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/C41D11.7
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Query: C41D11.7 CE08664 DNA-binding protein status:Partially_confirmed TR:O01976 protein_id:AAC48142.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
DEAD DEAD/DEAH box helicase 29.0 6.3e-08 1
AAA ATPase family associated with various 9.3 0.093 1
RNA_helicase RNA helicase 6.6 0.82 1
IstB IstB-like ATP binding protein 6.1 1.1 1
UK Virulence determinant 4.6 3.7 1
P2X_receptor ATP P2X receptor 3.8 4.4 1
Viral_helicase1 Viral (Superfamily 1) RNA helicase 2.3 8.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AAA 1/1 92 104 .. 1 13 [. 9.3 0.093
IstB 1/1 93 105 .. 52 64 .. 6.1 1.1
RNA_helicase 1/1 93 106 .. 126 139 .. 6.6 0.82
DEAD 1/1 64 129 .. 1 64 [. 29.0 6.3e-08
Viral_helicase1 1/1 460 474 .. 216 230 .. 2.3 8.2
UK 1/1 498 521 .. 133 156 .] 4.6 3.7
P2X_receptor 1/1 610 627 .. 378 395 .] 3.8 4.4
Alignments of top-scoring domains:
AAA: domain 1 of 1, from 92 to 104: score 9.3, E = 0.093
*->gvLLyGPPGtGKT<-*
v+ GPPGtGKT
C41D11.7 92 LVCIQGPPGTGKT 104
IstB: domain 1 of 1, from 93 to 105: score 6.1, E = 1.1
*->lvLlGPpGvGKTH<-*
+++ GPpG+GKT+
C41D11.7 93 VCIQGPPGTGKTF 105
RNA_helicase: domain 1 of 1, from 93 to 106: score 6.6, E = 0.82
*->vylhGaPGqGKSll<-*
v+++G+PG+GK+++
C41D11.7 93 VCIQGPPGTGKTFT 106
DEAD: domain 1 of 1, from 64 to 129: score 29.0, E = 6.3e-08
*->kalkklgfekptpiQaeaipaileg..rDvlvqApTGSGKTlAfllP
k+ g+ ++ Q+ ai+ +l+++++ v +q+p G+GKT l
C41D11.7 64 SMEKEAGIPFSNEKQRTAIKMALNEnrKLVCIQGPPGTGKTFTLTLL 110
ileallkgpqalvlaPTRE<-*
++ +++++q++vlaPTRE
C41D11.7 111 LCRLIQQKKQVVVLAPTRE 129
Viral_helicase1: domain 1 of 1, from 460 to 474: score 2.3, E = 8.2
*->tvhevQGltfdsVtl<-*
tv +vQG+++++V++
C41D11.7 460 TVDSVQGKEYEVVIF 474
UK: domain 1 of 1, from 498 to 521: score 4.6, E = 3.7
*->itsADkKFsvFgKGYLmRsmqKDD<-*
it A + F g GYL+ +KD+
C41D11.7 498 ITRAKRHFMFIGNGYLLAESKKDE 521
P2X_receptor: domain 1 of 1, from 610 to 627: score 3.8, E = 4.4
*->KFeeVedtkagaaselea<-*
K+e+ ++ ++ +asel++
C41D11.7 610 KYEYKRGSTEQLASELDQ 627