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/K08A2.5
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Query:  K08A2.5  CE21034   nuclear hormone receptor status:Partially_confirmed TR:Q9N5J5 protein_id:AAF39914.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
hormone_rec   Ligand-binding domain of nuclear hormon    99.8    7.6e-30   1
Glt_symporter Sodium/glutamate symporter                 10.8      0.033   1
DUF156        Uncharacterized BCR, COG1937                4.1        7.8   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
DUF156          1/1      25    41 ..    48    64 .]     4.1      7.8
Glt_symporter   1/1     185   195 ..   368   378 .]    10.8    0.033
hormone_rec     1/1      60   232 ..    22   203 .]    99.8  7.6e-30

Alignments of top-scoring domains:
DUF156: domain 1 of 1, from 25 to 41: score 4.1, E = 7.8
                   *->eaeqslaellealkall<-*
                      ++++s++ l++al++++
     K08A2.5    25    GRTASVEQLIAALRRYV    41

Glt_symporter: domain 1 of 1, from 185 to 195: score 10.8, E = 0.033
                   *->NMqaVTerFGp<-*
                      NM++VT+rFG+
     K08A2.5   185    NMTSVTSRFGN    195

hormone_rec: domain 1 of 1, from 60 to 232: score 99.8, E = 7.6e-30
                   *->leDQiiLLkhswlelllLrlayrsykekkataDgsdtllfpdGtdid
                      ++D+ +LLk++  +++++++a r+ +  +      d +++++ ++i+
     K08A2.5    60    IHDKTTLLKSVIGPFTIFNIAARTAQISD-----GDLICLCNKSTIN 101

                   rdsl.........gsselirrifelliklrvnvlaplieLkldeeEyalL
                   r+ +++  +++  g++   r i +l+ + +        +L l++ E+  L
     K08A2.5   102 RQPArhlldtnlvGNNFVGRVIDDLVFPTK--------KLALTNPEITIL 143

                   kAIvLfnPsdvpgLsesarelveklqekylsaLlqycllnypd.slssdg
                   +A+++++P d++gLs++  + +  +++++++aL++ ++ n ++ +   +
     K08A2.5   144 SALIILDP-DARGLSQETSQALLGIRDRVQNALFNLIRDNSNNmT---SV 189

                   psRFakLLlllpvlrslssdlkehlfflkrlfnlpkvppLlkell<-*
                   +sRF++LLll+p l +lss++ e+ ++l + f     ++Ll el+
     K08A2.5   190 TSRFGNLLLLFPPLAKLSSLIGEN-VQLAKMF-GIPIDSLLVELY    232



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