3.404  -0.642  1.00  0.00              
ATOM    110  CA  THR   103       7.790   2.399  -1.731  1.00  0.00              
ATOM    111  C   THR   103       6.448   1.678  -1.631  1.00  0.00              
ATOM    112  O   THR   103       6.386   0.614  -1.046  1.00  0.00              
ATOM    113  N   LEU   104       5.421   2.262  -2.185  1.00  0.00              
ATOM    114  CA  LEU   104       4.088   1.608  -2.121  1.00  0.00              
ATOM    115  C   LEU   104       3.903   0.699  -3.335  1.00  0.00              
ATOM    116  O   LEU   104       3.711   1.185  -4.431  1.00  0.00              
ATOM    117  N   ALA   105       3.967  -0.583  -3.099  1.00  0.00              
ATOM    118  CA  ALA   105       3.809  -1.585  -4.163  1.00  0.00              
ATOM    119  C   ALA   105       2.465  -1.406  -4.866  1.00  0.00              
ATOM    120  O   ALA   105       1.444  -1.797  -4.335  1.00  0.00              
END
