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/C08B11.5
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Query:  C08B11.5  CE24791  locus:sap-49 Poly(A) RNA binding protein status:Confirmed TR:Q8T8N6 protein_id:CAB60993.1

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    157.4    7.1e-45   2

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
rrm        1/2      25    96 ..     1    77 []    74.8  1.5e-20
rrm        2/2     112   184 ..     1    77 []    82.8  6.3e-23

Alignments of top-scoring domains:
rrm: domain 1 of 2, from 25 to 96: score 74.8, E = 1.5e-20
                   *->lfVgNLppdvteedLkdlFskfGpivsikivkDhiekpketgkskGf
                      ++Vg+L + v+e+ L +l+ + Gp+vs++++kD     ++t ++ Gf
    C08B11.5    25    IYVGGLDEKVSESILWELMVQAGPVVSVNMPKD-----RVTANHQGF 66

                   aFVeFeseedAekAlealnGkelggrklrv<-*
                   +FVeF  eedA+ A++ ln ++l+g++++v
    C08B11.5    67 GFVEFMGEEDADYAIKILNMIKLYGKPIKV    96

rrm: domain 2 of 2, from 112 to 184: score 82.8, E = 6.3e-23
                   *->lfVgNLppdvteedLkdlFskfGpivsi.kivkDhiekpketgkskG
                      +fVgNL p+v+e+ L+d Fs fG i+ ++ki++D        g skG
    C08B11.5   112    IFVGNLDPEVDEKLLYDTFSAFGVILQVpKIMRD-----VDSGTSKG 153

                   faFVeFeseedAekAlealnGkelggrklrv<-*
                   faF++F+s e+ + Alea+nG++l +r ++v
    C08B11.5   154 FAFINFASFEASDTALEAMNGQFLCNRAITV    184



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