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/F38A3.1
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Query: F38A3.1 CE02213 collagen status:Partially_confirmed TR:Q20135 protein_id:CAA90187.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 89.0 5.6e-23 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 16.7 0.0015 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 26 62 .. 1 37 [. 16.7 0.0015
Collagen 1/3 116 146 .. 1 31 [. 19.4 0.00078
Collagen 2/3 166 224 .. 1 60 [] 40.0 1.6e-09
Collagen 3/3 232 291 .. 1 60 [] 45.9 4e-11
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 26 to 62: score 16.7, E = 0.0015
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvya<-*
++A l +++++p y+++++ q+ ++ e+d++K+++
F38A3.1 26 TIAAALIAVIAIPAFYSYVQHVQSKLDSEVDFCKHRS 62
Collagen: domain 1 of 3, from 116 to 146: score 19.4, E = 0.00078
*->GppGppGppGppGppGppGppGpaGapGppG<-*
G++Gp+GppG pG +G+ G+ G++G+pG G
F38A3.1 116 GAAGPQGPPGRPGNDGNDGQSGNPGSPGQDG 146
Collagen: domain 2 of 3, from 166 to 224: score 40.0, E = 1.6e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p+GppG+pG +G+pG+ G pG++G++ pGppG+pGp G+pG++G
F38A3.1 166 -PAGPPGAPGQAGAPGNDGRPGQSGGAAIPGPPGPPGPSGQPGQDGH 211
pGppGapGapGpp<-*
pG++G+pG pG+
F38A3.1 212 PGQDGQPGQPGES 224
Collagen: domain 3 of 3, from 232 to 291: score 45.9, E = 4e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+G+pG+ G+pGp Gp G pG++G +G pG pG++G +G+pG+pG
F38A3.1 232 GPAGQPGSQGEPGPSGPDGRPGQPGQAGQPGGPGDAGNDGQPGQPGG 278
pGppGapGapGpp<-*
pG++G++G+ G
F38A3.1 279 PGEDGEDGDSGSS 291