Citrus Sinensis ID: 030447

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------
Protein Sequence
MEDGNGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccEEEEEEEcccEEEEEEccccEEEEHHccccccEEEEEccccHHHHHHHHHHcccccccccccEEEEEccccEEccccccccHHHHHHHHHHccccccccccccccccEEEEcccccccEEEEEEcccccccEEEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHccccccccccccccEEEcccccccccEEEEEcccccccHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHccccEEEEEEHHHHcccHHHcccccEEEEccHHHHHHHHHHccccHHHccEEccccHHHHHHccccccEEEEEccccccccccEEEEEc
Coil and Loop (DISEMBL)
medgngydssmemeggngyngeptesclsgfvdngsrdsLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAiygqdpdvdrlrisishqsdpskRITDLLVNITKhvlkpkhqvlTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYsgeiteshvtyrcvw
Flexible Loop (DISEMBL)
medgngydssMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRIsishqsdpskriTDLLVNITKHvlkpkhqvltdqekekLLKKysieekqlprmlKKDAIAQYYGLERGQVVKVtysgeiteshvtyrcvw
Low Complexity Region (SEG)
MEDGNGYDSSmemeggngyngePTESCLSGFVDNGsrdslryylsrrTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Disordered region (IsUnstruct)
***************************LSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISI********RITDLLVNITKHVLKPKHQVLT******LLKKYSIE**QLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCV*
Disordered Region (DISOPRED)
*******************************VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Disordered Region (DISEMBL)
**************GGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Disordered Region (DISPRO)
******************YNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEDGNGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	177	2.2.26 [Sep-21-2011]
Q6CA26	212	DNA-directed RNA polymera	yes	no	0.672	0.561	0.378	7e-17
Q6BIJ0	214	DNA-directed RNA polymera	yes	no	0.864	0.714	0.333	1e-16
Q757H7	215	DNA-directed RNA polymera	yes	no	0.666	0.548	0.369	8e-16
P20434	215	DNA-directed RNA polymera	yes	no	0.870	0.716	0.324	2e-15
Q9P4B9	215	DNA-directed RNA polymera	N/A	no	0.870	0.716	0.305	3e-15
Q54EH2	197	DNA-directed RNA polymera	yes	no	0.429	0.385	0.519	4e-15
A8XGH1	211	DNA-directed RNA polymera	N/A	no	0.406	0.341	0.467	5e-15
Q9N5K2	211	DNA-directed RNA polymera	yes	no	0.406	0.341	0.467	6e-15
Q6CJ62	215	DNA-directed RNA polymera	yes	no	0.870	0.716	0.299	1e-14
Q2T9T3	210	DNA-directed RNA polymera	yes	no	0.971	0.819	0.279	1e-14

>sp|Q6CA26|RPAB1_YARLI DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=RPB5 PE=3 SV=1

 Score = 86.7 bits (213), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 45/119 (37%), Positives = 71/119 (59%)

Query: 56  RGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKH 115
           R + + +SE   +           P  +RL  S++  +  + + TDLLVNITKHVL P H
Sbjct: 91  RNFCIHISENKFATGILVYENNMTPSANRLIPSVAPATIDTFQETDLLVNITKHVLVPTH 150

Query: 116 QVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYR 174
             L+  EK+ LL++Y ++E QLPR+ ++D +A+Y GL RGQ+VK+    E +  + +YR
Sbjct: 151 IKLSGAEKKFLLERYRLKESQLPRIQREDPVARYLGLRRGQIVKIIRRSETSGRYASYR 209

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.
Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

>sp|Q6BIJ0|RPAB1_DEBHA DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=RPB5 PE=3 SV=1

 Score = 85.9 bits (211), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 52/156 (33%), Positives = 82/156 (52%), Gaps = 3/156 (1%)

Query: 19  YNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ 78
           +   PT   L  F D GS   L         + +   R + + +SE N S   F      
Sbjct: 59  FQANPTAESLEKFPDLGS---LWVEFCDEASVGIKTMRNFCIHISEKNFSTGIFIYQSSI 115

