REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0062AL084_1_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : DIFRANCESCO 
REMARK  ---------------------------------------------------------- 
TARGET T0062  
AUTHOR 7278-7379-8158  
METHOD  In order to explore Flavin Reductase's evolutionary relationship(s)   
METHOD  with other members of the Ferredoxin NADP Reductase superfamily (FNR)   
METHOD  we have employed an iterative strategy to primary sequence database (db)   
METHOD  searching. This approach combines conventional algorithms for detecting  
METHOD  pairwise sequence similarities such as BLAST, FASTA & SSEARCH with multiple   
METHOD  sequence alignments (CLUSTALW), profile analysis & secondary structure prediction   
METHOD  methods (PhD, DSC, etc). The general idea is to generate & refine evolving  
METHOD  regions of local similarities which can then be used in multiple rounds of   
METHOD  db scanning to identify distantly related members of this superfamily.  
METHOD  In addition, the library of HMMs of protein folds (FoReSst, typically used by   
METHOD  for CASP3 predictions), confirmed the proposed model below.   
METHOD  This the aforementioned combination of methods was used by Maria A. Cueto.  
METHOD  from Novartis Pharmaceuticals of Summit, NJ.  
REMARK  Flavin Reductase from E. Coli (sw:ubib_ecoli) contains two  
REMARK  domains. First, an N-terminal beta-barrel domain which may bind  
REMARK  a flavin cofactor on the outside. We have chosen the crystal  
REMARK  structure of the N-terminal domain of Phthalate Dioxygenase   
REMARK  Reductase (PDB code 2PIA; residues:8-74) to construct the structural alignment.  
REMARK  The second or C-terminal domain is an alpha/beta fold or pyrimidine  
REMARK  nucleotide binding domain. The crystal structure of the C-terminal  
REMARK  domain of Nitrate Reductase (PDB code 1CNF; residues:94-251) was used as    
REMARK  the parent template for generating the pairwise alignment.       
MODEL   1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2PIA 
ATOM      1  N   THR     2      -4.440  21.026  21.201  1.00  0.00              
ATOM      2  CA  THR     2      -5.005  22.344  20.975  1.00  0.00              
ATOM      3  C   THR     2      -6.021  22.615  22.043  1.00  0.00              
ATOM      4  O   THR     2      -6.644  21.692  22.569  1.00  0.00              
ATOM      5  N   LEU     3      -6.195  23.888  22.340  1.00  0.00              
ATOM      6  CA  LEU     3      -7.183  24.332  23.301  1.00  0.00              
ATOM      7  C   LEU     3      -8.437  24.775  22.556  1.00  0.00              
ATOM      8  O   LEU     3      -8.343  25.210  21.409  1.00  0.00              
ATOM      9  N   SER     4      -9.607  24.609  23.166  1.00  0.00              
ATOM     10  CA  SER     4     -10.827  25.139  22.560  1.00  0.00              
ATOM     11  C   SER     4     -11.182  26.525  23.066  1.00  0.00              
ATOM     12  O   SER     4     -11.577  26.710  24.210  1.00  0.00              
ATOM     13  N   CYS     5     -10.971  27.506  22.196  1.00  0.00              
ATOM     14  CA  CYS     5     -11.260  28.893  22.485  1.00  0.00              
ATOM     15  C   CYS     5     -12.533  29.309  21.765  1.00  0.00              
ATOM     16  O   CYS     5     -13.192  28.494  21.119  1.00  0.00              
ATOM     17  N   LYS     6     -12.916  30.563  21.951  1.00  0.00              
ATOM     18  CA  LYS     6     -14.140  31.105  21.392  1.00  0.00              
ATOM     19  C   LYS     6     -13.781  32.406  20.690  1.00  0.00              
ATOM     20  O   LYS     6     -12.944  33.153  21.186  1.00  0.00              
ATOM     21  N   VAL     7     -14.322  32.636  19.498  1.00  0.00              
