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/C29E4.1
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Query:  C29E4.1  CE00083   Cuticle collagen status:Confirmed SW:P34340 protein_id:AAA27958.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    79.4    2.5e-20   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    71.0      1e-19   1
HAMP          HAMP domain                                 8.0        1.3   1
OGFr_repeat   Opioid growth factor receptor repeat        4.7        7.1   1
YdjC          YdjC-like protein                           4.6        1.9   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
HAMP            1/1       4    38 ..     1    35 [.     8.0      1.3
YdjC            1/1      37    59 ..   295   317 .]     4.6      1.9
Col_cuticle_N   1/1      12    73 ..     1    66 []    71.0    1e-19
Collagen        1/3      94   123 ..     5    34 ..     9.2     0.48
OGFr_repeat     1/1     166   186 ..     1    20 []     4.7      7.1
Collagen        2/3     142   201 ..     1    60 []    41.6    6e-10
Collagen        3/3     208   267 ..     1    60 []    44.2  1.2e-10

Alignments of top-scoring domains:
HAMP: domain 1 of 1, from 4 to 38: score 8.0, E = 1.3
                   *->lllvlllalllalllalllarrltrPlrrLaeaaq<-*
                      ++ +++ ++ll++l +l+ ++ ++r ++ L++ ++
     C29E4.1     4    IGYIGASICLLGVLSSLFSISHIVRDINSLRDEVE    38

YdjC: domain 1 of 1, from 37 to 59: score 4.6, E = 1.9
                   *->aqqRleELevLTsptLrawlaqr<-*
                      +++R++E+ vL+++t    l++
     C29E4.1    37    VEGRVDEFKVLADDTWQRLLVLQ    59

Col_cuticle_N: domain 1 of 1, from 12 to 73: score 71.0, E = 1e-19
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      +++ vl++Lf++ +i+ dIns++dev++ +deFKv+add+W++++++
     C29E4.1    12    CLLGVLSSLFSISHIVRDINSLRDEVEGRVDEFKVLADDTWQRLLVL 58

                   qrnvrppskpasarfgrpf<-*
                   q+++++     ++ +++ f
     C29E4.1    59 QSPTGE----TENVMPSIF    73

Collagen: domain 1 of 3, from 94 to 123: score 9.2, E = 0.48
                   *->ppGppGppGppGppGppGpaGapGppGppG<-*
                      p+GppGppG pG++G  G  G  G  G++G
     C29E4.1    94    PAGPPGPPGLPGKRGDEGVVGDLGRSGASG    123

OGFr_repeat: domain 1 of 1, from 166 to 186: score 4.7, E = 7.1
                   *->sPsEtPG.PrPAGParDEPAk<-*
                       Ps   G+P PAGP +D  A+
     C29E4.1   166    GPSGDDGqPGPAGPLGDKGAQ    186

Collagen: domain 2 of 3, from 142 to 201: score 41.6, E = 6e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp+GppG  Gp Gp G pG  G  G+ G+ G pG++Gp G +G+ Gp
     C29E4.1   142    GPAGPPGQQGPVGPQGFPGVVGTCGPSGDDGQPGPAGPLGDKGAQGP 188

                   pGppGapGapGpp<-*
                   +G +Ga+G+ G p
     C29E4.1   189 KGFDGADGPDGMP    201

Collagen: domain 3 of 3, from 208 to 267: score 44.2, E = 1.2e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+ G+pG+pG  G+pG pG  G++G  G+ Gp+G+pG PG+ G++
     C29E4.1   208    GAVGQPGEPGWLGQPGLPGKHGEPGQDGEEGPKGAPGTPGSNGRDAY 254

                   pGppGapGapGpp<-*
                   pG+pG++G+pG++
     C29E4.1   255 PGQPGKAGEPGAV    267

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