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:            hmm2/seq/F14B4.3
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Query:  F14B4.3  CE05629   DNA-directed RNA polymerase I status:Partially_confirmed TR:Q27493 protein_id:CAA99827.1

Scores for sequence family classification (score includes all domains):
Model          Description                              Score    E-value  N
--------       -----------                              -----    ------- ---
RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6            451.7   6.7e-144   2
RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3            120.4    2.6e-33   1
RNA_pol_Rpb2_1 RNA polymerase beta subunit               96.7      5e-31   2
RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7             74.1    1.3e-21   1
RNA_pol_Rpb2_5 RNA polymerase Rpb2, domain 5             37.3    2.7e-11   1
RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2             10.0      0.039   1
OS-D           Insect pheromone-binding family, A10/O     5.6       0.72   1
RNA_pol_Rpb2_4 RNA polymerase Rpb2, domain 4              4.9        4.8   1
Tub            Tub family                                 4.2      0.055   1
Phytochelatin  Phytochelatin synthase                     2.4        6.8   1

Parsed for domains:
Model          Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------       ------- ----- -----    ----- -----      -----  -------
RNA_pol_Rpb2_1   1/2       4   153 ..     1   171 [.    87.7  4.2e-28
OS-D             1/1     143   156 ..    63    76 ..     5.6     0.72
RNA_pol_Rpb2_2   1/1     259   339 ..   108   208 ..    10.0    0.039
RNA_pol_Rpb2_1   2/2     344   411 ..   170   238 .]     8.9    0.019
RNA_pol_Rpb2_3   1/1     426   495 ..     1    74 []   120.4  2.6e-33
RNA_pol_Rpb2_4   1/1     589   601 ..    46    58 ..     4.9      4.8
RNA_pol_Rpb2_5   1/1     601   642 ..     1    77 []    37.3  2.7e-11
RNA_pol_Rpb2_6   1/2     647   758 ..     1   122 [.   158.3  4.2e-50
Phytochelatin    1/1     809   825 ..     1    13 [.     2.4      6.8
Tub              1/1     836   850 ..     1    15 [.     4.2    0.055
RNA_pol_Rpb2_6   2/2     846  1005 ..   249   437 .]   296.5  2.7e-94
RNA_pol_Rpb2_7   1/1    1007  1119 ..     1    92 []    74.1  1.3e-21

Alignments of top-scoring domains:
RNA_pol_Rpb2_1: domain 1 of 2, from 4 to 153: score 87.7, E = 4.2e-28
                RF    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
                   *->glveqqldSFneFleeglqeiieefkkiesekeaqhatesdeedeel
                      ++ + ++dSF+ ++++g q    +++ +  ek   +        ++
     F14B4.3     4    DIASYHVDSFDFLVSKGCQ---FAAQAVPAEKFRLK--------NGD 39

                RF xxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxx
                   elslkveqiklkkPkikedvad.gkekelypkearlrnltYsselyvdve
                    + +k+ + +l+kP+++++ + +  +  l+p e+r+r ltY+++l v +
     F14B4.3    40 AVTMKFTSAQLHKPTLDTGAKLtSDTLPLLPAECRQRGLTYAGNLKVGID 89

                RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
                   ltvkkkeeeeekevseeekekeevfiGklPiMlrskacvlsglseeelve
                   ++v+ +           + +  e+ +Gk+PiMlrs+ c+l g+s +elv
     F14B4.3    90 VHVNGS-----------RLDIIEIILGKVPIMLRSEGCHLRGMSRKELVV 128

                RF xxxxxxxxxxxxxxxxxxxxxxxxx
                   lkEcpkdqGGyFivnGsekviiaqi<-*
                    +E+p ++GGyFivnGsekvi+  i
     F14B4.3   129 AGEEPIEKGGYFIVNGSEKVIRLLI    153

OS-D: domain 1 of 1, from 143 to 156: score 5.6, E = 0.72
                   *->kGaeKVIrfLIknk<-*
                      +G+eKVIr LI+n+
     F14B4.3   143    NGSEKVIRLLIANR    156

RNA_pol_Rpb2_2: domain 1 of 1, from 259 to 339: score 10.0, E = 0.039
                   *->eeaeviytqeeALdyIGkfRgvalgrgeekriqrareiLqsrfFDpk
                      +++e+i +qe A+  IG+     +++    r+   ++ L+
     F14B4.3   259    CQEEEILNQEAAIRAIGS----RFRVAVSDRVAPWEDDLE------- 294