Query: 79  DPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLP 138
            P  ++L  ++S  S  + +  DL+VNIT H L PKH  L   EK++LL++Y ++E QLP
Sbjct: 116 TPSANKLIPTVSPASIETFQEGDLVVNITHHDLVPKHIKLARDEKKELLERYRLKESQLP 175

Query: 139 RMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYR 174
           R+ ++D + +Y GL+RG+VVK+    E +  + +YR
Sbjct: 176 RIQREDPVGRYLGLKRGEVVKIIRRSETSGRYASYR 211

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

>sp|Q757H7|RPAB1_ASHGO DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB5 PE=3 SV=1

 Score = 83.2 bits (204), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 44/119 (36%), Positives = 70/119 (58%)

Query: 56  RGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKH 115
           + + + + E N     F    G  P   +L  S++  +  +   T L+VNIT H L PKH
Sbjct: 94  KNFVIHIGEKNFQTGIFIYQNGITPSALKLLPSVAPATIETFNETALVVNITHHELVPKH 153

Query: 116 QVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYR 174
             L+D+EK++LLK+Y ++E QLPR+ + D +A Y GL+RG+VVK+    E +  + +YR
Sbjct: 154 IKLSDEEKKELLKRYRLKESQLPRIQRMDPVALYLGLKRGEVVKIIRKSETSGRYASYR 212

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

>sp|P20434|RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB5 PE=1 SV=1

 Score = 81.6 bits (200), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 77/157 (49%), Gaps = 3/157 (1%)

Query: 18  GYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYG 77
            +   PTE  +S F D GS   L         + +   + + + + E N     F     
Sbjct: 59  SFQANPTEESISKFPDMGS---LWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNN 115

Query: 78  QDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQL 137
             P   +L  SI   +  +     L+VNIT H L PKH  L+  EK +LLK+Y ++E QL
Sbjct: 116 ITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQL 175

Query: 138 PRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYR 174
           PR+ + D +A Y GL+RG+VVK+    E +  + +YR
Sbjct: 176 PRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYR 212

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9P4B9|RPAB1_KLUMA DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Kluyveromyces marxianus GN=RPB5 PE=3 SV=1

 Score = 81.3 bits (199), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 48/157 (30%), Positives = 80/157 (50%), Gaps = 3/157 (1%)

Query: 18  GYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYG 77
            +   PTE  +  F + GS   L         + +   + + V ++E N     F    G
Sbjct: 59  SFQSNPTEESIEKFPEMGS---LWVEFCDEASVGVKTMKNFVVHITEKNFQTGIFIYQSG 115

Query: 78  QDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQL 137
             P  +++  + +     +     L+VNIT H L PKH  L+D EK++LLK+Y ++E QL
Sbjct: 116 ITPSANKILPTAAPAVIETFPEASLVVNITHHELVPKHIRLSDAEKKELLKRYRLKESQL 175

Query: 138 PRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYR 174
           PR+ + D +A Y GL+RG+V+K+    E +  + +YR
Sbjct: 176 PRIQRMDPVALYLGLKRGEVIKIIRKSETSGRYASYR 212

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Kluyveromyces marxianus (taxid: 4911)

>sp|Q54EH2|RPAB1_DICDI DNA-directed RNA polymerases I, II, and III subunit rpabc1 OS=Dictyostelium discoideum GN=polr2e PE=3 SV=2

 Score = 80.9 bits (198), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 53/77 (68%), Gaps = 1/77 (1%)

Query: 101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
           +LLVNIT H L PKH +LT +EK +LL +Y ++E QLPR+   D +A+YYGL RG VVK+
Sbjct: 121 ELLVNITHHQLVPKHILLTKEEKLELLTRYKMKESQLPRIQTNDPVARYYGLSRGHVVKI 180

