REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0065AL017_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : SJOLANDER-THOMAS 
REMARK  ---------------------------------------------------------- 
TARGET T0065  
AUTHOR 5827-4749-3439  
METHOD T0065 structure prediction  
METHOD  
METHOD For this target, our HMM library showed no significant hits.  
METHOD Threading, however, suggested 1pnra1 as a potentially similar  
METHOD structure.  HMMs were then constructed which confirmed a  
METHOD weak sequence similarity.  
METHOD  
METHOD As usual, we employed a two-pronged approach: (1) We scored the   
METHOD target against all the HMMs and threading models in our libraries,   
METHOD and (2) we gathered homologs to the target using PsiBLAST,   
METHOD constructed an HMM for the target and homologs   
METHOD (using UCSC's HMM software), and scored PDB.   
METHOD This yielded three sets of scores, which we then used   
METHOD to find a target-structure match.  
METHOD   
METHOD This target-structure prediction was primarily the result  
METHOD of agreement between the scoring of the threading models,  
METHOD and the scoring of PDB with an HMM for the target and its  
METHOD single homolog identifiable using BLAST.  
METHOD  
METHOD The alignment is automatic, produced by aligning the target  
METHOD and the structure, scop domain d1pnra1, to an HMM constructed  
METHOD for d1pnra1 and homologs. We used standard methods to create  
METHOD this HMM: (1) building an alignment using Gotoh's prrp  
METHOD software, (2) using modelfromalign from the UCSC HMM  
METHOD software to estimate an HMM from the alignment, and  
METHOD finally, (3) re-estimating this model using weights for  
METHOD the sequences to allow the HMM to generalize. The sequence  
METHOD weighting method employed used Henikoff weighting to  
METHOD establish the relative weights, and our own method of  
METHOD estimating the number of independent observations  
METHOD to establish the magnitude of the weights.  
METHOD  
METHOD The automatic alignment generated by threading agreed with  
METHOD the HMM alignment over the C-terminal half of the molecule.  
METHOD We felt that since there was an (albeit weak) sequence signal  
METHOD over the N-terminal portion as well, we decided to use the  
METHOD automatic HMM alignment.  
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1pnr_A 
ATOM      1  N   MET B   1      16.963   0.331  12.968  1.00  0.00              
ATOM      2  CA  MET B   1      16.628   1.700  13.426  1.00  0.00              
ATOM      3  C   MET B   1      15.242   1.573  14.095  1.00  0.00              
ATOM      4  O   MET B   1      14.993   2.178  15.149  1.00  0.00              
ATOM      5  N   LYS B   2      14.375   0.723  13.520  1.00  0.00              
ATOM      6  CA  LYS B   2      13.039   0.442  14.053  1.00  0.00              
ATOM      7  C   LYS B   2      13.183  -0.123  15.449  1.00  0.00              
ATOM      8  O   LYS B   2      12.382   0.130  16.377  1.00  0.00              
ATOM      9  N   ASN B   3      14.212  -0.925  15.596  1.00  0.00              
ATOM     10  CA  ASN B   3      14.354  -1.484  16.907  1.00  0.00              
ATOM     11  C   ASN B   3      14.734  -0.456  17.847  1.00  0.00              
ATOM     12  O   ASN B   3      14.250  -0.454  18.964  1.00  0.00              
ATOM     13  N   ALA B   4      14.059   2.745  17.653  1.00  0.00              
ATOM     14  CA  ALA B   4      12.921   3.640  17.865  1.00  0.00              
ATOM     15  C   ALA B   4      11.975   3.193  18.963  1.00  0.00              
ATOM     16  O   ALA B   4      11.468   3.967  19.789  1.00  0.00              
ATOM     17  N   LYS B   5      11.793   1.895  18.997  1.00  0.00              
ATOM     18  CA  LYS B   5      10.914   1.268  19.948  1.00  0.00              
