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/C34H4.4
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Query: C34H4.4 CE27821 cuticular collagen status:Partially_confirmed TR:O45140 protein_id:AAC04393.3
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do 72.6 3.6e-20 1
Collagen Collagen triple helix repeat (20 copies 58.0 1.9e-14 3
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 14 74 .. 1 66 [] 72.6 3.6e-20
Collagen 1/3 92 119 .. 1 28 [. 14.3 0.019
Collagen 2/3 135 190 .. 5 60 .] 42.1 4.4e-10
Collagen 3/3 191 226 .. 25 60 .] 17.3 0.0028
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 14 to 74: score 72.6, E = 3.6e-20
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
Sgv ++++L++++++++dIn+++ +vmd+m eF+ a++aW++M++
C34H4.4 14 SGVTIIVSLVAAGMLLQDINDLYYDVMDDMTEFRNTANEAWKDMIVP 60
qrnvrppskpasarfgrpf<-*
+v s +fgr++
C34H4.4 61 SGAVDA-----SLIFGRNK 74
Collagen: domain 1 of 3, from 92 to 119: score 14.3, E = 0.019
*->GppGppGppGppGppGppGppGpaGapG<-*
Gp+GppG+pG+pG++G pG++G +G+ G
C34H4.4 92 GPAGPPGAPGAPGEDGTPGQAGKNGGNG 119
Collagen: domain 2 of 3, from 135 to 190: score 42.1, E = 4.4e-10
*->ppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGppGpp
p+G+pGp+Gp+Gp+G+pG++G pG pG++G +G+PG++G+ G +G +
C34H4.4 135 PAGEPGPAGPDGPAGAPGADGQPGAPGNAGQDGAPGAAGEQGDAGAA 181
GapGapGpp<-*
G++G++G+p
C34H4.4 182 GQDGEAGAP 190
Collagen: domain 3 of 3, from 191 to 226: score 17.3, E = 0.0028
*->GapGppGppGepGpPGppGppGppGppGapGapGpp<-*
G +G+ Gp+G+pG +G +G+pG+ G++G G pG+
C34H4.4 191 GNAGSEGPAGAPGKDGEAGAPGQDGEAGGEGIPGQD 226