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