ATOM     19  C   LYS B   5      11.381   1.071  21.375  1.00  0.00              
ATOM     20  O   LYS B   5      10.595   1.127  22.303  1.00  0.00              
ATOM     21  N   GLN B   6      12.658   0.849  21.572  1.00  0.00              
ATOM     22  CA  GLN B   6      13.134   0.690  22.928  1.00  0.00              
ATOM     23  C   GLN B   6      12.966   2.066  23.578  1.00  0.00              
ATOM     24  O   GLN B   6      12.769   2.220  24.779  1.00  0.00              
ATOM     25  N   GLU B   7      13.036   3.067  22.715  1.00  0.00              
ATOM     26  CA  GLU B   7      12.960   4.471  23.076  1.00  0.00              
ATOM     27  C   GLU B   7      11.562   5.063  23.036  1.00  0.00              
ATOM     28  O   GLU B   7      11.291   6.082  23.619  1.00  0.00              
ATOM     29  N   HIS B   8      10.690   4.422  22.302  1.00  0.00              
ATOM     30  CA  HIS B   8       9.359   4.925  22.181  1.00  0.00              
ATOM     31  C   HIS B   8       9.228   6.276  21.585  1.00  0.00              
ATOM     32  O   HIS B   8       8.628   7.190  22.160  1.00  0.00              
ATOM     33  N   PHE B   9       9.783   6.338  20.374  1.00  0.00              
ATOM     34  CA  PHE B   9       9.758   7.534  19.523  1.00  0.00              
ATOM     35  C   PHE B   9       9.766   6.960  18.134  1.00  0.00              
ATOM     36  O   PHE B   9       9.906   5.757  17.942  1.00  0.00              
ATOM     37  N   GLU B  10       9.643   7.828  17.158  1.00  0.00              
ATOM     38  CA  GLU B  10       9.646   7.369  15.801  1.00  0.00              
ATOM     39  C   GLU B  10      11.061   7.279  15.285  1.00  0.00              
ATOM     40  O   GLU B  10      11.964   8.039  15.699  1.00  0.00              
ATOM     41  N   LEU B  11      11.191   6.365  14.329  1.00  0.00              
ATOM     42  CA  LEU B  11      12.413   6.141  13.661  1.00  0.00              
ATOM     43  C   LEU B  11      12.831   7.510  13.124  1.00  0.00              
ATOM     44  O   LEU B  11      14.017   7.879  13.148  1.00  0.00              
ATOM     45  N   ASP B  12      11.848   8.244  12.658  1.00  0.00              
ATOM     46  CA  ASP B  12      12.097   9.599  12.149  1.00  0.00              
ATOM     47  C   ASP B  12      12.889  10.342  13.275  1.00  0.00              
ATOM     48  O   ASP B  12      13.961  10.916  13.051  1.00  0.00              
ATOM     49  N   GLN B  13      12.400  10.235  14.499  1.00  0.00              
ATOM     50  CA  GLN B  13      13.082  10.883  15.580  1.00  0.00              
ATOM     51  C   GLN B  13      14.511  10.445  15.675  1.00  0.00              
ATOM     52  O   GLN B  13      15.425  11.242  15.559  1.00  0.00              
ATOM     53  N   GLU B  14      14.681   9.153  15.825  1.00  0.00              
ATOM     54  CA  GLU B  14      15.988   8.542  15.932  1.00  0.00              
ATOM     55  C   GLU B  14      16.895   9.006  14.810  1.00  0.00              
ATOM     56  O   GLU B  14      18.072   9.341  14.956  1.00  0.00              
ATOM     57  N   TRP B  15      16.338   9.036  13.645  1.00  0.00              
ATOM     58  CA  TRP B  15      17.216   9.455  12.611  1.00  0.00              
ATOM     59  C   TRP B  15      17.598  10.905  12.764  1.00  0.00              
ATOM     60  O   TRP B  15      18.671  11.312  12.419  1.00  0.00              
ATOM     61  N   VAL B  16      16.721  11.705  13.324  1.00  0.00              
ATOM     62  CA  VAL B  16      17.064  13.098  13.462  1.00  0.00              
ATOM     63  C   VAL B  16      18.147  13.284  14.480  1.00  0.00              
ATOM     64  O   VAL B  16      18.996  14.166  14.341  1.00  0.00              
ATOM     65  N   GLU B  17      18.118  12.480  15.522  1.00  0.00              
