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:            hmm4/seq/W02B12.3
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Query:  W02B12.3  CE03763  locus:rsp-1 pre-mRNA splicing factor like protein status:Confirmed TR:Q23121 protein_id:CAA91395.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
rrm      RNA recognition motif. (a.k.a. RRM, RBD, or     90.6    3.3e-25   3
XFP      D-xylulose 5-phosphate/D-fructose 6-phosphat     1.2        6.3   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
XFP        1/1      12    27 ..   214   229 ..     1.2      6.3
rrm        1/3       5    68 ..     1    77 []    69.8  4.5e-19
rrm        2/3     131   147 ..     1    17 [.     5.3      4.4
rrm        3/3     172   197 ..    52    77 .]    15.2   0.0052

Alignments of top-scoring domains:
XFP: domain 1 of 1, from 12 to 27: score 1.2, E = 6.3
                   *->aRisdeELrklFeGyG<-*
                      +R+s+ +++ +F+GyG
    W02B12.3    12    SRVSEKDIEHFFRGYG    27

rrm: domain 1 of 3, from 5 to 68: score 69.8, E = 4.5e-19
                   *->lfVgNLppdvteedLkdlFskfGpivsikivkDhiekpketgkskGf
                      +++g L+  v+e+d++ +F+ +G+i ++ +++             Gf
    W02B12.3     5    IYIGRLTSRVSEKDIEHFFRGYGQIRDVLLKN-------------GF 38

                   aFVeFeseedAekAlealnGkelggrklrv<-*
                   +FVeF++++dAe+A+ +lnGkelgg ++
    W02B12.3    39 GFVEFDDKRDAEDAVHDLNGKELGGERVIL    68

rrm: domain 2 of 3, from 131 to 147: score 5.3, E = 4.4
                   *->lfVgNLppdvteedLkd<-*
                      ++V NL+  ++++dLkd
    W02B12.3   131    VVVENLSSRISWQDLKD    147

rrm: domain 3 of 3, from 172 to 197: score 15.2, E = 0.0052
                   *->FeseedAekAlealnGkelggrklrv<-*
                      F++++d ++++e+++G+ l+grk++
    W02B12.3   172    FATPSDLKRCIEKCDGMDLNGRKIKM    197



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