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: hmm3/seq/F42G4.3b
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Query: F42G4.3b CE20775 LIM domain containing proteins status:Confirmed TR:Q9U3F5 protein_id:CAB03096.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
LIM LIM domain 93.9 3.5e-25 3
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
LIM 1/3 5 42 .. 22 62 .] 33.4 5.2e-08
LIM 2/3 44 101 .. 1 62 [] 41.6 2.4e-10
LIM 3/3 104 165 .. 1 56 [. 33.9 3.8e-08
Alignments of top-scoring domains:
LIM: domain 1 of 3, from 5 to 42: score 33.4, E = 5.2e-08
*->wHpeCFrCavCgkpLtegdefyekdgskelYCkhDyyklfg<-*
+H++CF+C +C k+L+ + fy +d+ k + C+ +y++ +
F42G4.3b 5 FHVDCFKCGQCSKTLAGAS-FYNIDD-K-PTCEGCYQNSLE 42
LIM: domain 2 of 3, from 44 to 101: score 41.6, E = 2.4e-10
*->CagCnkpIydrevvrralnkvwHpeCFrCavCgkpLtegdefyekdg
C +Cn+ I +++ ra + v+H++CF+C+ C+k L+ + d+
F42G4.3b 44 CTACNRAIS--DKLLRACGGVYHVNCFVCFSCKKSLDGI--PFTLDK 86
.skelYCkhDyyklfg<-*
++ C ++++++f+
F42G4.3b 87 dNN-VHCVPCFHDKFA 101
LIM: domain 3 of 3, from 104 to 165: score 33.9, E = 3.8e-08
*->CagCnkpIy......drevvrralnkvwHpeCFrCavCgkpLtegde
Ca C kpI +++++++ ++v +a++k++H++C +C +Cg +L+++ e
F42G4.3b 104 CALCSKPIVpqdgekESVRV-VAMDKSFHVDCYKCEDCGMQLSSKLE 149
...fyekdgskelYCkhD<-*
++++y +d+ l+Ck +
F42G4.3b 150 gqgCYPIDN-H-LLCKTC 165