ATOM     22  CA  VAL     7     -14.148  33.934  18.847  1.00  0.00              
ATOM     23  C   VAL     7     -15.053  34.982  19.506  1.00  0.00              
ATOM     24  O   VAL     7     -16.246  35.000  19.274  1.00  0.00              
ATOM     25  N   THR     8     -14.488  35.821  20.363  1.00  0.00              
ATOM     26  CA  THR     8     -15.277  36.822  21.079  1.00  0.00              
ATOM     27  C   THR     8     -15.625  38.027  20.211  1.00  0.00              
ATOM     28  O   THR     8     -16.582  38.746  20.477  1.00  0.00              
ATOM     29  N   SER     9     -14.798  38.284  19.210  1.00  0.00              
ATOM     30  CA  SER     9     -14.915  39.494  18.418  1.00  0.00              
ATOM     31  C   SER     9     -14.192  39.306  17.093  1.00  0.00              
ATOM     32  O   SER     9     -13.109  38.722  17.043  1.00  0.00              
ATOM     33  N   VAL    10     -14.872  39.663  16.013  1.00  0.00              
ATOM     34  CA  VAL    10     -14.296  39.632  14.675  1.00  0.00              
ATOM     35  C   VAL    10     -14.646  40.951  13.982  1.00  0.00              
ATOM     36  O   VAL    10     -15.816  41.316  13.924  1.00  0.00              
ATOM     37  N   GLU    11     -13.635  41.737  13.624  1.00  0.00              
ATOM     38  CA  GLU    11     -13.862  43.019  12.955  1.00  0.00              
ATOM     39  C   GLU    11     -12.929  43.160  11.759  1.00  0.00              
ATOM     40  O   GLU    11     -11.773  42.779  11.831  1.00  0.00              
ATOM     41  N   ALA    12     -13.420  43.727  10.670  1.00  0.00              
ATOM     42  CA  ALA    12     -12.558  44.148   9.565  1.00  0.00              
ATOM     43  C   ALA    12     -11.834  45.439   9.956  1.00  0.00              
ATOM     44  O   ALA    12     -12.472  46.392  10.378  1.00  0.00              
ATOM     45  N   ILE    13     -10.506  45.439   9.929  1.00  0.00              
ATOM     46  CA  ILE    13      -9.765  46.611  10.396  1.00  0.00              
ATOM     47  C   ILE    13      -8.993  47.353   9.309  1.00  0.00              
ATOM     48  O   ILE    13      -8.461  48.441   9.536  1.00  0.00              
ATOM     49  N   THR    14      -8.840  46.718   8.168  1.00  0.00              
ATOM     50  CA  THR    14      -8.289  47.390   7.011  1.00  0.00              
ATOM     51  C   THR    14      -8.890  46.686   5.831  1.00  0.00              
ATOM     52  O   THR    14      -9.595  45.695   5.992  1.00  0.00              
ATOM     53  N   ASP    15      -8.628  47.201   4.644  1.00  0.00              
ATOM     54  CA  ASP    15      -8.951  46.486   3.421  1.00  0.00              
ATOM     55  C   ASP    15      -8.318  45.083   3.494  1.00  0.00              
ATOM     56  O   ASP    15      -7.123  44.942   3.762  1.00  0.00              
ATOM     57  N   THR    16      -8.678  41.346   8.841  1.00  0.00              
ATOM     58  CA  THR    16      -9.624  41.181   9.948  1.00  0.00              
ATOM     59  C   THR    16      -8.909  40.915  11.265  1.00  0.00              
ATOM     60  O   THR    16      -7.936  40.177  11.289  1.00  0.00              
ATOM     61  N   VAL    17      -9.431  41.470  12.348  1.00  0.00              
ATOM     62  CA  VAL    17      -8.917  41.215  13.694  1.00  0.00              
ATOM     63  C   VAL    17      -9.802  40.209  14.431  1.00  0.00              
ATOM     64  O   VAL    17     -11.025  40.289  14.354  1.00  0.00              
ATOM     65  N   TYR    18      -9.187  39.226  15.078  1.00  0.00              
ATOM     66  CA  TYR    18      -9.930  38.272  15.905  1.00  0.00              
ATOM     67  C   TYR    18      -9.461  38.398  17.343  1.00  0.00              
