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/C09G5.3
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Query: C09G5.3 CE01483 collagen status:Partially_confirmed SW:Q09233 protein_id:CAA86756.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 82.6 3.4e-21 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 63.1 2.3e-17 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 76 .. 1 66 [] 63.1 2.3e-17
Collagen 1/3 92 121 .. 26 55 .. 15.5 0.0089
Collagen 2/3 139 198 .. 1 60 [] 39.5 2.2e-09
Collagen 3/3 204 263 .. 1 60 [] 42.8 2.8e-10
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 76: score 63.1, E = 2.3e-17
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S+ ++++++f+++++ +d+n++q +++ m +FK+++d +W+ M+ +
C09G5.3 14 SASVLVTTIFVCWNVTHDLNTLQAMSDRNMQDFKAISDRTWDKMMFK 60
qrnvrppskpasarfgrpf<-*
q+++ p++ s +fgr++
C09G5.3 61 QQSSPPSP---SLIFGRNK 76
Collagen: domain 1 of 3, from 92 to 121: score 15.5, E = 0.0089
*->apGppGppGepGpPGppGppGppGppGapG<-*
+ GppGppGe+G +G +G++G pG pG+ G
C09G5.3 92 PGGPPGPPGEKGNDGVDGVDGIPGFPGENG 121
Collagen: domain 2 of 3, from 139 to 198: score 39.5, E = 2.2e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+GppGp G+ Gp G+ G+ G++G pG+ G+ G pG G+pG Gp
C09G5.3 139 GPRGPPGPQGEEGPSGDVGEDGEPGVPGNDGADGTPGKSGAPGGKGP 185
pGppGapGapGpp<-*
+GppG pG pG+p
C09G5.3 186 QGPPGTPGRPGQP 198
Collagen: domain 3 of 3, from 204 to 263: score 42.8, E = 2.8e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G++Gp GppG+pG +G++G+ G +G G G pG+ G G +G pG
C09G5.3 204 GEAGPKGPPGAPGTDGRRGENGTDGDDGVDGQPGDEGDAGKDGTPGE 250
pGppGapGapGpp<-*
pGp+G+ G +G+p
C09G5.3 251 PGPQGEQGTEGQP 263