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/F57B1.4
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Query: F57B1.4 CE31962 collagen status:Confirmed TR:Q20921 protein_id:CAB01508.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 86.1 3.6e-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 1/4 129 158 .. 31 60 .] 17.8 0.0021
Collagen 2/4 177 236 .. 1 60 [] 47.6 1.3e-11
Collagen 3/4 241 267 .. 1 27 [. 15.0 0.012
Collagen 4/4 268 305 .. 23 60 .] 28.1 3.1e-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
F57B1.4 27 STIATLTAIVAVPMLYNYMQHVQSSLQSEVEFCAHRSNGLWDE 69
Collagen: domain 1 of 4, from 129 to 158: score 17.8, E = 0.0021
*->GppGepGpPGppGppGppGppGapGapGpp<-*
G++G++G+PG++G+pG G pGapG pG+
F57B1.4 129 GAAGPAGSPGQDGAPGNDGAPGAPGNPGQD 158
Collagen: domain 2 of 4, from 177 to 236: score 47.6, E = 1.3e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp G+pG Gp G+pG+pG++G++ pGppG++GpPGp G+pG+
F57B1.4 177 GPPGPSGAPGQKGPSGAPGAPGQSGGASLPGPPGPAGPPGPSGQPGS 223
pGppGapGapGpp<-*
G++GapGapG++
F57B1.4 224 NGNAGAPGAPGQV 236
Collagen: domain 3 of 4, from 241 to 267: score 15.0, E = 0.012
*->GppGppGppGppGppGppGppGpaGap<-*
G pGp+GppGppGp+G+pG+pG++G++
F57B1.4 241 GTPGPAGPPGPPGPAGAPGQPGQSGSA 267
Collagen: domain 4 of 4, from 268 to 305: score 28.1, E = 3.1e-06
*->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
++G+pGp+G++G+pG+PG+pG++G+pG++G +G++G++
F57B1.4 268 QPGGPGPQGDAGAPGAPGQPGQAGAPGQDGDSGSEGAC 305