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/H43I07.2
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Query:  H43I07.2  CE29979   transferase status:Partially_confirmed TR:Q9UAY9 protein_id:AAL38961.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain    193.8    2.7e-54   1
PNPase        Polyribonucleotide nucleotidyltransfera     4.2       0.97   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
RNA_pol_A_bac   1/1      99   247 ..     1   156 []   193.8  2.7e-54
PNPase          1/1     262   278 ..     1    17 [.     4.2     0.97

Alignments of top-scoring domains:
RNA_pol_A_bac: domain 1 of 1, from 99 to 247: score 193.8, E = 2.7e-54
                   *->VyIyengSvlqDEvvaHEfglIpGvsEDvleIilNlKelvvkisel.
                      +y y+n+Sv+qDEv++H++gl+p+ +++  +  ++ Ke vv i+e++
    H43I07.2    99    IYLYQNTSVIQDEVLCHRLGLLPLRVDPRGF--QFPKEKVVGINEKg 143

                   secadceegceecsvtltLdvkGpge.dA.k.s.DPk.lyqtlkVtAgDl
                   ++c+++ eg++ ++++++++v+++++++A ++++DPk+ly++++V+++ +
    H43I07.2   144 VDCDEEPEGDPAKNLIFKINVSCTKNrNAvPtAtDPKqLYHNSSVYSRAF 193

                   kseP.G.q......dpdVeivnpDilIatLrkgqeLelearakkGrGyvh
                   +++P ++q+++ +++++ ++v +Dil+a+Lr+gqe+e  ++a+kG+G++h
    H43I07.2   194 EWVPiAdQktqfteEAHPRMVSDDILVAKLRPGQEIEASCHAVKGIGRDH 243

                   AkRqenkeedrpiGrIpvDsifS<-*
                   Ak                   fS
    H43I07.2   244 AK-------------------FS    247

PNPase: domain 1 of 1, from 262 to 278: score 4.2, E = 0.97
                   *->LeekvaalaeerlseAy<-*
                      L++++ ++a+erl+ ++
    H43I07.2   262    LNAEISGEAAERLKSVF    278



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