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/Y57G11A.3
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Query: Y57G11A.3 CE14912 LIM domain containing proteins status:Partially_confirmed TR:O18220 protein_id:CAB16495.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
LIM LIM domain 44.8 3e-11 1
PolyA_pol Poly A polymerase family 7.3 1.1 1
IF-2B Initiation factor 2 subunit family 2.0 9.5 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
IF-2B 1/1 119 172 .. 1 39 [. 2.0 9.5
LIM 1/1 192 243 .. 1 56 [. 44.8 3e-11
PolyA_pol 1/1 237 258 .. 154 175 .] 7.3 1.1
Alignments of top-scoring domains:
IF-2B: domain 1 of 1, from 119 to 172: score 2.0, E = 9.5
*->vklsedvakaiksaqvRdqirrlvkkssll.................
++ed +++ k +q++ v+k +l++ +++ ++++++ ++
Y57G11A.3 119 STMDEDLEQKLKRMQKE--QIGGVGKETLAsakerfekgesdivvek 163
gapaigraa<-*
+a++i+r+a
Y57G11A.3 164 TAVDIERSA 172
LIM: domain 1 of 1, from 192 to 243: score 44.8, E = 3e-11
*->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefyekdg
C C+k +y+ e+v + + +H+ CF+C+ C k+Lt+++ f +++g
Y57G11A.3 192 CCICDKVVYPVEKVLANK-NLYHIQCFKCCKCAKKLTPTN-FNSHEG 236
skelYCkhD<-*
k l+Ck +
Y57G11A.3 237 -K-LLCKVH 243
PolyA_pol: domain 1 of 1, from 237 to 258: score 7.3, E = 1.1
*->qllreyglLevlfpeikksele<-*
+ll++ ++Lev++pei++++
Y57G11A.3 237 KLLCKVHMLEVFHPEIAHTMDP 258