REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0085AL019_1_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : UCSC-COMPBIO 
REMARK  ---------------------------------------------------------- 
TARGET T0085  
AUTHOR 9070-5088-8627  
REMARK   
REMARK Prediction date: Monday June 22, 1998  
REMARK Group name: UCSC-compbio  
REMARK Authors: Christian Barrett, Melissa Cline, Mark Diekhans, 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 There are four obvious heme-binding sites in T0085: CSSCHK, CVGCHV,  
METHOD CESCHG, and CSACHL.  
METHOD   
METHOD Our prediction for T0085 should be considered in three parts.    
METHOD   
METHOD The first part includes the first three heme-binding sites.  We are  
METHOD submitting an automatic alignment to 2cthA, which had a summed score  
METHOD of -63. For scores in this range, we had no false positives in our  
METHOD fold-recognition tests.  While 2cthA is a tetraheme protein, it does  
METHOD not appear that T0085 binds heme where 2cthA binds its second heme  
METHOD group.  
METHOD   
METHOD Since the 2cthA left much of T0085, including one heme-binding group,  
METHOD unaligned, we looked further down our list of hits until we found one  
METHOD that aligned well near the remaining heme-binding site.  
METHOD The 1ycc alignment looked good around the heme-binding site, but not so  
METHOD good on the back side of the heme, so we removed that part of the  
METHOD automatic alignment.  
METHOD   
METHOD In place of 1ycc for the fourth heme-binding site, we considered  
METHOD cytochromes 1cor and 1c52, since they associate electrostatically with  
METHOD phospholipid membranes, as T0085 does.  Because of what we considered  
METHOD structural problems, we chose to submit 1ycc plus an alignment to 1avc  
METHOD for the C-terminus instead.  
METHOD   
METHOD   
METHOD   
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1ycc 
ATOM      1  N   THR   116       4.753  11.979  -8.972  1.00  0.00              
ATOM      2  CA  THR   116       4.539  11.450  -7.559  1.00  0.00              
ATOM      3  C   THR   116       3.046  11.066  -7.543  1.00  0.00              
ATOM      4  O   THR   116       2.583  10.363  -8.470  1.00  0.00              
ATOM      5  N   PRO   117       2.356  11.639  -6.593  1.00  0.00              
ATOM      6  CA  PRO   117       0.885  11.557  -6.412  1.00  0.00              
ATOM      7  C   PRO   117       0.543  12.896  -5.726  1.00  0.00              
ATOM      8  O   PRO   117      -0.414  13.032  -4.931  1.00  0.00              
ATOM      9  N   ARG   118       1.408  13.846  -6.031  1.00  0.00              
ATOM     10  CA  ARG   118       1.536  15.207  -5.550  1.00  0.00              
ATOM     11  C   ARG   118       1.949  16.079  -6.750  1.00  0.00              
ATOM     12  O   ARG   118       2.985  15.659  -7.356  1.00  0.00              
ATOM     13  N   LYS   119       1.295  17.203  -6.966  1.00  0.00              
ATOM     14  CA  LYS   119       1.652  18.104  -8.067  1.00  0.00              
ATOM     15  C   LYS   119       1.650  19.520  -7.493  1.00  0.00              
ATOM     16  O   LYS   119       0.879  19.794  -6.563  1.00  0.00              
ATOM     17  N   ASP   120       2.474  20.348  -8.120  1.00  0.00              
ATOM     18  CA  ASP   120       2.669  21.736  -7.685  1.00  0.00              
ATOM     19  C   ASP   120       1.367  22.539  -7.820  1.00  0.00              
ATOM     20  O   ASP   120       0.628  22.328  -8.806  1.00  0.00              
ATOM     21  N   LEU   121       1.280  23.525  -6.925  1.00  0.00              
ATOM     22  CA  LEU   121       0.160  24.411  -6.856  1.00  0.00              
ATOM     23  C   LEU   121       0.735  25.794  -6.789  1.00  0.00              
ATOM     24  O   LEU   121       1.788  26.182  -7.372  1.00  0.00              
ATOM     25  N   ALA   122       0.036  26.620  -6.068  1.00  0.00              
ATOM     26  CA  ALA   122       0.309  28.022  -5.884  1.00  0.00              
ATOM     27  C   ALA   122       1.073  28.161  -4.550  1.00  0.00              
