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/C24F3.6
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Query: C24F3.6 CE18523 CUTICLE COLLAGEN 1 status:Partially_confirmed TR:Q9NAR3 protein_id:CAB97232.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 83.0 2.5e-21 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 26.0 2.7e-06 1
AmoA Putative ammonia monooxygenase 4.2 3.3 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
AmoA 1/1 25 44 .. 321 340 .] 4.2 3.3
Col_cuticle_N 1/1 21 58 .. 1 38 [. 26.0 2.7e-06
Collagen 1/3 95 124 .. 1 30 [. 14.9 0.013
Collagen 2/3 141 199 .. 1 60 [] 35.6 2.7e-08
Collagen 3/3 208 267 .. 1 60 [] 48.6 7.4e-12
Alignments of top-scoring domains:
AmoA: domain 1 of 1, from 25 to 44: score 4.2, E = 3.3
*->lLlvLlllpplirylsklrg<-*
+L+v +lp+ ++y+++ r
C24F3.6 25 VLSVCITLPMMYNYIHHTRK 44
Col_cuticle_N: domain 1 of 1, from 21 to 58: score 26.0, E = 2.7e-06
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyad<-*
S++Avl++++t+p++yn+I + + ++ ++ e+K +a+
C24F3.6 21 STIAVLSVCITLPMMYNYIHHTRKVMHSDIVECKSEAQ 58
Collagen: domain 1 of 3, from 95 to 124: score 14.9, E = 0.013
*->GppGppGppGppGppGppGppGpaGapGpp<-*
G+ GppG pG +G pG+pG+pG +G pG p
C24F3.6 95 GAQGPPGTPGSAGRPGKPGAPGLNGNPGRP 124
Collagen: domain 2 of 3, from 141 to 199: score 35.6, E = 2.7e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p GppGp+GppGp+G++Gp Gp+G+pGp Gp GepG Gp+GppGp
C24F3.6 141 -PEGPPGPAGPPGPDGNKGPLGPPGPPGPEGPNGEPGNKGPAGPPGP 186
pGppGapGapGpp<-*
G pG++G+pG++
C24F3.6 187 GGKPGPAGPPGEN 199
Collagen: domain 3 of 3, from 208 to 267: score 48.6, E = 7.4e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG+pG pG pG++Gp+G+pG +G+pG +G +G++G+PG+pG++G+
C24F3.6 208 GAPGEPGQPGQPGQRGPAGEPGKDGSPGGQGEKGASGEPGQPGRDGQ 254
pGppGapGapGpp<-*
pG pG+pG G p
C24F3.6 255 PGHPGQPGKDGRP 267