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/C44C10.1
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Query: C44C10.1 CE05408 collagen status:Partially_confirmed TR:Q18620 protein_id:CAA93642.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 104.6 2e-27 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 57.1 1.5e-15 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 25 88 .. 1 66 [] 57.1 1.5e-15
Collagen 1/3 112 149 .. 23 60 .] 18.2 0.0016
Collagen 2/3 159 218 .. 1 60 [] 52.9 4.7e-13
Collagen 3/3 226 285 .. 1 60 [] 49.3 4.7e-12
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 25 to 88: score 57.1, E = 1.5e-15
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
S A l+c++++p++yn+++++q+ ++ e+d+++ ++ ++W+e++ +
C44C10.1 25 SFTATLVCIIAAPMLYNYMQHMQSVMQSEVDFCRSRSGNIWREVTRT 71
qrnvrppskpasarfgrpf<-*
q+ + + s r +r+
C44C10.1 72 QVLAKVS--GGSVRSRRQA 88
Collagen: domain 1 of 3, from 112 to 149: score 18.2, E = 0.0016
*->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
+aG+pG pG Ge+G++G+pG+pG Gp+G++ p p+
C44C10.1 112 AAGPPGAPGQDGEDGSDGQPGAPGNDGPDGPAATPAPA 149
Collagen: domain 2 of 3, from 159 to 218: score 52.9, E = 4.7e-13
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
GppGp+Gp+Gp Gp G+pG G++GapG++G++G pG+PG++G++G
C44C10.1 159 GPPGPAGPAGPKGPNGNPGSDGQPGAPGNNGNAGGPGAPGQAGQDGH 205
pGppGapGapGpp<-*
pG++GapGapG +
C44C10.1 206 PGNAGAPGAPGRV 218
Collagen: domain 3 of 3, from 226 to 285: score 49.3, E = 4.7e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG pGp Gp+Gp+G pG+pG++G++G++Gp G++G+ G+pG+pG
C44C10.1 226 GAPGAPGPDGPAGPAGSPGAPGNPGSQGSQGPVGDNGAAGAPGQPGG 272
pGppGapGapGpp<-*
G+ Ga+G+ G+p
C44C10.1 273 NGNNGADGETGAP 285