

PFRMAT FRV1
REMARK ========================================================================
REMARK Threading results for target T0004, compared against a dataset of
REMARK Hidden Markov Models of structures. At present the dataset consists
REMARK of about 15 models. The test set consists of a non redundant set of
REMARK predicted secondary structure sequences. The secondary structure
REMARK prediction of the target sequence is included in the test set. A
REMARK score is assigned by the structural models to the sequences in the
REMARK test set. The scores are based on loglikelihood ratios. By ranking
REMARK the scores assigned by the models in ascending order (the lowest
REMARK negative score values get the highest ranks) a decision is taken
REMARK about the most probable fold for the target sequence.
REMARK
REMARK This target protein (pns1) is predicted to have either an 'OB fold' 
REMARK topology (the most likely one, with cumulative probability=0.6) or a 
REMARK 'Plait PTF' topology, with cum. prob.= 0.4 (we use 
REMARK the CATH  classification, to interprete of the word 'topology'). 
REMARK  
REMARK Provided are the alignments of this query sequence against two proteins 
REMARK with the OB fold topology: 1lts, chain D, and 1snc;
REMARK and against three proteins with Plait PTF topology: 1ptf, 2bop, chain A, 
REMARK and 2fxb. 
REMARK ========================================================================
AUTHOR 2225-3577-7739 Valentina Di Francesco, in Peter Munson's Analytical
AUTHOR 2225-3577-7739 Biostatistics Section at NIH, Bethesda, MD
REMARK ========================================================================
SEQRES T0004 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYL
SEQRES T0004 QMGQEVPVKVLEVDRQGRIRLSIKEATEQSQPAA
REMARK ========================================================================
TSCORE T0004 0 0.35  1LTS D 0
TSCORE T0004 0 0.25  1SNC x 0
TSCORE T0004 0 0.20  1PTF x 0
TSCORE T0004 0 0.05  2BOP A 0
TSCORE T0004 0 0.15  2FXB x 0
REMARK ========================================================================
TALIGN T0004 0     1  18              1LTS D  0  14  31     0.6  1
TALIGN T0004 0    19  39              1LTS D  0  34  54     0.6  1 
TALIGN T0004 0    40  78              1LTS D  0  65 103     0.6  1
TALIGN T0004 0     1  18              1LTS D  0  14  31     0.4  2 
TALIGN T0004 0    19  38              1LTS D  0  34  53     0.4  2
TALIGN T0004 0    39  78              1LTS D  0  64 103     0.4  2
TALIGN T0004 0     1  39              1SNC x  0   9  47     0.7  1
TALIGN T0004 0    40  63              1SNC x  0  54  77     0.7  1
TALIGN T0004 0    64  84              1SNC x  0  95 115     0.7  1
TALIGN T0004 0     1  18              1SNC x  0   9  26     0.3  2
TALIGN T0004 0    19  38              1SNC x  0  29  48     0.3  2
TALIGN T0004 0    39  53              1SNC x  0  55  69     0.3  2
TALIGN T0004 0    54  83              1SNC x  0  80 109     0.3  2
TALIGN T0004 0     1  11              1PTF x  0   1  11     1.0  1
TALIGN T0004 0    12  27              1PTF x  0  30  45     1.0  1
TALIGN T0004 0    42  83              1PTF x  0  46  87     1.0  1
TALIGN T0004 0     1  11              2BOP A  0 326 336     1.0  1
TALIGN T0004 0    14  27              2BOP A  0 352 365     1.0  1
TALIGN T0004 0    28  68              2BOP A  0 370 410     1.0  1
TALIGN T0004 0     1  11              2FXB x  0   1  11     1.0  1
TALIGN T0004 0    12  29              2FXB x  0  22  39     1.0  1
TALIGN T0004 0    37  75              2FXB x  0  43  81     1.0  1
REMARK ========================================================================


_______________________________________________________________________
Valentina Di Francesco                     Tel.  : (301) 402 0505
NIH/DCRT/Lab. of Structural Biology        Fax   : (301) 496 2172
12 South Drive MSC 5626                    email : valedf@helix.nih.gov
Bldg 12A - Room 2039
Bethesda, MD 20892 - 5626