ATOM     68  O   TYR    18      -8.261  38.456  17.609  1.00  0.00              
ATOM     69  N   ARG    19     -10.418  38.433  18.262  1.00  0.00              
ATOM     70  CA  ARG    19     -10.134  38.332  19.686  1.00  0.00              
ATOM     71  C   ARG    19     -10.623  36.976  20.176  1.00  0.00              
ATOM     72  O   ARG    19     -11.766  36.609  19.928  1.00  0.00              
ATOM     73  N   VAL    20      -9.709  36.178  20.707  1.00  0.00              
ATOM     74  CA  VAL    20     -10.001  34.805  21.114  1.00  0.00              
ATOM     75  C   VAL    20      -9.935  34.714  22.625  1.00  0.00              
ATOM     76  O   VAL    20      -9.007  35.234  23.227  1.00  0.00              
ATOM     77  N   ARG    21     -10.966  34.148  23.239  1.00  0.00              
ATOM     78  CA  ARG    21     -11.019  34.005  24.697  1.00  0.00              
ATOM     79  C   ARG    21     -11.383  32.575  25.074  1.00  0.00              
ATOM     80  O   ARG    21     -11.823  31.797  24.234  1.00  0.00              
ATOM     81  N   ILE    22     -11.104  32.190  26.313  1.00  0.00              
ATOM     82  CA  ILE    22     -11.535  30.893  26.802  1.00  0.00              
ATOM     83  C   ILE    22     -13.044  30.978  27.025  1.00  0.00              
ATOM     84  O   ILE    22     -13.528  31.953  27.603  1.00  0.00              
ATOM     85  N   VAL    23     -13.801  29.954  26.613  1.00  0.00              
ATOM     86  CA  VAL    23     -15.264  30.058  26.708  1.00  0.00              
ATOM     87  C   VAL    23     -15.874  30.155  28.125  1.00  0.00              
ATOM     88  O   VAL    23     -17.017  30.547  28.283  1.00  0.00              
ATOM     89  N   PRO    24     -15.124  29.782  29.157  1.00  0.00              
ATOM     90  CA  PRO    24     -15.616  29.916  30.526  1.00  0.00              
ATOM     91  C   PRO    24     -14.882  31.038  31.233  1.00  0.00              
ATOM     92  O   PRO    24     -14.906  31.132  32.451  1.00  0.00              
ATOM     93  N   ASP    25     -14.103  31.790  30.464  1.00  0.00              
ATOM     94  CA  ASP    25     -13.384  32.939  30.997  1.00  0.00              
ATOM     95  C   ASP    25     -12.096  32.647  31.752  1.00  0.00              
ATOM     96  O   ASP    25     -11.607  33.496  32.487  1.00  0.00              
ATOM     97  N   ALA    26     -11.552  31.443  31.611  1.00  0.00              
ATOM     98  CA  ALA    26     -10.310  31.104  32.295  1.00  0.00              
ATOM     99  C   ALA    26      -9.133  31.873  31.689  1.00  0.00              
ATOM    100  O   ALA    26      -9.142  32.182  30.492  1.00  0.00              
ATOM    101  N   ALA    27      -8.096  32.173  32.498  1.00  0.00              
ATOM    102  CA  ALA    27      -6.859  32.750  31.972  1.00  0.00              
ATOM    103  C   ALA    27      -6.183  31.806  30.996  1.00  0.00              
ATOM    104  O   ALA    27      -6.309  30.589  31.112  1.00  0.00              
ATOM    105  N   PHE    28      -5.594  32.386  29.958  1.00  0.00              
ATOM    106  CA  PHE    28      -4.956  31.630  28.892  1.00  0.00              
ATOM    107  C   PHE    28      -3.469  31.386  29.195  1.00  0.00              
ATOM    108  O   PHE    28      -2.875  32.057  30.038  1.00  0.00              
ATOM    109  N   SER    29      -2.854  30.403  28.534  1.00  0.00              
ATOM    110  CA  SER    29      -1.402  30.265  28.642  1.00  0.00              
ATOM    111  C   SER    29      -0.677  31.594  28.378  1.00  0.00              
ATOM    112  O   SER    29      -1.109  32.396  27.530  1.00  0.00              
ATOM    113  N   PHE    30       2.236  34.367  27.205  1.00  0.00              
