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/Y53C12B.5
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Query: Y53C12B.5 CE14902 locus:mab-3 DM DNA binding domain status:Partially_confirmed SW:O18214 protein_id:CAB16489.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
DM-domain DM DNA binding domain 189.6 5e-53 2
LytR_cpsA_psr Cell envelope-related transcriptional a 4.9 0.54 1
PHD PHD-finger 4.7 2.6 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PHD 1/1 20 34 .. 37 51 .] 4.7 2.6
DM-domain 1/2 24 70 .. 1 48 [] 96.6 2.3e-25
DM-domain 2/2 90 137 .. 1 48 [] 101.0 1.4e-26
LytR_cpsA_psr 1/1 239 252 .. 178 191 .] 4.9 0.54
Alignments of top-scoring domains:
PHD: domain 1 of 1, from 20 to 34: score 4.7, E = 2.6
*->eppegkWlCpeCtpk<-*
+++e +++C +C ++
Y53C12B.5 20 AEQEKNYYCQRCLNH 34
DM-domain: domain 1 of 2, from 24 to 70: score 96.6, E = 2.3e-25
*->RipyCqRCenHGekvpLKGHKryCpfrdCtCkkvCtlvekRRrlmal
+++yCqRC+nHGe++p+KGHK++C++++C+C++ Ct+ve+RR+l++l
Y53C12B.5 24 KNYYCQRCLNHGELKPRKGHKPDCRYLKCPCRE-CTMVEQRRQLNNL 69
q<-*
+
Y53C12B.5 70 L 70
DM-domain: domain 2 of 2, from 90 to 137: score 101.0, E = 1.4e-26
*->RipyCqRCenHGekvpLKGHKr.yCpfrdCtCkkvCtlvekRRrlma
R+p+C+RC++HG++vpL+GHKr++C+f++C+C+ Ctlve+RR+lma
Y53C12B.5 90 RDPHCARCSAHGVLVPLRGHKRtMCQFVTCECTL-CTLVEHRRNLMA 135
lq<-*
+q
Y53C12B.5 136 AQ 137
LytR_cpsA_psr: domain 1 of 1, from 239 to 252: score 4.9, E = 0.54
*->QqqvlkAlikklks<-*
Qqq+l+++i+ ++
Y53C12B.5 239 QQQFLMSIIQNMAP 252