ATOM     66  CA  GLU B  17      19.159  12.700  16.518  1.00  0.00              
ATOM     67  C   GLU B  17      20.500  12.143  16.098  1.00  0.00              
ATOM     68  O   GLU B  17      21.566  12.707  16.348  1.00  0.00              
ATOM     69  N   LEU B  18      20.433  11.025  15.438  1.00  0.00              
ATOM     70  CA  LEU B  18      21.650  10.441  14.989  1.00  0.00              
ATOM     71  C   LEU B  18      22.238  11.403  13.975  1.00  0.00              
ATOM     72  O   LEU B  18      23.434  11.503  13.848  1.00  0.00              
ATOM     73  N   MET B  19      21.460  12.134  13.221  1.00  0.00              
ATOM     74  CA  MET B  19      22.174  13.011  12.317  1.00  0.00              
ATOM     75  C   MET B  19      22.073  14.476  12.605  1.00  0.00              
ATOM     76  O   MET B  19      22.447  15.278  11.755  1.00  0.00              
ATOM     77  N   VAL B  20      21.562  14.803  13.794  1.00  0.00              
ATOM     78  CA  VAL B  20      21.437  16.197  14.252  1.00  0.00              
ATOM     79  C   VAL B  20      20.888  17.005  13.148  1.00  0.00              
ATOM     80  O   VAL B  20      21.418  18.006  12.743  1.00  0.00              
ATOM     81  N   GLU B  21      19.826  16.526  12.592  1.00  0.00              
ATOM     82  CA  GLU B  21      19.301  17.183  11.442  1.00  0.00              
ATOM     83  C   GLU B  21      18.021  18.022  11.681  1.00  0.00              
ATOM     84  O   GLU B  21      17.433  18.619  10.785  1.00  0.00              
ATOM     85  N   ALA B  25      17.600  18.075  12.925  1.00  0.00              
ATOM     86  CA  ALA B  25      16.432  18.870  13.316  1.00  0.00              
ATOM     87  C   ALA B  25      16.502  18.826  14.881  1.00  0.00              
ATOM     88  O   ALA B  25      17.138  17.898  15.416  1.00  0.00              
ATOM     89  N   ASN B  26      15.971  19.827  15.602  1.00  0.00              
ATOM     90  CA  ASN B  26      16.035  19.840  17.072  1.00  0.00              
ATOM     91  C   ASN B  26      15.266  18.742  17.784  1.00  0.00              
ATOM     92  O   ASN B  26      14.100  18.455  17.415  1.00  0.00              
ATOM     93  N   ILE B  27      15.863  18.154  18.830  1.00  0.00              
ATOM     94  CA  ILE B  27      15.096  17.129  19.578  1.00  0.00              
ATOM     95  C   ILE B  27      15.286  17.366  21.005  1.00  0.00              
ATOM     96  O   ILE B  27      16.367  17.599  21.422  1.00  0.00              
ATOM     97  N   SER B  28      14.221  17.311  21.756  1.00  0.00              
ATOM     98  CA  SER B  28      14.346  17.507  23.171  1.00  0.00              
ATOM     99  C   SER B  28      15.418  16.614  23.791  1.00  0.00              
ATOM    100  O   SER B  28      15.579  15.442  23.373  1.00  0.00              
ATOM    101  N   PRO B  29      16.120  17.192  24.771  1.00  0.00              
ATOM    102  CA  PRO B  29      17.208  16.534  25.502  1.00  0.00              
ATOM    103  C   PRO B  29      16.752  15.172  25.913  1.00  0.00              
ATOM    104  O   PRO B  29      17.346  14.135  25.601  1.00  0.00              
ATOM    105  N   GLU B  30      15.651  15.214  26.614  1.00  0.00              
ATOM    106  CA  GLU B  30      15.076  13.998  27.111  1.00  0.00              
ATOM    107  C   GLU B  30      14.889  12.990  26.028  1.00  0.00              
ATOM    108  O   GLU B  30      15.189  11.805  26.159  1.00  0.00              
ATOM    109  N   GLU B  31      14.390  13.473  24.922  1.00  0.00              
ATOM    110  CA  GLU B  31      14.152  12.545  23.888  1.00  0.00              
ATOM    111  C   GLU B  31      15.494  12.042  23.389  1.00  0.00              
ATOM    112  O   GLU B  31      15.793  10.806  23.320  1.00  0.00              
ATOM    113  N   ILE B  32      16.298  13.028  23.052  1.00  0.00              