ATOM    114  CA  PHE    30       3.103  34.531  26.033  1.00  0.00              
ATOM    115  C   PHE    30       3.951  35.785  26.192  1.00  0.00              
ATOM    116  O   PHE    30       3.681  36.620  27.048  1.00  0.00              
ATOM    117  N   ARG    31       5.012  35.902  25.403  1.00  0.00              
ATOM    118  CA  ARG    31       5.685  37.181  25.308  1.00  0.00              
ATOM    119  C   ARG    31       5.686  37.681  23.865  1.00  0.00              
ATOM    120  O   ARG    31       5.324  36.951  22.954  1.00  0.00              
ATOM    121  N   ALA    32       6.002  38.956  23.681  1.00  0.00              
ATOM    122  CA  ALA    32       6.082  39.544  22.345  1.00  0.00              
ATOM    123  C   ALA    32       6.857  38.698  21.331  1.00  0.00              
ATOM    124  O   ALA    32       7.883  38.103  21.652  1.00  0.00              
ATOM    125  N   GLY    33       6.361  38.670  20.101  1.00  0.00              
ATOM    126  CA  GLY    33       6.945  37.839  19.070  1.00  0.00              
ATOM    127  C   GLY    33       6.357  36.437  18.979  1.00  0.00              
ATOM    128  O   GLY    33       6.679  35.683  18.068  1.00  0.00              
ATOM    129  N   GLN    34       5.533  36.052  19.949  1.00  0.00              
ATOM    130  CA  GLN    34       4.997  34.689  19.980  1.00  0.00              
ATOM    131  C   GLN    34       3.970  34.402  18.875  1.00  0.00              
ATOM    132  O   GLN    34       3.210  35.277  18.464  1.00  0.00              
ATOM    133  N   TYR    35       3.943  33.150  18.434  1.00  0.00              
ATOM    134  CA  TYR    35       3.033  32.683  17.394  1.00  0.00              
ATOM    135  C   TYR    35       2.135  31.567  17.937  1.00  0.00              
ATOM    136  O   TYR    35       2.546  30.818  18.820  1.00  0.00              
ATOM    137  N   LEU    36       0.951  31.414  17.361  1.00  0.00              
ATOM    138  CA  LEU    36       0.135  30.237  17.621  1.00  0.00              
ATOM    139  C   LEU    36      -0.546  29.719  16.365  1.00  0.00              
ATOM    140  O   LEU    36      -0.591  30.403  15.339  1.00  0.00              
ATOM    141  N   MET    37      -0.945  28.459  16.410  1.00  0.00              
ATOM    142  CA  MET    37      -1.550  27.813  15.259  1.00  0.00              
ATOM    143  C   MET    37      -3.030  27.635  15.493  1.00  0.00              
ATOM    144  O   MET    37      -3.445  27.389  16.622  1.00  0.00              
ATOM    145  N   VAL    38      -3.805  28.006  14.481  1.00  0.00              
ATOM    146  CA  VAL    38      -5.265  27.987  14.514  1.00  0.00              
ATOM    147  C   VAL    38      -5.787  26.955  13.511  1.00  0.00              
ATOM    148  O   VAL    38      -5.278  26.860  12.396  1.00  0.00              
ATOM    149  N   VAL    39      -6.684  26.081  13.960  1.00  0.00              
ATOM    150  CA  VAL    39      -7.331  25.146  13.040  1.00  0.00              
ATOM    151  C   VAL    39      -8.489  25.873  12.350  1.00  0.00              
ATOM    152  O   VAL    39      -9.420  26.334  13.015  1.00  0.00              
ATOM    153  N   MET    40      -8.337  26.148  11.058  1.00  0.00              
ATOM    154  CA  MET    40      -9.336  26.939  10.334  1.00  0.00              
ATOM    155  C   MET    40     -10.491  26.056   9.805  1.00  0.00              
ATOM    156  O   MET    40     -10.376  24.824   9.826  1.00  0.00              
ATOM    157  N   ASP    41     -11.838  24.932   7.216  1.00  0.00              
ATOM    158  CA  ASP    41     -11.618  23.902   6.202  1.00  0.00              
ATOM    159  C   ASP    41     -10.668  22.762   6.600  1.00  0.00              
ATOM    160  O   ASP    41     -10.314  21.932   5.777  1.00  0.00              
