Motif confirmation by HMMer


hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
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HMM file:                 /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file:            hmm3/seq/F58H1.7
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Query:  F58H1.7  CE20895   low-density lipoprotein receptor status:Confirmed TR:Q18790 protein_id:CAB01419.1

Scores for sequence family classification (score includes all domains):
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
ldl_recept_a Low-density lipoprotein receptor domain     42.1    3.1e-11   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
ldl_recept_a   1/1      43    76 ..     9    43 .]    42.1  3.1e-11

Alignments of top-scoring domains:
ldl_recept_a: domain 1 of 1, from 43 to 76: score 42.1, E = 3.1e-11
                   *->FqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
                      F C sg+ C+p++++CDG+pDC D  DE    C a
     F58H1.7    43    FACPSGE-CVPIKYLCDGSPDCSDEYDENKSMCTA    76



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