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: hmm1/seq/B0336.3
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Query: B0336.3 CE29542 status:Partially_confirmed TR:Q10954 protein_id:AAK18852.2
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
zf-CCCH Zinc finger C-x8-C-x5-C-x3-H type (and simil 30.9 1.3e-07 1
rrm RNA recognition motif. (a.k.a. RRM, RBD, or 5.0 5.3 1
WHEP-TRS WHEP-TRS domain 3.9 9.7 1
DUF633 Family of unknown function (DUF633) 3.6 6.9 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
WHEP-TRS 1/1 71 86 .. 40 57 .] 3.9 9.7
zf-CCCH 1/1 207 233 .. 1 27 [] 30.9 1.3e-07
rrm 1/1 379 435 .. 11 77 .] 5.0 5.3
DUF633 1/1 546 582 .. 169 215 .] 3.6 6.9
Alignments of top-scoring domains:
WHEP-TRS: domain 1 of 1, from 71 to 86: score 3.9, E = 9.7
*->KaktGkdykPgtdlvdPa<-*
+a+t+k+y P++ ++P+
B0336.3 71 EALTSKSYMPAS--TAPT 86
zf-CCCH: domain 1 of 1, from 207 to 233: score 30.9, E = 1.3e-07
*->yktelCrffsrtGtCkyGdrCkFaHge<-*
+ +++C++f + G+C +Gd+C++ Hg+
B0336.3 207 SSRRRCKDFEERGYCIRGDQCPYYHGR 233
rrm: domain 1 of 1, from 379 to 435: score 5.0, E = 5.3
*->teedLkdlFskfGpivsikivkDhiekpketgkskGfaFVeFeseed
t +L ++F+ fG + +i++ ++ a V+++s+ d
B0336.3 379 TIAKLNEHFATFGTVDNIQVRYN---------GEIDSALVTYASKFD 416
AekAlealnGkelggrklrv<-*
A kA + +l++r ++v
B0336.3 417 AGKAYK-SPTPVLNNRFIKV 435
DUF633: domain 1 of 1, from 546 to 582: score 3.6, E = 6.9
*->alfkkKwqreleklkkilsqiseakdseqakaklqelsekIieviee
+++ kK++++ e ++ il +is +++ + ++I+++iee
B0336.3 546 KHLHKKIKACKEEVDGILLKIS----------EKSMVVDEIAAQIEE 582
<-*
B0336.3 - -