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: hmm3/seq/F54D1.3
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Query: F54D1.3 CE05938 collagen status:Predicted TR:Q20764 protein_id:CAB00860.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Col_cuticle_N Nematode cuticle collagen N-terminal do 94.9 8.1e-27 1
Collagen Collagen triple helix repeat (20 copies 89.0 5.6e-23 3
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 29 90 .. 1 66 [] 94.9 8.1e-27
Collagen 1/3 118 143 .. 35 60 .] 8.8 0.62
Collagen 2/3 164 222 .. 1 60 [] 50.0 2.9e-12
Collagen 3/3 234 293 .. 1 60 [] 47.2 1.7e-11
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 29 to 90: score 94.9, E = 8.1e-27
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
+++Avla+Lftvps+yn+In+ +d+v+d+++ F+v++d aW+eM+d+
F54D1.3 29 ASIAVLAVLFTVPSLYNTINEVHDQVLDGVSVFRVETDSAWTEMMDI 75
qrnvrppskpasarfgrpf<-*
q++v+pp+kp +++pf
F54D1.3 76 QVTVTPPTKP----RVNPF 90
Collagen: domain 1 of 3, from 118 to 143: score 8.8, E = 0.62
*->epGpPGppGppGppGppGapGapGpp<-*
+pGpPGppG+pG+pG pGapG+ G
F54D1.3 118 PPGPPGPPGQPGAPGVPGAPGPRGGD 143
Collagen: domain 2 of 3, from 164 to 222: score 50.0, E = 2.9e-12
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
p+Gp+Gp+G Gp+Gp+Gp G++G pG +G+ G+pG+PG+pG +G+
F54D1.3 164 -PAGPAGPAGSSGPAGPAGPSGQPGTPGQRGNDGFPGAPGAPGDNGQ 209
pGppGapGapGpp<-*
pG pG++GapG+p
F54D1.3 210 PGFPGQDGAPGQP 222
Collagen: domain 3 of 3, from 234 to 293: score 47.2, E = 1.7e-11
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+pG pG +Gp+Gp G G+pG++GapG++Gp+G +G+PG G +G+
F54D1.3 234 GAPGAPGNAGPAGPSGQDGFPGQDGAPGSAGPAGQDGFPGNNGSDGQ 280
pGppGapGapGpp<-*
pG pG pG pG
F54D1.3 281 PGAPGGPGLPGND 293