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/H27M09.2
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Query: H27M09.2 CE23831 RNA polymerase status:Confirmed TR:Q9N5K2 protein_id:AAF39906.1
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RNA_pol_Rpb5_N RNA polymerase Rpb5, N-terminal domain 201.2 1.6e-56 1
RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain 161.3 1.6e-44 1
DTW DTW domain 5.8 1.2 1
Rad50_zn_hook Rad50 zinc hook motif 5.6 6.5 1
MutS_V MutS domain V 2.2 8.9 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
DTW 1/1 18 56 .. 305 349 .] 5.8 1.2
RNA_pol_Rpb5_N 1/1 2 96 .. 1 118 [] 201.2 1.6e-56
MutS_V 1/1 146 164 .. 227 245 .] 2.2 8.9
Rad50_zn_hook 1/1 152 176 .. 32 57 .] 5.6 6.5
RNA_pol_Rpb5_C 1/1 138 211 .] 1 75 [] 161.3 1.6e-44
Alignments of top-scoring domains:
DTW: domain 1 of 1, from 18 to 56: score 5.8, E = 1.2
*->lLdelgedYeldkkpeaiaeaLlkvfeamireyqlakksentkek<-
+L++++++ ++ +++ L++++e+++ ++++++se+++ +
H27M09.2 18 VLQMVHDR-----GYLVAQDELDQPLETFK-VQYGDRPSEKKPAR 56
*
H27M09.2 - -
RNA_pol_Rpb5_N: domain 1 of 1, from 2 to 96: score 201.2, E = 1.6e-56
*->mddEeernikRlylaRRTvlQMLRDRGYlVFDsqeELnLRtLeeFka
+ddE e ++Rl+++R+TvlQM++DRGYlV +q+EL++ +Le+Fk
H27M09.2 2 ADDELE--TYRLWRIRKTVLQMVHDRGYLV--AQDELDQ-PLETFKV 43
kyGdkPsMgRpLLLLkdRerLrisaaiLhrsDSiKKfpnkdqlyVfFpee
+yGd+Ps+++p R++L+i++a h++D p +dq++VfFpe+
H27M09.2 44 QYGDRPSEKKP-----ARSDLTILVA--HNDD-----P-ADQMFVFFPED 80
pkDKmnVGVktIrvfvAeriq<-*
+k +G+ktI++++ +++q
H27M09.2 81 AK----IGIKTIKAIC-QQMQ 96
MutS_V: domain 1 of 1, from 146 to 164: score 2.2, E = 8.9
*->lPesVverArevLaeLEer<-*
+Pe+Vv A+e+++ L +
H27M09.2 146 VPEHVVMTAEEKAELLARY 164
Rad50_zn_hook: domain 1 of 1, from 152 to 176: score 5.6, E = 6.5
*->Lgteeekkelikeykseldrlpeelk<-*
+ t eek+el+ +yk++ ++lp+ ++
H27M09.2 152 M-TAEEKAELLARYKLKDSQLPRIQQ 176
RNA_pol_Rpb5_C: domain 1 of 1, from 138 to 211: score 161.3, E = 1.6e-44
*->vdvtdHELVPeHeIlpeEEvkeLLkrYnIkieQLPkIkasDPvakel
v++t+HELVPeH++++ EE+ eLL+rY++k +QLP+I+ DPva+++
H27M09.2 138 VNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPVARYF 184
GAkKeGDVVKIvRKSpTaGesvyYRLVi<-*
G+ +G+VVKI+R+S+TaG++++YRLV+
H27M09.2 185 GLR-RGQVVKIIRPSETAGRYITYRLVV 211