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



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