ATOM    114  CA  ILE B  32      17.643  12.807  22.545  1.00  0.00              
ATOM    115  C   ILE B  32      18.390  11.804  23.391  1.00  0.00              
ATOM    116  O   ILE B  32      19.006  10.877  22.909  1.00  0.00              
ATOM    117  N   ARG B  33      18.322  11.961  24.689  1.00  0.00              
ATOM    118  CA  ARG B  33      19.041  11.005  25.515  1.00  0.00              
ATOM    119  C   ARG B  33      18.547   9.627  25.320  1.00  0.00              
ATOM    120  O   ARG B  33      19.290   8.753  24.868  1.00  0.00              
ATOM    121  N   LYS B  34      17.274   9.479  25.651  1.00  0.00              
ATOM    122  CA  LYS B  34      16.573   8.221  25.522  1.00  0.00              
ATOM    123  C   LYS B  34      16.951   7.403  24.283  1.00  0.00              
ATOM    124  O   LYS B  34      17.039   6.148  24.308  1.00  0.00              
ATOM    125  N   TYR B  35      17.182   8.148  23.206  1.00  0.00              
ATOM    126  CA  TYR B  35      17.557   7.535  21.968  1.00  0.00              
ATOM    127  C   TYR B  35      18.925   6.939  22.100  1.00  0.00              
ATOM    128  O   TYR B  35      19.145   5.749  21.834  1.00  0.00              
ATOM    129  N   LEU B  36      19.860   7.775  22.500  1.00  0.00              
ATOM    130  CA  LEU B  36      21.192   7.287  22.654  1.00  0.00              
ATOM    131  C   LEU B  36      21.218   6.059  23.540  1.00  0.00              
ATOM    132  O   LEU B  36      21.916   5.080  23.258  1.00  0.00              
ATOM    133  N   LEU B  37      20.406   6.132  24.580  1.00  0.00              
ATOM    134  CA  LEU B  37      20.257   5.053  25.548  1.00  0.00              
ATOM    135  C   LEU B  37      20.085   3.727  24.805  1.00  0.00              
ATOM    136  O   LEU B  37      20.862   2.773  24.905  1.00  0.00              
ATOM    137  N   LEU B  38      19.017   3.722  24.036  1.00  0.00              
ATOM    138  CA  LEU B  38      18.683   2.591  23.279  1.00  0.00              
ATOM    139  C   LEU B  38      19.817   2.331  22.344  1.00  0.00              
ATOM    140  O   LEU B  38      20.248   1.168  22.266  1.00  0.00              
ATOM    141  N   ASN B  39      20.246   3.378  21.619  1.00  0.00              
ATOM    142  CA  ASN B  39      21.279   3.232  20.629  1.00  0.00              
ATOM    143  C   ASN B  39      22.358   2.447  21.252  1.00  0.00              
ATOM    144  O   ASN B  39      22.926   1.529  20.659  1.00  0.00              
ATOM    145  N   LYS B  40      22.597   2.773  22.501  1.00  0.00              
ATOM    146  CA  LYS B  40      23.618   1.983  23.115  1.00  0.00              
ATOM    147  C   LYS B  40      23.344   0.565  23.456  1.00  0.00              
ATOM    148  O   LYS B  40      23.961  -0.311  22.845  1.00  0.00              
ATOM    149  N   LYS B  41      22.446   0.314  24.400  1.00  0.00              
ATOM    150  CA  LYS B  41      22.198  -1.089  24.742  1.00  0.00              
ATOM    151  C   LYS B  41      21.895  -1.973  23.561  1.00  0.00              
ATOM    152  O   LYS B  41      22.388  -3.087  23.403  1.00  0.00              
ATOM    153  N   SER B  42      21.099  -1.441  22.679  1.00  0.00              
ATOM    154  CA  SER B  42      20.767  -2.193  21.517  1.00  0.00              
ATOM    155  C   SER B  42      22.036  -2.421  20.726  1.00  0.00              
ATOM    156  O   SER B  42      22.063  -3.211  19.763  1.00  0.00              
ATOM    157  N   ALA B  43      23.089  -1.704  21.106  1.00  0.00              
ATOM    158  CA  ALA B  43      24.346  -1.827  20.406  1.00  0.00              
ATOM    159  C   ALA B  43      24.188  -1.542  18.928  1.00  0.00              
ATOM    160  O   ALA B  43      24.675  -2.303  18.114  1.00  0.00              
ATOM    161  N   HIS B  44      24.417  -0.089  15.002  1.00  0.00              
