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: hmm5/seq/Y106G6D.7
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Query: Y106G6D.7 CE24110 RNA recognition motif. (aka RRM, RBD, or RNP domain) status:Partially_confirmed TR:Q9U304 protein_id:CAA20980.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
rrm RNA recognition motif. (a.k.a. RRM, RBD, or 36.8 2.3e-09 3
AF-4 AF-4 proto-oncoprotein 2.7 0.91 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
rrm 1/3 41 71 .. 46 77 .] 1.6 52
rrm 2/3 608 628 .. 1 21 [. 4.3 8.2
AF-4 1/1 895 905 .. 1 11 [. 2.7 0.91
rrm 3/3 874 945 .. 1 77 [] 30.7 1.4e-07
Alignments of top-scoring domains:
rrm: domain 1 of 3, from 41 to 71: score 1.6, E = 52
*->GfaFVeFeseedAekAlealnGkelggrklrv<-*
G FV F s +dA A+ + ++ g ++r
Y106G6D.7 41 GEVFVGFSSDDDARLAMT-KDRLMIHGAEVRL 71
rrm: domain 2 of 3, from 608 to 628: score 4.3, E = 8.2
*->lfVgNLppdvteedLkdlFsk<-*
+ V+N p+ + +e+L + Fs+
Y106G6D.7 608 VQVTNVPFRMKDEELLEWFSE 628
AF-4: domain 1 of 1, from 895 to 905: score 2.7, E = 0.91
*->YeeDRNaLRir<-*
Ye+DRN Rir
Y106G6D.7 895 YEPDRNSIRIR 905
rrm: domain 3 of 3, from 874 to 945: score 30.7, E = 1.4e-07
*->lfVgNLppdvteedLkdlFskfGpi.vsikivkDhiekpketgkskG
l ++++p+dvt ed+ ++F ++ p ++si+i + g G
Y106G6D.7 874 LSCNGFPKDVTLEDVVEFFNDYEPDrNSIRIRRG------DDGVMTG 914
faFVeFeseedAekAlealnGkelggrklrv<-*
+ ++e A +A +l+G++l++ ++ v
Y106G6D.7 915 ECMLACQNQENARRASMDLDGQKLRNSVISV 945