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/W09G10.1
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Query: W09G10.1 CE28512 collagen status:Partially_confirmed TR:O16640 protein_id:AAB66109.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies) 63.3 6.4e-16 3
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Collagen 1/3 57 94 .. 23 60 .] 17.2 0.003
Collagen 2/3 95 154 .. 1 60 [] 50.0 2.9e-12
Collagen 3/3 155 181 .. 34 60 .] 11.7 0.1
Alignments of top-scoring domains:
Collagen: domain 1 of 3, from 57 to 94: score 17.2, E = 0.003
*->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
p+G pG GppG+pG PG+pG++G G pG+ G++G+p
W09G10.1 57 PRGQPGYGGPPGPPGLPGQPGQNGNGGRPGNNGPMGQP 94
Collagen: domain 2 of 3, from 95 to 154: score 50.0, E = 2.9e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+ G pG +G pG pG G +G++G+ G++G++GpPG+ GppG
W09G10.1 95 GEPGREGQPGKAGGPGSPGRDGIRGSKGSTGDKGPNGPPGQNGPPGW 141
pGppGapGapGpp<-*
+G +G++G+ G p
W09G10.1 142 AGRDGNIGPQGTP 154
Collagen: domain 3 of 3, from 155 to 181: score 11.7, E = 0.1
*->GepGpPGppGppGppGppGapGapGpp<-*
G +G+PG pG +G+pG +G+pG+ G+p
W09G10.1 155 GGRGEPGGPGTDGFPGFAGNPGPDGAP 181