ATOM     28  O   ALA   122       0.492  28.041  -3.458  1.00  0.00              
ATOM     29  N   LYS   123       2.314  28.619  -4.733  1.00  0.00              
ATOM     30  CA  LYS   123       3.142  28.944  -3.549  1.00  0.00              
ATOM     31  C   LYS   123       2.535  30.154  -2.852  1.00  0.00              
ATOM     32  O   LYS   123       2.707  30.317  -1.620  1.00  0.00              
ATOM     33  N   LYS   124       1.977  31.088  -3.540  1.00  0.00              
ATOM     34  CA  LYS   124       1.448  32.275  -2.866  1.00  0.00              
ATOM     35  C   LYS   124       0.245  31.764  -2.051  1.00  0.00              
ATOM     36  O   LYS   124       0.003  32.268  -0.985  1.00  0.00              
ATOM     37  N   GLY   125      -0.600  30.985  -2.711  1.00  0.00              
ATOM     38  CA  GLY   125      -1.802  30.491  -1.978  1.00  0.00              
ATOM     39  C   GLY   125      -1.387  29.714  -0.738  1.00  0.00              
ATOM     40  O   GLY   125      -1.984  29.796   0.372  1.00  0.00              
ATOM     41  N   GLN   126      -0.359  28.955  -0.915  1.00  0.00              
ATOM     42  CA  GLN   126       0.341  28.060   0.111  1.00  0.00              
ATOM     43  C   GLN   126       0.887  28.928   1.197  1.00  0.00              
ATOM     44  O   GLN   126       0.673  28.461   2.383  1.00  0.00              
ATOM     45  N   ASP   127       1.399  30.087   0.961  1.00  0.00              
ATOM     46  CA  ASP   127       1.925  31.019   1.984  1.00  0.00              
ATOM     47  C   ASP   127       0.781  31.426   2.881  1.00  0.00              
ATOM     48  O   ASP   127       1.121  31.471   4.088  1.00  0.00              
ATOM     49  N   PHE   128      -0.349  31.732   2.356  1.00  0.00              
ATOM     50  CA  PHE   128      -1.494  32.216   3.180  1.00  0.00              
ATOM     51  C   PHE   128      -2.164  31.068   3.922  1.00  0.00              
ATOM     52  O   PHE   128      -2.738  31.321   4.992  1.00  0.00              
ATOM     53  N   HIS   129      -2.010  29.901   3.345  1.00  0.00              
ATOM     54  CA  HIS   129      -2.490  28.709   4.043  1.00  0.00              
ATOM     55  C   HIS   129      -1.596  28.577   5.261  1.00  0.00              
ATOM     56  O   HIS   129      -2.072  28.323   6.402  1.00  0.00              
ATOM     57  N   PHE   130      -0.335  28.667   5.088  1.00  0.00              
ATOM     58  CA  PHE   130       0.660  28.547   6.225  1.00  0.00              
ATOM     59  C   PHE   130       0.327  29.472   7.330  1.00  0.00              
ATOM     60  O   PHE   130       0.131  29.213   8.520  1.00  0.00              
ATOM     61  N   GLU   131       0.138  30.766   6.936  1.00  0.00              
ATOM     62  CA  GLU   131      -0.175  31.848   7.878  1.00  0.00              
ATOM     63  C   GLU   131      -1.419  31.560   8.621  1.00  0.00              
ATOM     64  O   GLU   131      -1.455  31.594   9.864  1.00  0.00              
ATOM     65  N   GLU   132      -2.503  31.221   8.001  1.00  0.00              
ATOM     66  CA  GLU   132      -3.745  30.939   8.735  1.00  0.00              
ATOM     67  C   GLU   132      -3.808  29.624   9.440  1.00  0.00              
ATOM     68  O   GLU   132      -4.693  29.482  10.291  1.00  0.00              
ATOM     69  N   ARG   133      -3.100  28.589   9.054  1.00  0.00              
ATOM     70  CA  ARG   133      -3.224  27.241   9.633  1.00  0.00              
ATOM     71  C   ARG   133      -2.038  26.664  10.344  1.00  0.00              
ATOM     72  O   ARG   133      -2.215  25.780  11.226  1.00  0.00              
ATOM     73  N   CYS   134      -0.854  27.109  10.064  1.00  0.00              
ATOM     74  CA  CYS   134       0.358  26.597  10.695  1.00  0.00              
ATOM     75  C   CYS   134       1.212  27.560  11.560  1.00  0.00              
ATOM     76  O   CYS   134       1.941  27.067  12.395  1.00  0.00              
ATOM     77  N   SER   135       1.210  28.820  11.265  1.00  0.00              
