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:            hmm5/seq/W08D2.6
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Query:  W08D2.6  CE06561   collagen status:Partially_confirmed TR:Q23222 protein_id:CAA94234.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    77.0    1.1e-19   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    65.9    3.4e-18   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      24    85 ..     1    66 []    65.9  3.4e-18
Collagen        1/3     145   170 ..    30    55 ..    14.9    0.013
Collagen        2/3     190   248 ..     1    60 []    43.8  1.5e-10
Collagen        3/3     257   316 ..     1    60 []    34.2  6.6e-08

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 24 to 85: score 65.9, E = 3.4e-18
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      S++A+++cL+++ s+y  ++++++e++d m e ++  dd+W+e++ +
     W08D2.6    24    SAIALISCLLVLSSVYRNVQDYWTELDDQMVEVRKDLDDMWREIMHI 70

                   qrnvrppskpasarfgrpf<-*
                   q+n+ ++      r +rp
     W08D2.6    71 QSNSLGS----VFRARRPA    85

Collagen: domain 1 of 3, from 145 to 170: score 14.9, E = 0.013
                   *->pGppGepGpPGppGppGppGppGapG<-*
                      +Gp+G++G+PG pGp+G pG +G+pG
     W08D2.6   145    AGPQGAKGAPGLPGPNGVPGLDGKPG    170

Collagen: domain 2 of 3, from 190 to 248: score 43.8, E = 1.5e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                       p GppG+pGp G pG++G +G +G pG pG  G+pG PG  Gp+G+
     W08D2.6   190    -PQGPPGSPGPMGHPGARGMKGSDGQPGQPGKDGDPGKPGEMGPNGF 235

                   pGppGapGapGpp<-*
                   +G  G++G pG+
     W08D2.6   236 QGKVGPDGFPGEK    248

Collagen: domain 3 of 3, from 257 to 316: score 34.2, E = 6.6e-08
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+pGp G +G++G pG+ G pG++G+ GppG++G++G PGp+G+ G+
     W08D2.6   257    GRPGPKGQKGETGHPGAQGTPGHNGPTGPPGDAGPDGGPGPQGEQGA 303

                   pGppGapGapGpp<-*
                    G pG  G  G p
     W08D2.6   304 DGGPGSEGKVGRP    316



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