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:            hmm1/seq/C02B8.6
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Query:  C02B8.6  CE29656   DNA repair protein RAD16 (yeast, weak) status:Partially_confirmed SW:Q11096 protein_id:AAA81439.2

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
WWE      WWE domain                                     104.1    1.2e-28   1
zf-C3HC4 Zinc finger, C3HC4 type (RING finger)           25.1    4.9e-08   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
zf-C3HC4   1/1       5    43 ..     1    50 []    25.1  4.9e-08
WWE        1/1     244   321 ..     1    88 []   104.1  1.2e-28

Alignments of top-scoring domains:
zf-C3HC4: domain 1 of 1, from 5 to 43: score 25.1, E = 4.9e-08
                   *->CrICleelkepsndfplilpCgHsGslkyfCrsClerWls..gnttv
                      C IC++++  p+      l C+H      fC+ C++  +++++  +
     C02B8.6     5    CTICHNTPNRPV-----RLDCNHE-----FCYICIKGSIQndM-LN- 39

                   kCplC<-*
                    C +C
     C02B8.6    40 -CAVC    43

WWE: domain 1 of 1, from 244 to 321: score 104.1, E = 1.2e-28
                   *->slappstvagekvvvWeyerSkddnggWwpYdprvsrdIEnAyaagk
                      +++++++va+ ++++W y+   ++++gWw++d+r+++dIE+++ a+k
     C02B8.6   244    NVQANFNVAR-VKFFWLYS---SRGDGWWRFDQRCEKDIEDEFLANK 286

                   kfgsvtldqvsicgrhYtidfetmtqyrqetgssttRpVrR<-*
                   +    +++ ++ +g++Y++df +m+q+++++  +++R+++R
     C02B8.6   287 P----NME-MYLFGKPYILDFVAMRQWQKGNL-DAWRQIKR    321



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