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



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