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/C34F6.3
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Query:  C34F6.3  CE15672   collagen status:Partially_confirmed TR:O17642 protein_id:CAB03942.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    65.0    2.3e-16   4
Col_cuticle_N Nematode cuticle collagen N-terminal do     5.5        3.3   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      24    57 ..     1    34 [.     5.5      3.3
Collagen        1/4      96   121 ..     1    26 [.    16.2   0.0056
Collagen        2/4     142   201 ..     1    60 []    26.6  8.1e-06
Collagen        3/4     207   259 ..     8    60 .]    42.4  3.7e-10
Collagen        4/4     260   271 ..    49    60 .]     2.2       40

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 24 to 57: score 5.5, E = 3.3
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFK<-*
                      S+vA l +++++p     ++s  + + +e+ ++K
     C34F6.3    24    STVATLIAIIAIPLFCVHMQSVTSGLSEELLFCK    57

Collagen: domain 1 of 4, from 96 to 121: score 16.2, E = 0.0056
                   *->GppGppGppGppGppGppGppGpaGa<-*
                      Gp+G pG  G+pG +G++G+pG++Ga
     C34F6.3    96    GPAGVPGQEGAPGNDGKAGQPGAPGA    121

Collagen: domain 2 of 4, from 142 to 201: score 26.6, E = 8.1e-06
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      GppG  G+pGp GppGppG pG+ G+pG  G++G+pGp GppG++Gp
     C34F6.3   142    GPPGAVGGPGPKGPPGPPGGPGELGGPGRGGNRGPPGPRGPPGEAGP 188

                   pGppGapGapGpp<-*
                    G+ G+pG +G+
     C34F6.3   189 DGEGGRPGQAGQT    201

Collagen: domain 3 of 4, from 207 to 259: score 42.4, E = 3.7e-10
                   *->ppGppGppGppGppGpaGapGppGppGepGpPGppGppGppGppGap
                      ppG pG+pG+pG pG++G+ G +G+pG +GpPGppG +G +G+pG++
     C34F6.3   207    PPGQPGQPGEPGSPGEPGPDGRAGHPGRNGPPGPPGDNGGQGEPGKD 253

                   GapGpp<-*
                   G+ G++
     C34F6.3   254 GEDGEN    259

Collagen: domain 4 of 4, from 260 to 271: score 2.2, E = 40
                   *->GppGapGapGpp<-*
                      G +Ga+G++G +
     C34F6.3   260    GAAGAAGPKGSC    271

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