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: hmm4/seq/W05G11.3
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Query: W05G11.3 CE14628 cuticular collagen status:Partially_confirmed TR:O44904 protein_id:AAC71147.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 97.4 2.9e-25 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 74.4 1e-20 1
Poty_coat Potyvirus coat protein 6.8 0.6 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Poty_coat 1/1 37 51 .. 224 238 .] 6.8 0.6
Col_cuticle_N 1/1 14 76 .. 1 66 [] 74.4 1e-20
Collagen 1/3 95 123 .. 32 60 .] 18.8 0.0011
Collagen 2/3 142 201 .. 1 60 [] 47.4 1.5e-11
Collagen 3/3 207 266 .. 1 60 [] 47.1 1.8e-11
Alignments of top-scoring domains:
Poty_coat: domain 1 of 1, from 37 to 51: score 6.8, E = 0.6
*->dDVnrnmHsLlGvrg<-*
dDV ++mHs++G +
W05G11.3 37 DDVLQDMHSFRGLAN 51
Col_cuticle_N: domain 1 of 1, from 14 to 76: score 74.4, E = 1e-20
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
+ A+l++L++++++y++In+++d+v+++m++F+++a+daW++Mv+
W05G11.3 14 LSTAILGSLLYAGVLYSEINELRDDVLQDMHSFRGLANDAWRSMVQA 60
qrnvrppskpasarfgrpf<-*
+++v + a + fg+ f
W05G11.3 61 NAPVNG---GALPDFGSIF 76
Collagen: domain 1 of 3, from 95 to 123: score 18.8, E = 0.0011
*->ppGepGpPGppGppGppGppGapGapGpp<-*
p+G+pGpPG+pG +G G+ G++G+ G+
W05G11.3 95 PAGPPGPPGAPGDAGLDGENGQAGPNGQD 123
Collagen: domain 2 of 3, from 142 to 201: score 47.4, E = 1.5e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp+Gp Gp+G+pG+ G++G +GapG G pG pG++G +G+pG
W05G11.3 142 GAPGPQGPDGPAGAPGADGQAGSPGAPGQDGQPGGPGAQGDAGAPGN 188
pGppGapGapGpp<-*
G pG++GapG++
W05G11.3 189 DGTPGQDGAPGQN 201
Collagen: domain 3 of 3, from 207 to 266: score 47.1, E = 1.8e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G++G pGp Gp+G +G +G+pG++G pG +G +G +G+PG+pG++G
W05G11.3 207 GAAGAPGPQGPAGNAGQAGQPGADGQPGAQGSAGIAGAPGQPGKAGE 253
pGppGapGapGpp<-*
G++G+ G G+p
W05G11.3 254 DGEAGENGTDGEP 266