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: hmm2/seq/F13E6.4
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Query: F13E6.4 CE03201 RSP5 like protein status:Predicted TR:Q19404 protein_id:CAA92121.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
WW WW domain 49.7 3.2e-12 1
RNA_pol_Rpb2_5 RNA polymerase Rpb2, domain 5 4.3 2.4 1
Syndecan Syndecan domain 0.1 9.1 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
RNA_pol_Rpb2_5 1/1 26 66 .. 14 77 .] 4.3 2.4
WW 1/1 220 249 .. 1 30 [] 49.7 3.2e-12
Syndecan 1/1 392 421 .. 324 358 .. 0.1 9.1
Alignments of top-scoring domains:
RNA_pol_Rpb2_5: domain 1 of 1, from 26 to 66: score 4.3, E = 2.4
*->YlDaEEEEtamIAmtpeDLe.srqmkagyeieeededpgiednrRvk
YlD+++ a+I+++ e+ +++q++
F13E6.4 26 YLDPNQSIHALISCS-EKKYeKNQNQ--------------------- 50
pkpneeithtyTHcEIhP<-*
k+n+ + y+H+ P
F13E6.4 51 -KKNPL-PSSYYHQKRNP 66
WW: domain 1 of 1, from 220 to 249: score 49.7, E = 3.2e-12
*->lppgWeerkdpdGrpYYyNhnTktTqWekP<-*
+p gWe+ +d+dG Y+ +hn+ktT+W++P
F13E6.4 220 MPQGWEMCYDSDGVRYFKDHNSKTTTWDDP 249
Syndecan: domain 1 of 1, from 392 to 421: score 0.1, E = 9.1
*->pdlvnEtspentaaaapepTlgrgqrPdiGLidNt<-*
+d++ E++ + ++ p l+ ++ P ++++N+
F13E6.4 392 DDSAMEVDY--SMVSHPQQ-LQHQHQP--HMHNNM 421