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 mainly low scores were achieved. There 
METHOD   were a number of immunoglobuline-like fold amongst the best 10 
METHOD   hits, but also a number of cupredoxin-like folds. It was not 
METHOD   not clear how to decide which of either might be the right fold, 
METHOD   it was decided to submit both and as well make a prediciton claiming 
METHOD   the fold of the N-terminal domain is not yet in the database of 
METHOD   known structures. 
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 mainly low scores were achieved. There 
METHOD   were a number of immunoglobuline-like fold amongst the best 10 
METHOD   hits, but also a number of cupredoxin-like folds. It was not 
METHOD   not clear how to decide which of either might be the right fold, 
METHOD   it was decided to submit both and as well make a prediciton claiming 
METHOD   the fold of the N-terminal domain is not yet in the database of 
METHOD   known structures. 
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 3 
PARENT NONE 
TER 
END 
