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).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file: hmm5/seq/Y47D3B.9
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: Y47D3B.9 CE19173 status:Partially_confirmed TR:Q9XWZ9 protein_id:CAA21044.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
zf-BED BED zinc finger 93.3 7.5e-26 2
E6 Early Protein (E6) 3.0 9.7 1
ku Ku70/Ku80 beta-barrel domain 2.9 5.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
ku 1/1 109 122 .. 224 237 .] 2.9 5.3
zf-BED 1/2 186 230 .. 1 52 [] 40.2 3e-10
E6 1/1 370 381 .. 1 12 [. 3.0 9.7
zf-BED 2/2 353 396 .. 1 52 [] 59.2 7.9e-16
Alignments of top-scoring domains:
ku: domain 1 of 1, from 109 to 122: score 2.9, E = 5.3
*->teeqldlakqlidk<-*
teeq+++a +li++
Y47D3B.9 109 TEEQQAAALSLIQS 122
zf-BED: domain 1 of 2, from 186 to 230: score 40.2, E = 3e-10
*->SkvWkhFtkve..eeedgkevegkakCkhCgkklsrkkksGTSnLir
++vW++F+ +++++ + g ++C+hC + + + +nL++
Y47D3B.9 186 HPVWDFFKDMKdsTGAGG------VICLHCSWSGDDR---SPNNLRT 223
HLrrkHp<-*
HL+++H+
Y47D3B.9 224 HLKKFHS 230
E6: domain 1 of 1, from 370 to 381: score 3.0, E = 9.7
*->CvFCkkfLtraE<-*
C++C k+L r++
Y47D3B.9 370 CIYCWKVLKRND 381
zf-BED: domain 2 of 2, from 353 to 396: score 59.2, E = 7.9e-16
*->SkvWkhFtkveeeedgkevegkakCkhCgkklsrkkksGTSnLirHL
S++W+h++++ +e++ ++C++C+k+l+r+ +s+T++++ H+
Y47D3B.9 353 SEIWEHYKCL--NEKQ-----NVECIYCWKVLKRN-DSSTKSMWGHM 391
rrkHp<-*
+++H+
Y47D3B.9 392 NAYHQ 396