ATOM    161  N   GLU    42     -10.239  22.729   7.853  1.00  0.00              
ATOM    162  CA  GLU    42      -9.360  21.654   8.286  1.00  0.00              
ATOM    163  C   GLU    42      -7.875  21.984   8.272  1.00  0.00              
ATOM    164  O   GLU    42      -7.072  21.281   8.894  1.00  0.00              
ATOM    165  N   ARG    43      -7.503  23.058   7.582  1.00  0.00              
ATOM    166  CA  ARG    43      -6.112  23.488   7.559  1.00  0.00              
ATOM    167  C   ARG    43      -5.690  24.099   8.873  1.00  0.00              
ATOM    168  O   ARG    43      -6.527  24.568   9.642  1.00  0.00              
ATOM    169  N   LYS    45      -4.395  24.091   9.136  1.00  0.00              
ATOM    170  CA  LYS    45      -3.832  24.771  10.295  1.00  0.00              
ATOM    171  C   LYS    45      -2.910  25.890   9.860  1.00  0.00              
ATOM    172  O   LYS    45      -2.059  25.685   9.010  1.00  0.00              
ATOM    173  N   ARG    46      -3.107  27.081  10.427  1.00  0.00              
ATOM    174  CA  ARG    46      -2.385  28.279  10.006  1.00  0.00              
ATOM    175  C   ARG    46      -1.807  29.010  11.215  1.00  0.00              
ATOM    176  O   ARG    46      -2.428  29.041  12.280  1.00  0.00              
ATOM    177  N   PRO    47      -0.608  29.570  11.054  1.00  0.00              
ATOM    178  CA  PRO    47       0.112  30.231  12.151  1.00  0.00              
ATOM    179  C   PRO    47      -0.072  31.748  12.112  1.00  0.00              
ATOM    180  O   PRO    47       0.102  32.360  11.073  1.00  0.00              
ATOM    181  N   PHE    48      -0.433  32.347  13.245  1.00  0.00              
ATOM    182  CA  PHE    48      -0.602  33.794  13.317  1.00  0.00              
ATOM    183  C   PHE    48       0.129  34.363  14.532  1.00  0.00              
ATOM    184  O   PHE    48       0.284  33.667  15.521  1.00  0.00              
ATOM    185  N   SER    49       0.684  35.569  14.403  1.00  0.00              
ATOM    186  CA  SER    49       1.358  36.258  15.522  1.00  0.00              
ATOM    187  C   SER    49       0.383  36.901  16.488  1.00  0.00              
ATOM    188  O   SER    49      -0.561  37.559  16.059  1.00  0.00              
ATOM    189  N   MET    50       0.693  36.840  17.780  1.00  0.00              
ATOM    190  CA  MET    50      -0.120  37.518  18.794  1.00  0.00              
ATOM    191  C   MET    50       0.240  38.992  18.758  1.00  0.00              
ATOM    192  O   MET    50       1.410  39.333  18.661  1.00  0.00              
ATOM    193  N   ALA    51      -0.750  39.875  18.704  1.00  0.00              
ATOM    194  CA  ALA    51      -0.425  41.294  18.649  1.00  0.00              
ATOM    195  C   ALA    51      -0.968  42.146  19.794  1.00  0.00              
ATOM    196  O   ALA    51      -0.771  43.364  19.822  1.00  0.00              
ATOM    197  N   SER    52      -1.559  41.495  20.796  1.00  0.00              
ATOM    198  CA  SER    52      -1.957  42.214  21.994  1.00  0.00              
ATOM    199  C   SER    52      -0.850  42.276  23.041  1.00  0.00              
ATOM    200  O   SER    52       0.209  41.665  22.885  1.00  0.00              
ATOM    201  N   THR    53      -1.037  43.177  24.007  1.00  0.00              
ATOM    202  CA  THR    53      -0.120  43.376  25.124  1.00  0.00              
ATOM    203  C   THR    53       0.048  42.054  25.859  1.00  0.00              
ATOM    204  O   THR    53      -0.932  41.527  26.399  1.00  0.00              
ATOM    205  N   PRO    54       1.298  41.632  26.044  1.00  0.00              
ATOM    206  CA  PRO    54       1.604  40.320  26.623  1.00  0.00              
