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/C24F3.6
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Query:  C24F3.6  CE18523   CUTICLE COLLAGEN 1 status:Partially_confirmed TR:Q9NAR3 protein_id:CAB97232.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    83.0    2.5e-21   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    26.0    2.7e-06   1
AmoA          Putative ammonia monooxygenase              4.2        3.3   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
AmoA            1/1      25    44 ..   321   340 .]     4.2      3.3
Col_cuticle_N   1/1      21    58 ..     1    38 [.    26.0  2.7e-06
Collagen        1/3      95   124 ..     1    30 [.    14.9    0.013
Collagen        2/3     141   199 ..     1    60 []    35.6  2.7e-08
Collagen        3/3     208   267 ..     1    60 []    48.6  7.4e-12

Alignments of top-scoring domains:
AmoA: domain 1 of 1, from 25 to 44: score 4.2, E = 3.3
                   *->lLlvLlllpplirylsklrg<-*
                      +L+v  +lp+ ++y+++ r
     C24F3.6    25    VLSVCITLPMMYNYIHHTRK    44

Col_cuticle_N: domain 1 of 1, from 21 to 58: score 26.0, E = 2.7e-06
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyad<-*
                      S++Avl++++t+p++yn+I + +  ++ ++ e+K +a+
     C24F3.6    21    STIAVLSVCITLPMMYNYIHHTRKVMHSDIVECKSEAQ    58

Collagen: domain 1 of 3, from 95 to 124: score 14.9, E = 0.013
                   *->GppGppGppGppGppGppGppGpaGapGpp<-*
                      G+ GppG pG +G pG+pG+pG +G pG p
     C24F3.6    95    GAQGPPGTPGSAGRPGKPGAPGLNGNPGRP    124

Collagen: domain 2 of 3, from 141 to 199: score 35.6, E = 2.7e-08
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                       p GppGp+GppGp+G++Gp Gp+G+pGp Gp GepG  Gp+GppGp
     C24F3.6   141    -PEGPPGPAGPPGPDGNKGPLGPPGPPGPEGPNGEPGNKGPAGPPGP 186

                   pGppGapGapGpp<-*
                    G pG++G+pG++
     C24F3.6   187 GGKPGPAGPPGEN    199

Collagen: domain 3 of 3, from 208 to 267: score 48.6, E = 7.4e-12
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+pG+pG pG pG++Gp+G+pG +G+pG +G +G++G+PG+pG++G+
     C24F3.6   208    GAPGEPGQPGQPGQRGPAGEPGKDGSPGGQGEKGASGEPGQPGRDGQ 254

                   pGppGapGapGpp<-*
                   pG pG+pG  G p
     C24F3.6   255 PGHPGQPGKDGRP    267



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