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/EGAP7.1
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Query: EGAP7.1 CE07013 locus:dpy-3 cuticular collagen status:Partially_confirmed TR:Q19079 protein_id:AAB00598.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 91.8 9.5e-24 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 63.9 1.3e-17 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 22 83 .. 1 66 [] 63.9 1.3e-17
Collagen 1/3 109 142 .. 23 56 .. 18.9 0.001
Collagen 2/3 157 215 .. 1 60 [] 43.8 1.5e-10
Collagen 3/3 225 284 .. 1 60 [] 45.2 6e-11
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 22 to 83: score 63.9, E = 1.3e-17
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
++v+ la+++ vp +yn ++++q+ + e+d++K++++d W+eMv+v
EGAP7.1 22 AIVSMLATVIIVPLVYNHVQHLQSVMNSEVDFCKTRSRDLWREMVTV 68
qrnvrppskpasarfgrpf<-*
q+++++ + ar++r+
EGAP7.1 69 QSATGG----IPARTARRT 83
Collagen: domain 1 of 3, from 109 to 142: score 18.9, E = 0.001
*->paGapGppGppGepGpPGppGppGppGppGapGa<-*
+ G+pGppGppG +G+PG+pG+pG pGppG++Ga
EGAP7.1 109 QVGPPGPPGPPGRDGRPGAPGRPGNPGPPGRDGA 142
Collagen: domain 2 of 3, from 157 to 215: score 43.8, E = 1.5e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
ppGppGp+GppGp+G pGp+G+aG G G pG pGpPGp Gp G+
EGAP7.1 157 -PPGPPGPAGPPGPKGLPGPQGDAGTSGQDGVPGLPGPPGPSGPQGA 202
pGppGapGapGpp<-*
pG pG++G+ G+p
EGAP7.1 203 PGVPGEKGPTGEP 215
Collagen: domain 3 of 3, from 225 to 284: score 45.2, E = 6e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGppGppGp+GppGppG G++G++GppG pG+pG+ G++G pGp
EGAP7.1 225 GPPGPPGPPGPQGPPGPPGKDGQPGKAGPPGLPGDPGEKGSDGLPGP 271
pGppGapGapGpp<-*
G +G+ G+pG+p
EGAP7.1 272 HGGTGPRGPPGQP 284