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/C15A11.6
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Query:  C15A11.6  CE08174   collagen status:Partially_confirmed TR:Q93207 protein_id:CAB01958.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do    84.4    1.1e-23   1
Collagen      Collagen triple helix repeat (20 copies    77.8    6.9e-20   3
7tm_1         7 transmembrane receptor (rhodopsin fam     2.6          3   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      14    75 ..     1    66 []    84.4  1.1e-23
Collagen        1/3      92   126 ..    26    60 .]    19.8  0.00058
Collagen        2/3     139   198 ..     1    60 []    35.4    3e-08
Collagen        3/3     204   263 ..     1    60 []    38.4  4.6e-09
7tm_1           1/1      65   304 ..   186   212 ..     2.6        3

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 75: score 84.4, E = 1.1e-23
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      Sg++v+++L++v++iy+dInsf +++++e++eFK++a+daWn+M++
    C15A11.6    14    SGIVVFGALISVFHIYSDINSFVEDSHRELGEFKGFANDAWNSMINQ 60

                   qrnvrppskpasarfgrpf<-*
                    ++vr+    a++ fgr+
    C15A11.6    61 DDSVRM----ARSVFGRRR    75

Collagen: domain 1 of 3, from 92 to 126: score 19.8, E = 0.00058
                   *->apGppGppGepGpPGppGppGppGppGapGapGpp<-*
                      ++GppGppG++G  G++G+pG++G pG+pG +Gp
    C15A11.6    92    PAGPPGPPGASGDKGHDGQPGQAGKPGQPGVAGPS    126

Collagen: domain 2 of 3, from 139 to 198: score 35.4, E = 3e-08
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G pGp+G+pG pGp+Gp G pG++   G +GppG+pGp G++G pG+
    C15A11.6   139    GLPGPAGAPGQPGPKGPNGNPGAPAQGGGQGPPGPPGPAGSAGSPGQ 185

                   pGppGapGapGpp<-*
                   +G pG+pG+pG+
    C15A11.6   186 AGAPGNPGSPGKS    198

Collagen: domain 3 of 3, from 204 to 263: score 38.4, E = 4.6e-09
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G pGp G+pG +GppG+pG+pG   apGp+GppG++Gp G+pG+pG+
    C15A11.6   204    GLPGPSGAPGSQGPPGAPGQPGSGNAPGPAGPPGPAGPNGQPGHPGQ 250

                   pGppGapGapGpp<-*
                    G+pGapG  G p
    C15A11.6   251 DGQPGAPGNDGTP    263

7tm_1: domain 1 of 1, from 65 to 304: score 2.6, E = 3
                   *->rIlrtlrkrarkgas................................
                      r++r ++ r+r+ ++++ + +++ ++ + +++++++ ++++++++++
    C15A11.6    65    RMARSVFGRRRQKKQsqcncgqqasncpagppgppgasgdkghdgqp 111

                   ..................................................
                   ++ +++++++  +++++++++  + +++ +++ + ++++++++++++++
    C15A11.6   112 gqagkpgqpgvagpshhqkqecikcpqglpgpagapgqpgpkgpngnpga 161

                   ..................................................
                   + +++++++++++++ ++ +++++ + ++++++++++++++++ +++++
    C15A11.6   162 paqgggqgppgppgpagsagspgqagapgnpgspgksgqrgrglpgpsga 211

                   ..................................................
                   ++++++++ ++++++++ +++ +++++ ++++++++++++++++ +++++
    C15A11.6   212 pgsqgppgapgqpgsgnapgpagppgpagpngqpghpgqdgqpgapgndg 261

                   ...............................kkrsskerkaak<-*
                   +++++    + +++++  ++++ ++++   +kkr+ +++++ak
    C15A11.6   262 tpgsdaaycpcptrssvlrhrnvnrhraaasKKRVVAKKRVAK    304



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