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/F44E2.4
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Query: F44E2.4 CE28232 status:Partially_confirmed TR:Q8TA82 protein_id:AAK67236.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
ldl_recept_a Low-density lipoprotein receptor domain 46.6 1.3e-12 1
DUF19 Domain of unknown function DUF19 4.6 0.68 1
Herpes_UL43 Herpesvirus UL43 protein 2.0 9.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
ldl_recept_a 1/1 9 43 .. 1 39 [. 46.6 1.3e-12
Herpes_UL43 1/1 124 133 .. 1 11 [. 2.0 9.2
DUF19 1/1 421 446 .. 1 26 [. 4.6 0.68
Alignments of top-scoring domains:
ldl_recept_a: domain 1 of 1, from 9 to 43: score 46.6, E = 1.3e-12
*->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEsle<-*
C p+ F C++g+ CIp++w+ DG+ DCeDGSDE e
F44E2.4 9 AACP-PNTFTCADGS-CIPSDWKGDGEKDCEDGSDE--E 43
Herpes_UL43: domain 1 of 1, from 124 to 133: score 2.0, E = 9.2
*->GcvgsgagCip<-*
cvg+++gC+p
F44E2.4 124 -CVGNQKGCMP 133
DUF19: domain 1 of 1, from 421 to 446: score 4.6, E = 0.68
*->CTevtslkatkClyrlgdFlekvdfL<-*
CTe+ + a++Cl++l ++ +k+ ++
F44E2.4 421 CTEEQENGALGCLVELVEINKKLTAF 446