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/C09G5.3
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Query:  C09G5.3  CE01483   collagen status:Partially_confirmed SW:Q09233 protein_id:CAA86756.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    82.6    3.4e-21   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    63.1    2.3e-17   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      14    76 ..     1    66 []    63.1  2.3e-17
Collagen        1/3      92   121 ..    26    55 ..    15.5   0.0089
Collagen        2/3     139   198 ..     1    60 []    39.5  2.2e-09
Collagen        3/3     204   263 ..     1    60 []    42.8  2.8e-10

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 76: score 63.1, E = 2.3e-17
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      S+ ++++++f+++++ +d+n++q  +++ m +FK+++d +W+ M+ +
     C09G5.3    14    SASVLVTTIFVCWNVTHDLNTLQAMSDRNMQDFKAISDRTWDKMMFK 60

                   qrnvrppskpasarfgrpf<-*
                   q+++ p++   s +fgr++
     C09G5.3    61 QQSSPPSP---SLIFGRNK    76

Collagen: domain 1 of 3, from 92 to 121: score 15.5, E = 0.0089
                   *->apGppGppGepGpPGppGppGppGppGapG<-*
                      + GppGppGe+G +G +G++G pG pG+ G
     C09G5.3    92    PGGPPGPPGEKGNDGVDGVDGIPGFPGENG    121

Collagen: domain 2 of 3, from 139 to 198: score 39.5, E = 2.2e-09
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp+GppGp G+ Gp G+ G+ G++G pG+ G+ G pG  G+pG  Gp
     C09G5.3   139    GPRGPPGPQGEEGPSGDVGEDGEPGVPGNDGADGTPGKSGAPGGKGP 185

                   pGppGapGapGpp<-*
                   +GppG pG pG+p
     C09G5.3   186 QGPPGTPGRPGQP    198

Collagen: domain 3 of 3, from 204 to 263: score 42.8, E = 2.8e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G++Gp GppG+pG +G++G+ G +G  G  G pG+ G  G +G pG
     C09G5.3   204    GEAGPKGPPGAPGTDGRRGENGTDGDDGVDGQPGDEGDAGKDGTPGE 250

                   pGppGapGapGpp<-*
                   pGp+G+ G +G+p
     C09G5.3   251 PGPQGEQGTEGQP    263



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