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: hmm4/seq/R11B5.1
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Query: R11B5.1 CE28759 status:Partially_confirmed TR:Q21928 protein_id:AAA83513.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
TBC TBC domain 114.6 2.7e-32 1
Birna_VP5 Birnavirus VP5 protein 7.4 0.77 1
SAA_proteins Serum amyloid A protein 2.4 9.2 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Birna_VP5 1/1 141 156 .. 123 138 .] 7.4 0.77
SAA_proteins 1/1 216 224 .. 103 111 .] 2.4 9.2
TBC 1/1 295 523 .. 1 341 [] 114.6 2.7e-32
Alignments of top-scoring domains:
Birna_VP5: domain 1 of 1, from 141 to 156: score 7.4, E = 0.77
*->CterdhkrrhLrRksv<-*
Cte d kr+ L R+s+
R11B5.1 141 CTESDSKRSSLDRRSE 156
SAA_proteins: domain 1 of 1, from 216 to 224: score 2.4, E = 9.2
*->RPpGLPeKY<-*
RP GLP+K
R11B5.1 216 RPSGLPSKS 224
TBC: domain 1 of 1, from 295 to 523: score 114.6, E = 2.7e-32
*->vrqgvpsslRgkVWklllgaqelnnclltdnfkgldlfglvpvllla
+ qgvp+ +Rg++W l +g+q ++
R11B5.1 295 WWQGVPAKVRGELWFLTIGNQIEIT---------------------- 319
dkdeYeellnknkektvqdqneKssvgirrldyVEAVEKHPLSDDNDKTK
k Y+ l ++ +ek +
R11B5.1 320 -KELYDGLMDQAEEKIAKQ------------------------------- 337
GSLekgsdekalklredldkIekDlsRTfpdeiffqtrlaeqqlkkdqdl
L + + a + ++ +I +D+ RTf fq
R11B5.1 338 --LAEQNKNSAERKETSVTQIHLDATRTFTSLGMFQ-------------- 371
daydkDEfddeddkneppsikqLrrlLvaYswknpqehlgYvQGMnvils
+p ++L lL+aY++ +p+ +gYvQ+M++i++
R11B5.1 372 --------------KDGPYYDHLLKLLSAYAILRPD--IGYVQSMTFIAA 405
pLLlflkhgvdldeideeqAFwclvkLmdnylpqkyflndlsglnedlrv
+LL+++ d AF+ +++L+d+ l ++f + + e
R11B5.1 406 VLLIQM---------DPYPAFISFANLLDRSLQSAFFGLKQPQMTEYFIA 446
LdslvkeslPeLyshlkkkenktgsgkKknllaldltllifafpwfLtlF
d+ ++ lP L hl k d+ +++++++w+ +
R11B5.1 447 YDRYLEQELPALHQHLDKL---------------DVRPDLYLIEWTFAMY 481
arelPleivlrIwDilftyYlgshflifvalAiLkllkskllkh<-*
a +lPl+++ rIwD++f + g fl++ al iL ++kll
R11B5.1 482 AKSLPLDVTCRIWDVYFRD--GEEFLFKAALGILRMYEPKLLTM 523