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/F02E9.4
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Query: F02E9.4 CE09187 locus:pqn-28 status:Partially_confirmed TR:O01319 protein_id:CAB04052.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
PAH Paired amphipathic helix repeat 80.5 3.5e-20 1
Nebulin Nebulin repeat 7.8 3 1
CDRN Cysteine-rich D. radiodurans N-terminus fam 6.8 2.3 1
Replicase Replicase family 5.4 2.5 1
CHMI 5-carboxymethyl-2-hydroxymuconate isomerase 4.8 1.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PAH 1/1 304 350 .. 1 47 [] 80.5 3.5e-20
Nebulin 1/1 514 528 .. 15 29 .] 7.8 3
Replicase 1/1 759 783 .. 232 261 .] 5.4 2.5
CDRN 1/1 997 1018 .. 1 22 [. 6.8 2.3
CHMI 1/1 1020 1027 .. 1 8 [. 4.8 1.8
Alignments of top-scoring domains:
PAH: domain 1 of 1, from 304 to 350: score 80.5, E = 3.5e-20
*->pekYneFLeiLndykaeridkpeviarVseLlkghpdLllgFnvFLp
+Y+ FLei++d++a+ri++p+vi++V+eLl+++p+L+lgFn+FLp
F02E9.4 304 VPVYHRFLEIMKDFRAQRIETPDVIEQVAELLYDSPELVLGFNTFLP 350
<-*
F02E9.4 - -
Nebulin: domain 1 of 1, from 514 to 528: score 7.8, E = 3
*->qSdvkYKedyEkeKg<-*
+Sd +YK+d Ek ++
F02E9.4 514 MSDQQYKKDMEKLRK 528
Replicase: domain 1 of 1, from 759 to 783: score 5.4, E = 2.5
*->tiwgrchRgdgqlvyeatlpeiQaarGRkg<-*
+++ d+++v + +lp+iQ++rG +
F02E9.4 759 RPEN-----DMDAVMRKDLPAIQPKRGLRD 783
CDRN: domain 1 of 1, from 997 to 1018: score 6.8, E = 2.3
*->rllsasLEqFsELrvRRnstAt<-*
++l+ ++Eq +E r++ nst t
F02E9.4 997 KPLVNQIEQICEERRKNNSTDT 1018
CHMI: domain 1 of 1, from 1020 to 1027: score 4.8, E = 1.8
*->PHlilEct<-*
PHlilE+t
F02E9.4 1020 PHLILEYT 1027