PFRMAT     AL 
TARGET     T0071 
AUTHOR     7545-6133-3082 
REMARK 
METHOD   The information that T0071 is a two domain protein was given 
METHOD   as well as an approximate domain-boundary. Both domains were 
METHOD   analysed independently. 
METHOD   blastp was used to find homologous sequences of which a multiple 
METHOD   sequences alignment was build and used as seed for HMMer. The 
METHOD   resulting hmm was used to search against a version of pdb which 
METHOD   only contains proteins of less than 90% homology. No significant 
METHOD   hits were found during this procedure. 
METHOD   A specifically developed neural network scored all alignments on 
METHOD   basis of their secondary structure overlap. 
METHOD   For the N-terminal part a number of immunoglobuline-like folds 
METHOD   (three) were among the top ten scores. Although the scores 
METHOD   were not very high and thus no confident prediction was possible, 
METHOD   it was decide to use the immunoglobuline like fold with the highest 
METHOD   score as the parent for the N-terminal part of the protein. 
METHOD   For the C-terminal part all scores were very low (only one score 
METHOD   above 0) and there was no common fold amongst the top 10 hits. 
METHOD   Thus it was concluded, that the C-terminal domain has a structure 
METHOD   not yet present in the database. 
MODEL 1 
PARENT 1wit 
L       22      L       1 
Q       23      K       2 
I       24      P       3 
G       25      K       4 
L       26      I       5 
K       27      L       6 
S       28      T       7 
E       29      A       8 
F       30      S       9 
R       31      R       10 
Q       32      K       11 
N       33      I       12 
L       34      K       13 
G       35      I       14 
R       36      K       15 
M       37      A       16 
F       38      G       17 
F       40      F       18 
Y       41      T       19 
G       42      H       20 
N       43      N       21 
K       44      L       22 
T       45      E       23 
S       46      V       24 
T       47      D       25 
Q       48      F       26 
F       49      I       27 
L       50      G       28 
N       51      A       29 
F       52      P       30 
T       53      D       31 
P       54      P       32 
T       55      T       33 
L       56      A       34 
I       57      T       35 
C       58      W       36 
L       62      T       37 
Q       63      V       38 
T       64      G       39 
N       65      D       40 
L       66      S       41 
N       67      G       42 
L       68      A       43 
Q       69      A       44 
T       70      L       45 
K       71      A       46 
P       72      P       47 
D       74      E       48 
P       75      L       49 
T       76      L       50 
V       77      V       51 
D       78      D       52 
G       79      A       53 
G       80      K       54 
A       81      S       55 
Q       82      S       56 
V       83      T       57 
Q       84      T       58 
Q       85      S       59 
V       86      I       60 
I       87      F       61 
N       88      F       62 
I       89      P       63 
E       90      S       64 
C       91      A       65 
I       92      K       66 
S       93      R       67 
T       96      A       68 
E       97      D       69 
A       98      S       70 
P       99      G       71 
V       100     N       72 
L       101     Y       73 
N       102     K       74 
I       103     L       75 
Q       104     K       76 
R       106     V       77 
Y       107     K       78 
G       108     N       79 
G       109     E       80 
T       110     L       81 
F       111     G       82 
Q       112     E       83 
V       114     D       84 
S       115     E       85 
V       116     A       86 
K       117     I       87 
L       118     F       88 
P       119     E       89 
I       120     V       90 
T       121     I       91 
L       122     V       92 
N       123     Q       93 
TER 
END 