ATOM    207  C   PRO    54       1.299  40.222  28.105  1.00  0.00              
ATOM    208  O   PRO    54       1.421  39.154  28.699  1.00  0.00              
ATOM    209  N   ASP    55       0.971  41.339  28.733  1.00  0.00              
ATOM    210  CA  ASP    55       0.597  41.274  30.127  1.00  0.00              
ATOM    211  C   ASP    55      -0.877  40.907  30.312  1.00  0.00              
ATOM    212  O   ASP    55      -1.284  40.483  31.385  1.00  0.00              
ATOM    213  N   GLU    56      -1.627  40.869  29.216  1.00  0.00              
ATOM    214  CA  GLU    56      -2.995  40.377  29.286  1.00  0.00              
ATOM    215  C   GLU    56      -3.061  38.854  29.373  1.00  0.00              
ATOM    216  O   GLU    56      -2.460  38.157  28.568  1.00  0.00              
ATOM    217  N   LYS    57      -3.940  38.354  30.230  1.00  0.00              
ATOM    218  CA  LYS    57      -4.056  36.922  30.473  1.00  0.00              
ATOM    219  C   LYS    57      -5.388  36.369  29.961  1.00  0.00              
ATOM    220  O   LYS    57      -5.656  35.178  30.059  1.00  0.00              
ATOM    221  N   GLY    58      -6.240  37.252  29.464  1.00  0.00              
ATOM    222  CA  GLY    58      -7.639  36.928  29.234  1.00  0.00              
ATOM    223  C   GLY    58      -8.023  36.677  27.769  1.00  0.00              
ATOM    224  O   GLY    58      -9.086  36.116  27.496  1.00  0.00              
ATOM    225  N   PHE    59      -7.191  37.139  26.835  1.00  0.00              
ATOM    226  CA  PHE    59      -7.489  37.000  25.417  1.00  0.00              
ATOM    227  C   PHE    59      -6.221  36.914  24.590  1.00  0.00              
ATOM    228  O   PHE    59      -5.155  37.315  25.042  1.00  0.00              
ATOM    229  N   ILE    60      -6.364  36.427  23.372  1.00  0.00              
ATOM    230  CA  ILE    60      -5.328  36.474  22.354  1.00  0.00              
ATOM    231  C   ILE    60      -5.911  37.315  21.209  1.00  0.00              
ATOM    232  O   ILE    60      -7.084  37.169  20.886  1.00  0.00              
ATOM    233  N   GLU    61      -5.135  38.234  20.643  1.00  0.00              
ATOM    234  CA  GLU    61      -5.605  38.996  19.476  1.00  0.00              
ATOM    235  C   GLU    61      -4.704  38.747  18.257  1.00  0.00              
ATOM    236  O   GLU    61      -3.491  38.844  18.357  1.00  0.00              
ATOM    237  N   LEU    62      -5.295  38.280  17.166  1.00  0.00              
ATOM    238  CA  LEU    62      -4.567  38.095  15.906  1.00  0.00              
ATOM    239  C   LEU    62      -5.212  38.917  14.769  1.00  0.00              
ATOM    240  O   LEU    62      -6.360  39.325  14.869  1.00  0.00              
ATOM    241  N   HIS    63      -4.436  39.211  13.735  1.00  0.00              
ATOM    242  CA  HIS    63      -4.923  39.955  12.577  1.00  0.00              
ATOM    243  C   HIS    63      -4.503  39.187  11.333  1.00  0.00              
ATOM    244  O   HIS    63      -3.338  38.794  11.204  1.00  0.00              
ATOM    245  N   ILE    64      -5.492  38.830  10.518  1.00  0.00              
ATOM    246  CA  ILE    64      -5.311  37.898   9.414  1.00  0.00              
ATOM    247  C   ILE    64      -5.675  38.593   8.107  1.00  0.00              
ATOM    248  O   ILE    64      -6.753  39.160   7.997  1.00  0.00              
ATOM    249  N   GLY    65      -4.727  38.674   7.186  1.00  0.00              
ATOM    250  CA  GLY    65      -5.010  39.152   5.838  1.00  0.00              
ATOM    251  C   GLY    65      -5.643  38.050   4.992  1.00  0.00              
ATOM    252  O   GLY    65      -5.184  36.921   4.977  1.00  0.00              
END
