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/D2023.7
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Query: D2023.7 CE09077 collagen status:Partially_confirmed TR:O17734 protein_id:CAB02874.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 86.9 2.1e-22 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 63.2 2.2e-17 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 73 .. 1 66 [] 63.2 2.2e-17
Collagen 1/3 110 138 .. 32 60 .] 24.9 2.4e-05
Collagen 2/3 156 215 .. 1 60 [] 42.8 2.8e-10
Collagen 3/3 224 283 .. 1 60 [] 34.2 6.3e-08
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 73: score 63.2, E = 2.2e-17
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S++ ++ +L++++siy+d++s+++++++emd FKv +dd W++M+ +
D2023.7 14 SSATLILSLYAIFSIYSDVQSIWSQLDQEMDQFKVTTDDLWTQMLGL 60
qrnvrppskpasarfgrpf<-*
+++++ s+r +r+
D2023.7 61 GAATV------SNRQRRQG 73
Collagen: domain 1 of 3, from 110 to 138: score 24.9, E = 2.4e-05
*->ppGepGpPGppGppGppGppGapGapGpp<-*
p+G++Gp+G++Gp+G pG +G++G pG++
D2023.7 110 PAGPSGPQGSAGPDGIPGIDGQDGFPGEN 138
Collagen: domain 2 of 3, from 156 to 215: score 42.8, E = 2.8e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pG++G pG +G +Gp G G+pG G pG pG+ GppGppG
D2023.7 156 GKPGSPGERGKPGLRGMRGPRGTGGSPGTDGYPGRPGEMGPPGPPGD 202
pGppGapGapGpp<-*
G pG G++G+
D2023.7 203 DGKPGSNGEKGQD 215
Collagen: domain 3 of 3, from 224 to 283: score 34.2, E = 6.3e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+GppG GppGp G++G Gp Ga+G pGp G +G++Gp GppG
D2023.7 224 GPRGPPGDSGPPGPEGDAGNDGPVGAAGAPGPDGINGFQGPGGPPGE 270
pGppGapGapGpp<-*
G pG++G G
D2023.7 271 EGKPGEDGKVGDD 283