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/Y38C1BA.3
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Query: Y38C1BA.3 CE21569 collagen status:Partially_confirmed TR:Q9N527 protein_id:AAF60502.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 74.2 6.4e-19 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 27.3 1.1e-06 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 20 59 .. 1 40 [. 27.3 1.1e-06
Collagen 1/4 95 125 .. 30 60 .] 18.9 0.0011
Collagen 2/4 141 199 .. 1 60 [] 35.6 2.7e-08
Collagen 3/4 207 255 .. 12 60 .] 35.9 2.2e-08
Collagen 4/4 256 271 .. 1 16 [. 7.0 1.9
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 20 to 59: score 27.3, E = 1.1e-06
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyadda<-*
S +A+l++++++p iyn ++s++ + ++m ++K a+d+
Y38C1BA.3 20 SFLAILSVCISMPIIYNFVDSIHQQTKRDMTFCKSTARDI 59
Collagen: domain 1 of 4, from 95 to 125: score 18.9, E = 0.0011
*->pGppGepGpPGppGppGppGppGapGapGpp<-*
pG+pG pG PG G+pG pG pG+pG pG p
Y38C1BA.3 95 PGHPGRPGLPGRNGKPGVPGAPGRPGTPGRP 125
Collagen: domain 2 of 4, from 141 to 199: score 35.6, E = 2.7e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
ppGppGp Gp+G G pG pG++G pG+pG pG+ Gp G+ G G+
Y38C1BA.3 141 -PPGPPGPQGPTGNSGQPGRPGNPGRPGSPGTPGPVGPNGASGDSGA 186
pGppGapGapGpp<-*
pG++G++G+pG p
Y38C1BA.3 187 PGNDGEKGEPGRP 199
Collagen: domain 3 of 4, from 207 to 255: score 35.9, E = 2.2e-08
*->pGppGppGppGpaGapGppGppGepGpPGppGppGppGppGapGapG
pG+pG+pG +G+ GapG+ G+pG +G+PG+ GppGppGppG+ G++G
Y38C1BA.3 207 PGEPGNPGDAGATGAPGDDGAPGRDGQPGQSGPPGPPGPPGNVGEAG 253
pp<-*
pp
Y38C1BA.3 254 PP 255
Collagen: domain 4 of 4, from 256 to 271: score 7.0, E = 1.9
*->GppGppGppGppGppG<-*
G+pG+pG pGp+G++G
Y38C1BA.3 256 GKPGQPGLPGPQGERG 271