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).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file: hmm2/seq/F33D11.3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: F33D11.3 CE09893 collagen status:Partially_confirmed TR:O44774 protein_id:AAB96697.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 89.0 5.8e-23 3
Col_cuticle_N Nematode cuticle collagen N-terminal do 63.3 2.1e-17 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 15 74 .. 1 66 [] 63.3 2.1e-17
Collagen 1/3 88 116 .. 32 60 .] 18.7 0.0012
Collagen 2/3 133 191 .. 1 60 [] 46.4 2.8e-11
Collagen 3/3 203 262 .. 1 60 [] 39.6 2.1e-09
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 15 to 74: score 63.3, E = 2.1e-17
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
+gvA++++L++++s++ + + f ++++de+++FK+y+d aW++M+++
F33D11.3 15 CGVAIISSLLVAGSLFFEAQGFLETSLDEIESFKHYSDVAWKDMISS 61
qrnvrppskpasarfgrpf<-*
+++ r+ +r + ++
F33D11.3 62 NTFDRK------KRDDEDK 74
Collagen: domain 1 of 3, from 88 to 116: score 18.7, E = 0.0012
*->ppGepGpPGppGppGppGppGapGapGpp<-*
ppGe+GpPG+pG pG+ G++G+pG G++
F33D11.3 88 PPGEAGPPGAPGTPGADGEAGNPGKDGAA 116
Collagen: domain 2 of 3, from 133 to 191: score 46.4, E = 2.8e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p+G+pGp Gp G+pG+pGp G++GapG++G+pG +G++G+ G+pG
F33D11.3 133 -PAGEPGPQGPDGAPGAPGPDGQPGAPGSNGNPGSAGEQGSEGEPGD 178
pGppGapGapGpp<-*
+G +G++G +G+p
F33D11.3 179 AGATGEIGVAGAP 191
Collagen: domain 3 of 3, from 203 to 262: score 39.6, E = 2.1e-09
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pGp Gp G+pG +G Gp G+ G+ G G +G+pG +G G +G
F33D11.3 203 GAPGPEGPIGEPGKDGQQGPHGDVGGDGTEGIQGAPGKDGENGSDGV 249
pGppGapGapGpp<-*
+G +GapGapGp
F33D11.3 250 AGSDGAPGAPGPD 262