                   RYdLGivGRenLnkhlglnepfenkrvlKaqdilymidrLLllklGrrep
                     +  ++ Re +++hl+ +e+       K++ ++ym+++L+ l +G++ p
     F14B4.3   295 --AGRFIIRECVLIHLDSDEE-------KFHTLAYMTQKLIALVKGECAP 335

                   DDiD<-*
                   + +D
     F14B4.3   336 ETPD    339

RNA_pol_Rpb2_1: domain 2 of 2, from 344 to 411: score 8.9, E = 0.019
                RF    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxx
                   *->qivrlageLlqslfrvllkklekdvreklqkllkkkskk.kelnlqr
                      q+ ++ g++l  ++r++++++   vr+kl+ + ++k+   +++++ +
     F14B4.3   344    QEASVSGHILLLILRERMENIIGMVRRKLEYMSSRKDFIlTSAAILK 390

                RF xxxxxxxxxxxxxxxxxxxxxxx
                   llkalvksaktitsglkeflatg<-*
                    l +       it+g+ +flatg
     F14B4.3   391 ALGNHTGG--EITRGMAYFLATG    411

RNA_pol_Rpb2_3: domain 1 of 1, from 426 to 495: score 120.4, E = 2.6e-33
                   *->glsQvldqtNplselshkRrvsrlGPGglsrerktfevRdlhpsqyG
                      g+s++++++N l+++sh+R+++r   G++++e++t++vR+l p+ +G
     F14B4.3   426    GFSVIAERINQLRFVSHFRAIHR---GAFFMEMRTTDVRKLRPEAWG 469

                   riCPieTPErGqncGLvnsLalyarin<-*
                   +iCP++TP+ G++cGL+n+ +  +ri+
     F14B4.3   470 FICPVHTPD-GAPCGLLNHVTASCRIV    495

RNA_pol_Rpb2_4: domain 1 of 1, from 589 to 601: score 4.9, E = 4.8
                   *->irInTDaGRicRP<-*
                      i+I  DaGR+ RP
     F14B4.3   589    IYILSDAGRLIRP    601

RNA_pol_Rpb2_5: domain 1 of 1, from 601 to 642: score 37.3, E = 2.7e-11
                   *->wddLlkeGPHvvEYlDaEEEEtamIAmtpeDLesrqmkagyeieeed
                      ++ +l++   +vE+++++E+++  +++ p
     F14B4.3   601    PVRNLAMD--AVEHIGTFEQVYLSVVLDP------------------ 627

                   edpgiednrRvkpkpneeithtyTHcEIhP<-*
                                  +e+++ +++H+E+hP
     F14B4.3   628 ---------------EEAEPGVTMHQELHP    642

RNA_pol_Rpb2_6: domain 1 of 2, from 647 to 758: score 158.3, E = 4.2e-50
                RF    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
                   *->gvvAsligfvehnqSprityqcamgeaaKqaigypllnyqiRsDqgt
                      +   +li+f++hnqSpr++yqc+mg   Kq++g+  +    R D+++
     F14B4.3   647    SFAGNLIPFPDHNQSPRNVYQCQMG---KQTMGTAVHAWHSRADNKM 690

                RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
                   cllqyPqvplvetvtkgqilaDGPatenGelplGqNalVAvmsweGYNyE
                   ++lq+Pq p+ +   ++ + +D       e+plG+Na+VAv+s++GY++E
     F14B4.3   691 YRLQFPQQPMLKLEAYEKYEMD-------EYPLGTNACVAVISYTGYDME 733

                RF xxxxxxxxxxxxxxxxxxxxxxxxx
                   DAiiiNkrlvergvftSihieeyei<-*
                   DA+ iNk++  rg++++++i+ + i
     F14B4.3   734 DAMTINKASYQRGFAHGTVIKVERI    758

Phytochelatin: domain 1 of 1, from 809 to 825: score 2.4, E = 6.8
                   *->qfqTQs....EPAyCGL<-*
                       f+T + +  EPAyCGL
     F14B4.3   809    DFRTHKfhyaEPAYCGL    825

Tub: domain 1 of 1, from 836 to 850: score 4.2, E = 0.055
                   *->PgPrdslvqCfIkRd<-*
                      +g +++l+q++I R+
     F14B4.3   836    SGAKHALIQWRIERN    850

	[output cut off at A = 10 top alignments]


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