Query: 161 TYSGEITESHVTYR-CV 176
               E    ++TYR CV
Sbjct: 181 VRPSETAGRYITYRLCV 197

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Dictyostelium discoideum (taxid: 44689)

>sp|A8XGH1|RPAB1_CAEBR DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis briggsae GN=rpb-5 PE=3 SV=1

 Score = 80.5 bits (197), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 55/77 (71%)

Query: 100 TDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVK 159
            +L+VNIT+H L P+H V+T +EK +LL +Y +++ QLPR+ + D +A+Y+GL RGQVVK
Sbjct: 134 AELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPVARYFGLRRGQVVK 193

Query: 160 VTYSGEITESHVTYRCV 176
           +    E    ++TYR V
Sbjct: 194 IIRPSETAGRYITYRLV 210

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Caenorhabditis briggsae (taxid: 6238)

>sp|Q9N5K2|RPAB1_CAEEL DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis elegans GN=rpb-5 PE=3 SV=1

 Score = 80.5 bits (197), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 55/77 (71%)

Query: 100 TDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVK 159
            +L+VNIT+H L P+H V+T +EK +LL +Y +++ QLPR+ + D +A+Y+GL RGQVVK
Sbjct: 134 AELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPVARYFGLRRGQVVK 193

Query: 160 VTYSGEITESHVTYRCV 176
           +    E    ++TYR V
Sbjct: 194 IIRPSETAGRYITYRLV 210

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Caenorhabditis elegans (taxid: 6239)

>sp|Q6CJ62|RPAB1_KLULA DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=RPB5 PE=3 SV=1

 Score = 79.7 bits (195), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 47/157 (29%), Positives = 80/157 (50%), Gaps = 3/157 (1%)

Query: 18  GYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYG 77
            +   PTE  +  F + GS   L         + +   + + V ++E N     F    G
Sbjct: 59  SFQSNPTEESIEKFPEMGS---LWVEFCDEASVGVKTMKNFVVHITEKNFQTGIFIYQSG 115

Query: 78  QDPDVDRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQL 137
             P  +++  + +     +     L+VNIT H L PKH  L++ EK++LLK+Y ++E QL
Sbjct: 116 ITPSANKILPTAAPAVIETFPEASLVVNITHHELVPKHIRLSEAEKKELLKRYRLKESQL 175

Query: 138 PRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYR 174
           PR+ + D +A Y GL+RG+V+K+    E +  + +YR
Sbjct: 176 PRIQRMDPVALYLGLKRGEVIKIIRKSETSGRYASYR 212

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

>sp|Q2T9T3|RPAB1_BOVIN DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Bos taurus GN=POLR2E PE=2 SV=1

 Score = 79.0 bits (193), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 90/179 (50%), Gaps = 7/179 (3%)

Query: 5   NGYDSSME----MEGGNGYNGEPTESCLSGFV--DNGSRDSLRYYLSRRTVLEMLKDRGY 58
           +G D ++E      GG    G P  + L+  V  ++   D +  +      + +   + Y
Sbjct: 31  DGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEPKVGIKTIKVY 90

Query: 59  AVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRIT-DLLVNITKHVLKPKHQV 117
              + E N++        G  P   +  + ++ +    + +  +LL+NIT+H L P+H V
Sbjct: 91  CQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVV 150

Query: 118 LTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCV 176
           +T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+    E    ++TYR V
Sbjct: 151 MTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV 209

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	177
351723899	237	uncharacterized protein LOC100306033 [Gl	0.864	0.645	0.509	1e-49
255576548	238	DNA-directed RNA polymerase II, putative	0.954	0.710	0.495	4e-49
388510192	248	unknown [Medicago truncatula]	0.988	0.705	0.463	4e-48
357509489	248	DNA-directed RNA polymerases I, II, and	0.988	0.705	0.463	4e-48
297739911	330	unnamed protein product [Vitis vinifera]	0.943	0.506	0.463	5e-48
359482221	229	PREDICTED: DNA-directed RNA polymerases	0.932	0.720	0.467	1e-47
224139746	216	predicted protein [Populus trichocarpa]	0.853	0.699	0.538	2e-47
15230206	222	rpb5 RNA polymerase subunit family prote	0.887	0.707	0.467	3e-44
21617912	222	putative DNA-directed RNA polymerase 23k	0.887	0.707	0.463	1e-43
297817026	222	eukaryotic rpb5 RNA polymerase subunit f	0.853	0.680	0.466	2e-43

