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/C35B8.1
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Query:  C35B8.1  CE02534   Cuticle collagen status:Partially_confirmed TR:Q18480 protein_id:AAC46553.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    93.3    3.7e-24   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    68.1    7.5e-19   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      12    73 ..     1    66 []    68.1  7.5e-19
Collagen        1/3     100   131 ..    29    60 .]    23.5  5.8e-05
Collagen        2/3     148   207 ..     1    60 []    37.4  8.4e-09
Collagen        3/3     217   276 ..     1    60 []    47.8  1.2e-11

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 12 to 73: score 68.1, E = 7.5e-19
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      S+v++ a+L++v++i+ndIn + +++  +m++FK+++d aW  ++++
     C35B8.1    12    SAVVITASLCSVLVIMNDINKLSEDISIGMENFKDVSDVAWGNIMVL 58

                   qrnvrppskpasarfgrpf<-*
                   + +vr++    sa   r+
     C35B8.1    59 HGGVRQQ----SASVHRDV    73

Collagen: domain 1 of 3, from 100 to 131: score 23.5, E = 5.8e-05
                   *->ppGppGepGpPGppGppGppGppGapGapGpp<-*
                      p+G pGe+G+PG +G pGp G++G++GapG +
     C35B8.1   100    PAGSPGEKGEPGLAGLPGPDGEDGKDGAPGVA    131

Collagen: domain 2 of 3, from 148 to 207: score 37.4, E = 8.4e-09
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp+Gp+G +GppGppG+ G pG++G pG++G pG+ G+PG  G pGp
     C35B8.1   148    GPRGPRGDAGPPGPPGNGGRPGQRGTPGEAGTPGPVGEPGETGGPGP 194

                   pGppGapGapGpp<-*
                   +G pG+ G+pG+p
     C35B8.1   195 QGRPGQRGEPGQP    207

Collagen: domain 3 of 3, from 217 to 276: score 47.8, E = 1.2e-11
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+pGp+Gp+G +G+pG+ G +G++G  G +G+pG +G+ G+ G++G+
     C35B8.1   217    GRPGPQGPRGQQGEPGKDGSKGNPGDEGRQGHPGKNGRTGAHGKDGA 263

                   pGppGapGapGpp<-*
                   pG  G+ G+ Gp
     C35B8.1   264 PGKCGKEGPIGPD    276



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