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:            hmm3/seq/F59F3.2
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Query:  F59F3.2  CE18797   collagen status:Partially_confirmed TR:Q21039 protein_id:CAA91992.1

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
Collagen Collagen triple helix repeat (20 copies)        51.6    1.1e-12   4

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
Collagen   1/4      24    53 ..    14    43 ..     3.1       23
Collagen   2/4      63    97 ..    26    60 .]    20.4  0.00041
Collagen   3/4      98   126 ..    11    39 ..    11.3     0.13
Collagen   4/4     132   191 ..     1    60 []    39.7  1.9e-09

Alignments of top-scoring domains:
Collagen: domain 1 of 4, from 24 to 53: score 3.1, E = 23
                   *->ppGppGppGpaGapGppGppGepGpPGppG<-*
                      p+Gp+GppG++G     G+pG++G +G +G
     F59F3.2    24    PKGPRGPPGDDGNSPTDGHPGDNGKDGTDG    53

Collagen: domain 2 of 4, from 63 to 97: score 20.4, E = 0.00041
                   *->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
                      +p p+GppGe+G  G +G+pG pG pG pG pG +
     F59F3.2    63    PPCPQGPPGEDGLRGEAGEPGRPGTPGDPGRPGTN    97

Collagen: domain 3 of 4, from 98 to 126: score 11.3, E = 0.13
                   *->ppGppGppGppGpaGapGppGppGepGpP<-*
                      +pG  G++Gp G++G  G++G+pGe+G++
     F59F3.2    98    EPGGIGARGPRGQSGRTGSKGDPGEAGQD    126

Collagen: domain 4 of 4, from 132 to 191: score 39.7, E = 1.9e-09
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G pGp G pG  G pG++G pG++G+p ppGp G+pGp G  G +G
     F59F3.2   132    GLPGPKGLPGSVGLPGARGDPGNNGKPAPPGPEGFPGPVGDLGDAGE 178

                   pGppGapGapGpp<-*
                    G +G pG  G p
     F59F3.2   179 YGLRGVPGRRGSP    191



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