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/C08F8.2
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Query: C08F8.2 CE19689 ATP-dependent RNA helicase status:Partially_confirmed TR:Q17828 protein_id:CAA97429.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
helicase_C Helicase conserved C-terminal domain 61.8 4.6e-16 1
e3_binding e3 binding domain 7.4 3.9 1
oxidored_q4 NADH-ubiquinone/plastoquinone oxidoreduct 4.5 4.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
e3_binding 1/1 91 103 .. 5 17 .. 7.4 3.9
helicase_C 1/1 378 455 .. 1 72 [] 61.8 4.6e-16
oxidored_q4 1/1 583 594 .. 71 82 .] 4.5 4.2
Alignments of top-scoring domains:
e3_binding: domain 1 of 1, from 91 to 103: score 7.4, E = 3.9
*->PaARkLArEkGiD<-*
P +R+LA+E+Gi+
C08F8.2 91 PMVRQLAKENGIN 103
helicase_C: domain 1 of 1, from 378 to 455: score 61.8, E = 4.6e-16
*->gikvarlhGglsqeeReeilekFrngks..kvLvaTdvaarGiDipd
gik a+++G+l++ + + +kF++ + + +vLvaTd++++G+++ +
C08F8.2 378 GIKPAVIYGDLPPGTKLAQAAKFNDPDDecNVLVATDAIGMGLNL-N 423
vnlVInydlpwnpes.....yiQRiGRaGRaG<-*
++ VI+ + + e ++ +Q +GRaGR+G
C08F8.2 424 IRRVIFNSCTRQTELlptyaALQIAGRAGRFG 455
oxidored_q4: domain 1 of 1, from 583 to 594: score 4.5, E = 4.2
*->LvYEWrqGaLeW<-*
L YEW LeW
C08F8.2 583 LTYEWLIDMLEW 594