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/W03G11.1
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Query: W03G11.1 CE26826 cuticle collagen status:Partially_confirmed TR:Q23150 protein_id:CAA91544.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 78.8 3.6e-20 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 22.5 2.8e-05 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 74 110 .. 1 37 [. 22.5 2.8e-05
Collagen 1/3 142 174 .. 28 60 .] 18.3 0.0015
Collagen 2/3 192 250 .. 1 60 [] 28.2 2.9e-06
Collagen 3/3 258 317 .. 1 60 [] 47.7 1.3e-11
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 74 to 110: score 22.5, E = 2.8e-05
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvya<-*
S+v+ l+++++vp++ +++s + ++de+++++v+a
W03G11.1 74 STVSTLTAIVAVPMLCLYLQSVSSSLQDEVNFCRVRA 110
Collagen: domain 1 of 3, from 142 to 174: score 18.3, E = 0.0015
*->GppGppGepGpPGppGppGppGppGapGapGpp<-*
G++GppG+pG++G++G++G+ G pG+pG+
W03G11.1 142 GSAGPPGPPGFDGSAGKDGSNGRPGNPGEDADG 174
Collagen: domain 2 of 3, from 192 to 250: score 28.2, E = 2.9e-06
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p+GppG+pGp G+ G +G+pG +G +G pG++G pGp Gp G pG+
W03G11.1 192 -PAGPPGRPGPDGENGGAGEPGRDGLAGRPGARGSPGPRGPSGNPGA 237
pGppGapGapGpp<-*
Gp+G+ G+ G
W03G11.1 238 DGPAGQLGPQGGS 250
Collagen: domain 3 of 3, from 258 to 317: score 47.7, E = 1.3e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG pG+ Gp GppG++G pG +G pG pG++Ge+Gp+G+pG+ G+
W03G11.1 258 GEPGAPGAQGPKGPPGAAGRPGRDGQPGAPGDQGENGPDGAPGKSGS 304
pGppGapGapGpp<-*
G+pGapG +G +
W03G11.1 305 DGQPGAPGKEGSR 317