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: hmm3/seq/F57B1.3
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Query: F57B1.3 CE11290 collagen status:Partially_confirmed TR:Q20922 protein_id:CAB01509.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 87.0 2e-22 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 40.6 1.2e-10 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 27 69 .. 1 43 [. 40.6 1.2e-10
Collagen 1/4 125 154 .. 31 60 .] 17.8 0.0021
Collagen 2/4 173 232 .. 1 60 [] 47.3 1.7e-11
Collagen 3/4 237 262 .. 1 26 [. 14.7 0.015
Collagen 4/4 263 301 .. 22 60 .] 29.6 1.2e-06
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 27 to 69: score 40.6, E = 1.2e-10
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWne<-*
S++A l+++++vp++yn++++ q+ ++ e++++ ++++ W+e
F57B1.3 27 STIATLTAIVAVPMLYNYMQHVQSSLQSEVEFCAHRSNGLWDE 69
Collagen: domain 1 of 4, from 125 to 154: score 17.8, E = 0.0021
*->GppGepGpPGppGppGppGppGapGapGpp<-*
G++G++G+PG++G+pG G pGapG pG+
F57B1.3 125 GAAGPAGSPGQDGAPGNDGAPGAPGNPGQD 154
Collagen: domain 2 of 4, from 173 to 232: score 47.3, E = 1.7e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp G+pG Gp G+pG pG+ G++ pGppG++GpPGp G+pG+
F57B1.3 173 GPPGPSGAPGQKGPSGAPGVPGQTGGASLPGPPGPAGPPGPSGQPGS 219
pGppGapGapGpp<-*
G++GapGapG++
F57B1.3 220 NGNAGAPGAPGQV 232
Collagen: domain 3 of 4, from 237 to 262: score 14.7, E = 0.015
*->GppGppGppGppGppGppGppGpaGa<-*
G pGp+GppGppGp+G+pG+pG++G+
F57B1.3 237 GTPGPAGPPGPPGPAGAPGQPGQSGS 262
Collagen: domain 4 of 4, from 263 to 301: score 29.6, E = 1.2e-06
*->GpaGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
G++G+pGp+G++G+pG+PG+pG++G+pG++G +G++G++
F57B1.3 263 GQPGGPGPQGDAGAPGAPGQPGQAGAPGQDGDSGSEGAC 301