ATOM    162  CA  HIS B  44      25.335   0.498  14.081  1.00  0.00              
ATOM    163  C   HIS B  44      24.441   0.877  12.904  1.00  0.00              
ATOM    164  O   HIS B  44      23.882   0.088  12.166  1.00  0.00              
ATOM    165  N   PRO B  45      24.283   2.144  12.731  1.00  0.00              
ATOM    166  CA  PRO B  45      23.467   2.670  11.669  1.00  0.00              
ATOM    167  C   PRO B  45      23.971   2.103  10.362  1.00  0.00              
ATOM    168  O   PRO B  45      25.158   2.029  10.184  1.00  0.00              
ATOM    169  N   GLY B  46      23.104   1.685   9.453  1.00  0.00              
ATOM    170  CA  GLY B  46      23.572   1.150   8.168  1.00  0.00              
ATOM    171  C   GLY B  46      23.936   2.141   7.039  1.00  0.00              
ATOM    172  O   GLY B  46      23.086   2.900   6.473  1.00  0.00              
ATOM    173  N   PRO B  47      25.212   2.137   6.665  1.00  0.00              
ATOM    174  CA  PRO B  47      25.590   3.053   5.606  1.00  0.00              
ATOM    175  C   PRO B  47      25.007   2.532   4.340  1.00  0.00              
ATOM    176  O   PRO B  47      24.768   3.309   3.388  1.00  0.00              
ATOM    177  N   ALA B  48      24.785   1.225   4.264  1.00  0.00              
ATOM    178  CA  ALA B  48      24.266   0.882   2.983  1.00  0.00              
ATOM    179  C   ALA B  48      22.871   1.413   2.697  1.00  0.00              
ATOM    180  O   ALA B  48      22.584   1.913   1.584  1.00  0.00              
ATOM    181  N   ALA B  49      22.045   1.308   3.739  1.00  0.00              
ATOM    182  CA  ALA B  49      20.696   1.782   3.634  1.00  0.00              
ATOM    183  C   ALA B  49      20.836   3.247   3.290  1.00  0.00              
ATOM    184  O   ALA B  49      20.290   3.764   2.267  1.00  0.00              
ATOM    185  N   ARG B  50      21.550   3.937   4.185  1.00  0.00              
ATOM    186  CA  ARG B  50      21.734   5.365   3.969  1.00  0.00              
ATOM    187  C   ARG B  50      22.144   5.796   2.603  1.00  0.00              
ATOM    188  O   ARG B  50      21.573   6.716   2.021  1.00  0.00              
ATOM    189  N   SER B  51      23.122   5.133   2.036  1.00  0.00              
ATOM    190  CA  SER B  51      23.563   5.573   0.744  1.00  0.00              
ATOM    191  C   SER B  51      22.570   5.377  -0.283  1.00  0.00              
ATOM    192  O   SER B  51      22.529   6.115  -1.303  1.00  0.00              
ATOM    193  N   HIS B  52      21.810   4.332   0.000  1.00  0.00              
ATOM    194  CA  HIS B  52      20.749   3.899  -0.894  1.00  0.00              
ATOM    195  C   HIS B  52      19.855   5.066  -1.124  1.00  0.00              
ATOM    196  O   HIS B  52      19.486   5.321  -2.261  1.00  0.00              
ATOM    197  N   THR B  53      19.573   5.807  -0.050  1.00  0.00              
ATOM    198  CA  THR B  53      18.715   6.994  -0.161  1.00  0.00              
ATOM    199  C   THR B  53      19.380   8.301  -0.569  1.00  0.00              
ATOM    200  O   THR B  53      19.052   8.883  -1.629  1.00  0.00              
ATOM    201  N   VAL B  54      20.285   8.763   0.298  1.00  0.00              
ATOM    202  CA  VAL B  54      21.001  10.030   0.114  1.00  0.00              
ATOM    203  C   VAL B  54      21.809  10.072  -1.157  1.00  0.00              
ATOM    204  O   VAL B  54      22.208  11.122  -1.575  1.00  0.00              
ATOM    205  N   ASN B  55      22.063   8.934  -1.783  1.00  0.00              
ATOM    206  CA  ASN B  55      22.821   8.919  -3.045  1.00  0.00              
ATOM    207  C   ASN B  55      24.307   9.186  -3.156  1.00  0.00              
ATOM    208  O   ASN B  55      24.771   9.912  -4.070  1.00  0.00              
END