ATOM     78  CA  SER   135       2.001  29.900  11.851  1.00  0.00              
ATOM     79  C   SER   135       1.751  30.001  13.408  1.00  0.00              
ATOM     80  O   SER   135       2.735  30.352  14.077  1.00  0.00              
ATOM     81  N   ALA   136       0.602  29.594  13.777  1.00  0.00              
ATOM     82  CA  ALA   136       0.280  29.620  15.246  1.00  0.00              
ATOM     83  C   ALA   136       1.303  28.768  15.978  1.00  0.00              
ATOM     84  O   ALA   136       1.586  29.240  17.148  1.00  0.00              
ATOM     85  N   CYS   137       1.836  27.744  15.351  1.00  0.00              
ATOM     86  CA  CYS   137       2.710  26.846  16.049  1.00  0.00              
ATOM     87  C   CYS   137       4.123  26.680  15.616  1.00  0.00              
ATOM     88  O   CYS   137       4.997  26.000  16.162  1.00  0.00              
ATOM     89  N   HIS   138       4.362  27.143  14.337  1.00  0.00              
ATOM     90  CA  HIS   138       5.633  26.927  13.618  1.00  0.00              
ATOM     91  C   HIS   138       6.141  28.126  12.830  1.00  0.00              
ATOM     92  O   HIS   138       5.413  28.988  12.358  1.00  0.00              
ATOM     93  N   LEU   139       7.442  28.112  12.741  1.00  0.00              
ATOM     94  CA  LEU   139       8.219  29.067  11.877  1.00  0.00              
ATOM     95  C   LEU   139       8.869  28.233  10.744  1.00  0.00              
ATOM     96  O   LEU   139       8.987  27.036  10.872  1.00  0.00              
ATOM     97  N   ASN   140       9.173  28.910   9.634  1.00  0.00              
ATOM     98  CA  ASN   140       9.823  28.199   8.531  1.00  0.00              
ATOM     99  C   ASN   140      11.224  28.668   8.163  1.00  0.00              
ATOM    100  O   ASN   140      11.992  27.958   7.483  1.00  0.00              
ATOM    101  N   TYR   141      11.537  29.811   8.624  1.00  0.00              
ATOM    102  CA  TYR   141      12.804  30.461   8.281  1.00  0.00              
ATOM    103  C   TYR   141      14.017  29.836   8.930  1.00  0.00              
ATOM    104  O   TYR   141      14.046  29.366  10.027  1.00  0.00              
ATOM    105  N   GLU   142      15.124  29.937   8.212  1.00  0.00              
ATOM    106  CA  GLU   142      16.425  29.452   8.766  1.00  0.00              
ATOM    107  C   GLU   142      16.744  30.347   9.932  1.00  0.00              
ATOM    108  O   GLU   142      16.719  31.546   9.790  1.00  0.00              
ATOM    109  N   GLY   143      17.017  29.777  11.114  1.00  0.00              
ATOM    110  CA  GLY   143      17.277  30.701  12.252  1.00  0.00              
ATOM    111  C   GLY   143      16.040  31.173  12.969  1.00  0.00              
ATOM    112  O   GLY   143      16.104  32.106  13.815  1.00  0.00              
ATOM    113  N   SER   144      14.897  30.597  12.598  1.00  0.00              
ATOM    114  CA  SER   144      13.582  30.803  13.187  1.00  0.00              
ATOM    115  C   SER   144      13.591  29.878  14.463  1.00  0.00              
ATOM    116  O   SER   144      14.205  28.801  14.474  1.00  0.00              
ATOM    117  N   PRO   145      12.868  30.375  15.434  1.00  0.00              
ATOM    118  CA  PRO   145      12.749  29.589  16.645  1.00  0.00              
ATOM    119  C   PRO   145      11.696  28.543  16.639  1.00  0.00              
ATOM    120  O   PRO   145      10.656  28.516  15.971  1.00  0.00              
ATOM    121  N   TRP   146      11.862  27.575  17.589  1.00  0.00              
ATOM    122  CA  TRP   146      10.827  26.611  17.941  1.00  0.00              
ATOM    123  C   TRP   146       9.759  27.414  18.642  1.00  0.00              
ATOM    124  O   TRP   146      10.149  28.313  19.480  1.00  0.00              
ATOM    125  N   LYS   147       8.531  26.968  18.433  1.00  0.00              
ATOM    126  CA  LYS   147       7.414  27.551  19.257  1.00  0.00              
ATOM    127  C   LYS   147       6.750  26.400  19.942  1.00  0.00              
ATOM    128  O   LYS   147       7.426  25.487  20.501  1.00  0.00              
END
