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: hmm1/seq/B0491.2
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Query: B0491.2 CE02104 locus:sqt-1 cuticle collagen SQT-1 status:Confirmed SW:P12114 protein_id:CAA90084.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 80.9 9.8e-21 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 31.4 6.2e-08 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 13 71 .. 1 66 [] 31.4 6.2e-08
Collagen 1/3 125 151 .. 23 49 .. 12.7 0.052
Collagen 2/3 175 234 .. 1 60 [] 42.1 4.5e-10
Collagen 3/3 240 299 .. 1 60 [] 42.0 4.6e-10
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 13 to 71: score 31.4, E = 6.2e-08
*->SgvAvlacLftvps.iyndInsfqdevmdemdeFKvyaddaWneMvd
+vA l ++f + s+iy++++ f++ ++ em+ F++ ++ W+++v+
B0491.2 13 VTVATLMVCFMTMStIYSEVDGFREKLDTEMNVFRQSTNGLWKDIVV 59
vqrnvrppskpasarfgrpf<-*
++r++ +r++
B0491.2 60 IGRSSKR--------VRRQY 71
Collagen: domain 1 of 3, from 125 to 151: score 12.7, E = 0.052
*->paGapGppGppGepGpPGppGppGppG<-*
paG+ Gp+G pG pG +G pG +G pG
B0491.2 125 PAGPSGPKGVPGVPGLDGVPGLDGVPG 151
Collagen: domain 2 of 3, from 175 to 234: score 42.1, E = 4.5e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppG G+pGp+G pGp+G+ G++G G pG+pGe G+ G+ G+ G
B0491.2 175 GPPGALGRPGPRGLPGPRGQNGNPGRDGQPGHPGEQGSSGQIGKIGE 221
pGppGapGapGpp<-*
pGppG++G +
B0491.2 222 PGPPGEKGRDAEH 234
Collagen: domain 3 of 3, from 240 to 299: score 42.0, E = 4.6e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp+G Gp+Gp+G G Gp+G+pG Gp G++G +G +Gp+G
B0491.2 240 GPKGPRGDQGPTGPAGQNGLHGPPGEPGTVGPEGPSGKQGRQGPDGT 286
pGppGapGapGpp<-*
+G++G++G pG+
B0491.2 287 QGETGPDGRPGKD 299