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: hmm2/seq/F15H10.1
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Query: F15H10.1 CE05638 locus:col-12 collagen status:Partially_confirmed SW:P20630 protein_id:CAA98257.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 89.0 5.6e-23 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 47.1 1.4e-12 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 26 68 .. 1 43 [. 47.1 1.4e-12
Collagen 1/4 128 157 .. 31 60 .] 17.8 0.0021
Collagen 2/4 176 235 .. 1 60 [] 53.0 4.6e-13
Collagen 3/4 239 264 .. 18 43 .. 12.9 0.047
Collagen 4/4 267 304 .. 23 60 .] 28.6 2.2e-06
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 26 to 68: score 47.1, E = 1.4e-12
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWne<-*
S++A l+++++vp++yn++++ q+ ++ e+++++++++ W+e
F15H10.1 26 STIATLTAIIAVPMLYNYMQHVQSSLQSEVEFCQHRSNGLWDE 68
Collagen: domain 1 of 4, from 128 to 157: score 17.8, E = 0.0021
*->GppGepGpPGppGppGppGppGapGapGpp<-*
G++G++G+PG++G+pG G pGapG pG+
F15H10.1 128 GAAGPAGSPGQDGAPGNDGAPGAPGNPGQD 157
Collagen: domain 2 of 4, from 176 to 235: score 53.0, E = 4.6e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp G+pG Gp G+pG+pG++G++ pGppG++GpPGp+G+pG+
F15H10.1 176 GPPGPSGAPGQKGPSGAPGAPGQSGGAALPGPPGPAGPPGPAGQPGS 222
pGppGapGapGpp<-*
G++GapGapG++
F15H10.1 223 NGNAGAPGAPGQV 235
Collagen: domain 3 of 4, from 239 to 264: score 12.9, E = 0.047
*->pGppGpaGapGppGppGepGpPGppG<-*
pG pGpaG+pG+pGp+G+pG+PG++G
F15H10.1 239 PGTPGPAGPPGSPGPAGAPGQPGQAG 264
Collagen: domain 4 of 4, from 267 to 304: score 28.6, E = 2.2e-06
*->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
++G+pGp+G++G+pG+PG+pG++G+pG++G++G++G++
F15H10.1 267 QPGGPGPQGDAGAPGAPGAPGQAGAPGQDGESGSEGAC 304