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/B0222.6
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Query: B0222.6 CE30585 status:Partially_confirmed TR:Q17458 protein_id:AAA92323.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do 96.8 2.3e-27 1
Collagen Collagen triple helix repeat (20 copies 85.0 7e-22 3
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 25 86 .. 1 66 [] 96.8 2.3e-27
Collagen 1/3 114 139 .. 35 60 .] 17.0 0.0036
Collagen 2/3 165 224 .. 1 60 [] 49.2 4.8e-12
Collagen 3/3 227 286 .. 1 60 [] 35.4 3.1e-08
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 25 to 86: score 96.8, E = 2.3e-27
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
+++Av+a+Lftvps+yn+In+ +d+v+d+++ F+v++d aW+eM+d+
B0222.6 25 ATFAVFAVLFTVPSLYNTINEVHDQVLDGVSVFRVETDSAWTEMMDI 71
qrnvrppskpasarfgrpf<-*
q++v+pp+kp +++pf
B0222.6 72 QITVTPPTKP----RVNPF 86
Collagen: domain 1 of 3, from 114 to 139: score 17.0, E = 0.0036
*->epGpPGppGppGppGppGapGapGpp<-*
+pGpPGppG+pG+pG pGapG++G
B0222.6 114 PPGPPGPPGQPGAPGTPGAPGPKGDD 139
Collagen: domain 2 of 3, from 165 to 224: score 49.2, E = 4.8e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
Gp+Gp Gp+Gp+Gp+G pG+pG+aG pG+ G pG+pG G++G+pG+
B0222.6 165 GPAGPEGPAGPAGPDGQPGAPGNAGNPGSDGQPGAPGDNGQDGAPGQ 211
pGppGapGapGpp<-*
G+pGapG G++
B0222.6 212 DGQPGAPGQDGQR 224
Collagen: domain 3 of 3, from 227 to 286: score 35.4, E = 3.1e-08
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG pG+pG +Gp+Gp+G+ G++G G pGp+G++G++G+pG +G+
B0222.6 227 GAPGGPGAPGNAGPAGPAGQDGAPGQDGQPGPAGPAGQDGAPGNAGS 273
pGppGapGapGpp<-*
G+pGapG pG p
B0222.6 274 DGQPGAPGGPGLP 286