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:            hmm4/seq/T10B10.1
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Query:  T10B10.1  CE06399  locus:col-41 collagen status:Partially_confirmed TR:Q22369 protein_id:CAA96674.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    84.8    8.2e-22   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    70.3    1.7e-19   1
HAMP          HAMP domain                                 4.8        9.6   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
HAMP            1/1       4    38 ..     1    35 [.     4.8      9.6
Col_cuticle_N   1/1      12    76 ..     1    66 []    70.3  1.7e-19
Collagen        1/3      94   123 ..    14    43 ..    10.9     0.16
Collagen        2/3     142   201 ..     1    60 []    45.5  5.2e-11
Collagen        3/3     208   267 ..     1    60 []    44.0  1.3e-10

Alignments of top-scoring domains:
HAMP: domain 1 of 1, from 4 to 38: score 4.8, E = 9.6
                   *->lllvlllalllalllalllarrltrPlrrLaeaaq<-*
                      l+ ++++++ll+++ al  +  +++ +++L++ ++
    T10B10.1     4    LGYIGAGVCLLGVFSALCSIGHIVQDINNLRSEVE    38

Col_cuticle_N: domain 1 of 1, from 12 to 76: score 70.3, E = 1.7e-19
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      +++ v+++L+++++i++dIn++++ev++ +deFKv+add+W++++ +
    T10B10.1    12    CLLGVFSALCSIGHIVQDINNLRSEVEGRVDEFKVLADDTWDRLLIL 58

                   qrnvrppskpasarfgrpf<-*
                   q++++++ +p  + + r++
    T10B10.1    59 QSPTGESANP-VPSLLRNK    76

Collagen: domain 1 of 3, from 94 to 123: score 10.9, E = 0.16
                   *->ppGppGppGpaGapGppGppGepGpPGppG<-*
                      p+G+pGppG++G++G+ G+pG+ G+ G+ G
    T10B10.1    94    PAGAPGPPGNPGKRGDEGHPGDEGRRGASG    123

Collagen: domain 2 of 3, from 142 to 201: score 45.5, E = 5.2e-11
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp+GppGp G+ Gp G pG +G++G+ G+ G+pG  G+PG +G+ Gp
    T10B10.1   142    GPAGPPGPDGDSGPEGFPGLQGQSGPSGEDGAPGQEGAPGDQGEQGP 188

                   pGppGapGapGpp<-*
                   +G +G +G+ G+p
    T10B10.1   189 KGYDGTDGPDGQP    201

Collagen: domain 3 of 3, from 208 to 267: score 44.0, E = 1.3e-10
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G +G+pG+pG  G+pG pG+ G++G+ G+ Gp+G+pG PG +G++ +
    T10B10.1   208    GQAGQPGEPGWLGEPGLPGQHGEPGKDGEEGPQGAPGTPGNAGHDAF 254

                   pGppGapGapGpp<-*
                   pG pG++G pG+p
    T10B10.1   255 PGTPGQAGKPGAP    267



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