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/F44E2.4
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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



[DB home][top]