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/K02D7.3
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Query:  K02D7.3  CE17996   cuticular collagen status:Partially_confirmed TR:O45105 protein_id:AAC02608.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    67.9    3.5e-17   4
Col_cuticle_N Nematode cuticle collagen N-terminal do    40.9    9.8e-11   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      27    69 ..     1    43 [.    40.9  9.8e-11
Collagen        1/4     126   158 ..    28    60 .]    17.8   0.0021
Collagen        2/4     174   233 ..     1    60 []    42.7    3e-10
Collagen        3/4     237   264 ..    18    45 ..    12.9    0.048
Collagen        4/4     265   302 ..    23    60 .]    17.8   0.0021

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 27 to 69: score 40.9, E = 9.8e-11
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWne<-*
                      S++A l ++++vp++yn+I++ q+ ++ e++++ ++++  W+e
     K02D7.3    27    STIATLIAIVAVPMLYNYIQHVQSSLQSEVEFCAHRSNGLWDE    69

Collagen: domain 1 of 4, from 126 to 158: score 17.8, E = 0.0021
                   *->GppGppGepGpPGppGppGppGppGapGapGpp<-*
                      G++Gp+G pG++G+pG +G+pG pG+pG   +
     K02D7.3   126    GSAGPAGSPGQDGAPGNDGAPGAPGNPGQDAQD    158

Collagen: domain 2 of 4, from 174 to 233: score 42.7, E = 3e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      GppGp G+pG  Gp G+pG+pG +G++  pGppG++GpPGp G+pG+
     K02D7.3   174    GPPGPSGAPGQKGPSGAPGQPGRSGGASLPGPPGPAGPPGPSGQPGS 220

                   pGppGapGapGpp<-*
                    G++GapGapG +
     K02D7.3   221 NGNAGAPGAPGHV    233

Collagen: domain 3 of 4, from 237 to 264: score 12.9, E = 0.048
                   *->pGppGpaGapGppGppGepGpPGppGpp<-*
                      pG pGpaG+pGp+Gp+G+pG+PG++G++
     K02D7.3   237    PGTPGPAGPPGPAGPAGAPGQPGQAGHA    264

Collagen: domain 4 of 4, from 265 to 302: score 17.8, E = 0.0021
                   *->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
                      ++G pGp+G++G+pG+PG+pG +G+pG++G +G  G++
     K02D7.3   265    QPGQPGPQGDAGAPGAPGQPGSAGQPGNDGGDGGQGAC    302



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