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/F54D1.3
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Query:  F54D1.3  CE05938   collagen status:Predicted TR:Q20764 protein_id:CAB00860.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do    94.9    8.1e-27   1
Collagen      Collagen triple helix repeat (20 copies    89.0    5.6e-23   3

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      29    90 ..     1    66 []    94.9  8.1e-27
Collagen        1/3     118   143 ..    35    60 .]     8.8     0.62
Collagen        2/3     164   222 ..     1    60 []    50.0  2.9e-12
Collagen        3/3     234   293 ..     1    60 []    47.2  1.7e-11

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 29 to 90: score 94.9, E = 8.1e-27
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      +++Avla+Lftvps+yn+In+ +d+v+d+++ F+v++d aW+eM+d+
     F54D1.3    29    ASIAVLAVLFTVPSLYNTINEVHDQVLDGVSVFRVETDSAWTEMMDI 75

                   qrnvrppskpasarfgrpf<-*
                   q++v+pp+kp    +++pf
     F54D1.3    76 QVTVTPPTKP----RVNPF    90

Collagen: domain 1 of 3, from 118 to 143: score 8.8, E = 0.62
                   *->epGpPGppGppGppGppGapGapGpp<-*
                      +pGpPGppG+pG+pG pGapG+ G
     F54D1.3   118    PPGPPGPPGQPGAPGVPGAPGPRGGD    143

Collagen: domain 2 of 3, from 164 to 222: score 50.0, E = 2.9e-12
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                       p+Gp+Gp+G  Gp+Gp+Gp G++G pG +G+ G+pG+PG+pG +G+
     F54D1.3   164    -PAGPAGPAGSSGPAGPAGPSGQPGTPGQRGNDGFPGAPGAPGDNGQ 209

                   pGppGapGapGpp<-*
                   pG pG++GapG+p
     F54D1.3   210 PGFPGQDGAPGQP    222

Collagen: domain 3 of 3, from 234 to 293: score 47.2, E = 1.7e-11
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+pG pG +Gp+Gp G  G+pG++GapG++Gp+G +G+PG  G +G+
     F54D1.3   234    GAPGAPGNAGPAGPSGQDGFPGQDGAPGSAGPAGQDGFPGNNGSDGQ 280

                   pGppGapGapGpp<-*
                   pG pG pG pG
     F54D1.3   281 PGAPGGPGLPGND    293



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