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/F54D1.4
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Query: F54D1.4 CE20866 locus:nhr-7 nuclear hormone receptor status:Confirmed SW:Q20765 protein_id:CAB00862.3
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
zf-C4 Zinc finger, C4 type (two domains) 126.2 1.2e-36 1
Acyl_transf_2 Acyl transferase 3.9 1.9 1
hormone_rec Ligand-binding domain of nuclear hormon 3.5 4.1 1
Pox_polyA_pol Poxvirus poly(A) polymerase catalytic s 2.7 4.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
zf-C4 1/1 7 83 .. 1 77 [] 126.2 1.2e-36
Pox_polyA_pol 1/1 260 285 .. 1 35 [. 2.7 4.8
hormone_rec 1/1 280 330 .. 105 155 .. 3.5 4.1
Acyl_transf_2 1/1 373 401 .. 266 294 .] 3.9 1.9
Alignments of top-scoring domains:
zf-C4: domain 1 of 1, from 7 to 83: score 126.2, E = 1.2e-36
*->elCkVCGDkASGyHYGvlTCEGCKGFFrRsiqknlviYsCkrnkdCv
++C+VCGD + HYGvl+C GCKGFFrR+++ + Y C+++k+C+
F54D1.4 7 RICAVCGDTPAKIHYGVLACFGCKGFFRRAVKDGRNKYVCRFEKNCE 53
IdKrnRnrCQyCRLkKCLeVGMskeaVrfg<-*
++K Rn+C+yCR++KCL VGM+ + Vr +
F54D1.4 54 VTKFERNACRYCRFRKCLLVGMNPDYVRPD 83
Pox_polyA_pol: domain 1 of 1, from 260 to 285: score 2.7, E = 4.8
*->MNaaPdqntfPniilellreYLGRpPslneYhmlK<-*
+ + i+++ ++YL pPs+ eY +lK
F54D1.4 260 LTQK---------IADVFETYLRKPPSIIEYSVLK 285
hormone_rec: domain 1 of 1, from 280 to 330: score 3.5, E = 4.1
*->EyalLkAIvLfnPsdvpgLsesarelveklqekylsaLlqycllnyp
Ey LkA + ++ + + Ls+s e ++ +e++++ L++ ++++++
F54D1.4 280 EYSVLKAYIVLSA-ESTVLSNSLNESLSLARENLSELLFKVIKHSRN 325
d.sls<-*
++s+s
F54D1.4 326 KtSIS 330
Acyl_transf_2: domain 1 of 1, from 373 to 401: score 3.9, E = 1.9
*->ldvdiiEPdFEdLtiatvnERRlKneies<-*
+ dii P+ dL + t n R+l ++ s
F54D1.4 373 ILTDIINPEVSDLLLTTANCRKLSTQMGS 401