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:            hmm2/seq/EGAP7.1
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Query:  EGAP7.1  CE07013  locus:dpy-3 cuticular collagen status:Partially_confirmed TR:Q19079 protein_id:AAB00598.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    91.8    9.5e-24   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    63.9    1.3e-17   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      22    83 ..     1    66 []    63.9  1.3e-17
Collagen        1/3     109   142 ..    23    56 ..    18.9    0.001
Collagen        2/3     157   215 ..     1    60 []    43.8  1.5e-10
Collagen        3/3     225   284 ..     1    60 []    45.2    6e-11

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 22 to 83: score 63.9, E = 1.3e-17
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      ++v+ la+++ vp +yn ++++q+ +  e+d++K++++d W+eMv+v
     EGAP7.1    22    AIVSMLATVIIVPLVYNHVQHLQSVMNSEVDFCKTRSRDLWREMVTV 68

                   qrnvrppskpasarfgrpf<-*
                   q+++++    + ar++r+
     EGAP7.1    69 QSATGG----IPARTARRT    83

Collagen: domain 1 of 3, from 109 to 142: score 18.9, E = 0.001
                   *->paGapGppGppGepGpPGppGppGppGppGapGa<-*
                      + G+pGppGppG +G+PG+pG+pG pGppG++Ga
     EGAP7.1   109    QVGPPGPPGPPGRDGRPGAPGRPGNPGPPGRDGA    142

Collagen: domain 2 of 3, from 157 to 215: score 43.8, E = 1.5e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                       ppGppGp+GppGp+G pGp+G+aG  G  G pG pGpPGp Gp G+
     EGAP7.1   157    -PPGPPGPAGPPGPKGLPGPQGDAGTSGQDGVPGLPGPPGPSGPQGA 202

                   pGppGapGapGpp<-*
                   pG pG++G+ G+p
     EGAP7.1   203 PGVPGEKGPTGEP    215

Collagen: domain 3 of 3, from 225 to 284: score 45.2, E = 6e-11
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      GppGppGppGp+GppGppG  G++G++GppG pG+pG+ G++G pGp
     EGAP7.1   225    GPPGPPGPPGPQGPPGPPGKDGQPGKAGPPGLPGDPGEKGSDGLPGP 271

                   pGppGapGapGpp<-*
                    G +G+ G+pG+p
     EGAP7.1   272 HGGTGPRGPPGQP    284



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