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/F54C9.4
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Query: F54C9.4 CE20864 locus:col-38 collagen status:Partially_confirmed TR:Q20754 protein_id:CAA90250.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 88.4 8.1e-23 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 66.8 1.9e-18 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 13 77 .. 1 66 [] 66.8 1.9e-18
Collagen 1/3 98 129 .. 14 45 .. 13.4 0.033
Collagen 2/3 146 205 .. 1 60 [] 46.6 2.6e-11
Collagen 3/3 215 274 .. 1 60 [] 44.7 8.6e-11
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 13 to 77: score 66.8, E = 1.9e-18
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S+vAv+++L+++ si+ dI+++++e+ ++++ Kv++ddaWn+M+
F54C9.4 13 SLVAVFGALVAMHSIVVDIDTMREEIVTGVHDMKVMSDDAWNRMIGF 59
qrnvrppskpasarfgrpf<-*
+ ++ + sa+f++ f
F54C9.4 60 TKPSLDSESR-SAAFASVF 77
Collagen: domain 1 of 3, from 98 to 129: score 13.4, E = 0.033
*->ppGppGppGpaGapGppGppGepGpPGppGpp<-*
ppGppGppG +G++G++Gp+G++G++G+ G+
F54C9.4 98 PPGPPGPPGLPGGRGDQGPSGDKGRDGASGVS 129
Collagen: domain 2 of 3, from 146 to 205: score 46.6, E = 2.6e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppG+ Gp G+ G+pG pG+ G aG G+ G+pGe+G G +Gp G
F54C9.4 146 GPPGETGPDGDIGEPGFPGASGSAGQCGEDGAPGEAGITGEQGPQGE 192
pGppGapGapGpp<-*
pG +G G+ G+
F54C9.4 193 PGTEGSEGPTGQD 205
Collagen: domain 3 of 3, from 215 to 274: score 44.7, E = 8.6e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G pG pG pG +G+pG+ G G +G++Gp+Gp+G++G+PG + +G+
F54C9.4 215 GQPGTPGWPGSQGEPGKNGDSGVDGEQGPQGPQGPDGQPGRDADNGQ 261
pGppGapGapGpp<-*
pG pG++G+ Gp
F54C9.4 262 PGLPGKDGSIGPD 274