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: hmm5/seq/W08D2.6
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Query: W08D2.6 CE06561 collagen status:Partially_confirmed TR:Q23222 protein_id:CAA94234.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 77.0 1.1e-19 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 65.9 3.4e-18 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 24 85 .. 1 66 [] 65.9 3.4e-18
Collagen 1/3 145 170 .. 30 55 .. 14.9 0.013
Collagen 2/3 190 248 .. 1 60 [] 43.8 1.5e-10
Collagen 3/3 257 316 .. 1 60 [] 34.2 6.6e-08
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 24 to 85: score 65.9, E = 3.4e-18
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++A+++cL+++ s+y ++++++e++d m e ++ dd+W+e++ +
W08D2.6 24 SAIALISCLLVLSSVYRNVQDYWTELDDQMVEVRKDLDDMWREIMHI 70
qrnvrppskpasarfgrpf<-*
q+n+ ++ r +rp
W08D2.6 71 QSNSLGS----VFRARRPA 85
Collagen: domain 1 of 3, from 145 to 170: score 14.9, E = 0.013
*->pGppGepGpPGppGppGppGppGapG<-*
+Gp+G++G+PG pGp+G pG +G+pG
W08D2.6 145 AGPQGAKGAPGLPGPNGVPGLDGKPG 170
Collagen: domain 2 of 3, from 190 to 248: score 43.8, E = 1.5e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p GppG+pGp G pG++G +G +G pG pG G+pG PG Gp+G+
W08D2.6 190 -PQGPPGSPGPMGHPGARGMKGSDGQPGQPGKDGDPGKPGEMGPNGF 235
pGppGapGapGpp<-*
+G G++G pG+
W08D2.6 236 QGKVGPDGFPGEK 248
Collagen: domain 3 of 3, from 257 to 316: score 34.2, E = 6.6e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp G +G++G pG+ G pG++G+ GppG++G++G PGp+G+ G+
W08D2.6 257 GRPGPKGQKGETGHPGAQGTPGHNGPTGPPGDAGPDGGPGPQGEQGA 303
pGppGapGapGpp<-*
G pG G G p
W08D2.6 304 DGGPGSEGKVGRP 316