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/B0491.2
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Query:  B0491.2  CE02104  locus:sqt-1 cuticle collagen SQT-1 status:Confirmed SW:P12114 protein_id:CAA90084.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    80.9    9.8e-21   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    31.4    6.2e-08   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      13    71 ..     1    66 []    31.4  6.2e-08
Collagen        1/3     125   151 ..    23    49 ..    12.7    0.052
Collagen        2/3     175   234 ..     1    60 []    42.1  4.5e-10
Collagen        3/3     240   299 ..     1    60 []    42.0  4.6e-10

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 13 to 71: score 31.4, E = 6.2e-08
                   *->SgvAvlacLftvps.iyndInsfqdevmdemdeFKvyaddaWneMvd
                       +vA l ++f + s+iy++++ f++ ++ em+ F++ ++  W+++v+
     B0491.2    13    VTVATLMVCFMTMStIYSEVDGFREKLDTEMNVFRQSTNGLWKDIVV 59

                   vqrnvrppskpasarfgrpf<-*
                   ++r++           +r++
     B0491.2    60 IGRSSKR--------VRRQY    71

Collagen: domain 1 of 3, from 125 to 151: score 12.7, E = 0.052
                   *->paGapGppGppGepGpPGppGppGppG<-*
                      paG+ Gp+G pG pG +G pG +G pG
     B0491.2   125    PAGPSGPKGVPGVPGLDGVPGLDGVPG    151

Collagen: domain 2 of 3, from 175 to 234: score 42.1, E = 4.5e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      GppG  G+pGp+G pGp+G+ G++G  G pG+pGe G+ G+ G+ G
     B0491.2   175    GPPGALGRPGPRGLPGPRGQNGNPGRDGQPGHPGEQGSSGQIGKIGE 221

                   pGppGapGapGpp<-*
                   pGppG++G   +
     B0491.2   222 PGPPGEKGRDAEH    234

Collagen: domain 3 of 3, from 240 to 299: score 42.0, E = 4.6e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp+Gp+G  Gp+Gp+G  G  Gp+G+pG  Gp G++G +G +Gp+G
     B0491.2   240    GPKGPRGDQGPTGPAGQNGLHGPPGEPGTVGPEGPSGKQGRQGPDGT 286

                   pGppGapGapGpp<-*
                   +G++G++G pG+
     B0491.2   287 QGETGPDGRPGKD    299



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