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).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file: hmm2/seq/F14B4.3
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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]