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: hmm3/seq/H27M09.4
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: H27M09.4 CE25036 status:Partially_confirmed TR:Q9N5K5 protein_id:AAF39908.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Collagen Collagen triple helix repeat (20 copies 58.0 1.8e-14 4
Col_cuticle_N Nematode cuticle collagen N-terminal do 24.5 7e-06 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Col_cuticle_N 1/1 21 60 .. 1 40 [. 24.5 7e-06
Collagen 1/4 133 168 .. 1 36 [. 8.6 0.72
Collagen 2/4 182 241 .. 1 60 [] 43.1 2.4e-10
Collagen 3/4 246 271 .. 1 26 [. 11.6 0.1
Collagen 4/4 273 310 .. 23 60 .] 18.9 0.001
Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 21 to 60: score 24.5, E = 7e-06
*->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyadda<-*
S+ Av+++L+++p+iyn + s+q+e+ +e +++ ++++d+
H27M09.4 21 STCAVVSSLVALPMIYNMVISIQSEISQETGFCMMRSRDM 60
Collagen: domain 1 of 4, from 133 to 168: score 8.6, E = 0.72
*->GppGppGppGppGppGppGppGpaGapGppGppGep<-*
G++GppGppG+ G +G+ G +G++ + G G G++
H27M09.4 133 GKAGPPGPPGDDGKDGNDGSAGNDAKNGKDGGVGPS 168
Collagen: domain 2 of 4, from 182 to 241: score 43.1, E = 2.4e-10
*->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
G+ G+ G+pG+ Gp Gp+G pG +G G +G pG +Gp G +G+pGp
H27M09.4 182 GAQGLGGAPGAKGPQGPRGSPGLSGVDGRRGEPGMSGPAGTQGEPGP 228
pGppGapGapGpp<-*
+GppG++G+ G +
H27M09.4 229 QGPPGKKGDDGRV 241
Collagen: domain 3 of 4, from 246 to 271: score 11.6, E = 0.1
*->GppGppGppGppGppGppGppGpaGa<-*
GppG G+pGp+G +G++Gp+G +G+
H27M09.4 246 GPPGAGGAPGPQGRKGERGPKGVPGS 271
Collagen: domain 4 of 4, from 273 to 310: score 18.9, E = 0.001
*->paGapGppGppGepGpPGppGppGppGppGapGapGpp<-*
++G +Gp G++G +G+ G +G+ G +Gp G +G+ G +
H27M09.4 273 HPGVQGPTGDQGRKGRAGRKGETGGQGPIGSKGPNGDC 310