>gi|351723899|ref|NP_001236527.1| uncharacterized protein LOC100306033 [Glycine max] gi|255627335|gb|ACU14012.1| unknown [Glycine max]

 Score =  200 bits (509), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 108/212 (50%), Positives = 131/212 (61%), Gaps = 59/212 (27%)

Query: 25  ESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR 84
           + CLS FVDNGS +S RYYLSRRT LEMLKDRGY++   EI+LS+ DFR I+GQ PD DR
Sbjct: 26  KGCLSKFVDNGSVESHRYYLSRRTTLEMLKDRGYSIPSHEIDLSLSDFRDIHGQFPDPDR 85

Query: 85  LRISISHQSDPSKRI----------------------------TDLLVNITKHV------ 110
           LR+S++H ++ SKRI                            T L++ +  H+      
Sbjct: 86  LRLSLTHATNSSKRILVIFCGPGVVKVTAIRNTAGQIINRDTLTGLILIVENHITSQALK 145

Query: 111 -------------------------LKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDA 145
                                    LKPKHQVLTD++K  LLKKY+IEEKQLPRML+ DA
Sbjct: 146 AVNLFSFKVEIFQITDLLVNITKHVLKPKHQVLTDKQKINLLKKYNIEEKQLPRMLQTDA 205

Query: 146 IAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           IA+YYGLERGQVVKVTYSGE+T+ HVTYRCVW
Sbjct: 206 IARYYGLERGQVVKVTYSGEVTQMHVTYRCVW 237

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255576548|ref|XP_002529165.1| DNA-directed RNA polymerase II, putative [Ricinus communis] gi|223531389|gb|EEF33224.1| DNA-directed RNA polymerase II, putative [Ricinus communis]

 Score =  199 bits (505), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 116/234 (49%), Positives = 142/234 (60%), Gaps = 65/234 (27%)

Query: 3   DGNGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVAL 62
           +GNG D+S        +N E    C S + D+G+ ++ RYYLSRRTVLEML+DRGY+V  
Sbjct: 11  NGNGTDASER------FNMEGLGKCFSSYADDGTHETHRYYLSRRTVLEMLRDRGYSVPS 64

Query: 63  SEINLSVQDF------------------------------------------RAIYGQDP 80
           SEI+LS+Q+F                                          RAI GQ  
Sbjct: 65  SEIDLSLQEFRAIHGPNPDIDRLKFSATHTSDPSKRMLVLFGGPGIIKVSTIRAIAGQIV 124

Query: 81  DVDRL-------RISISHQSDPSK----------RITDLLVNITKHVLKPKHQVLTDQEK 123
           + D L       +  I++Q+  +           +ITDLLVNITKHVLKPKHQVLTD+EK
Sbjct: 125 NKDSLTGLILVLQNQITNQAMKAVDLFKFKVEMFQITDLLVNITKHVLKPKHQVLTDREK 184

Query: 124 EKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           +KLLK Y IEEKQLPR+L+KDAIA+YYGLE+GQVVKVTYSGEITESHVTYRCVW
Sbjct: 185 QKLLKDYCIEEKQLPRLLRKDAIARYYGLEKGQVVKVTYSGEITESHVTYRCVW 238

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510192|gb|AFK43162.1| unknown [Medicago truncatula]

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 114/246 (46%), Positives = 142/246 (57%), Gaps = 71/246 (28%)

Query: 2   EDGNGYD-------SSMEMEGGNGYNGEPT----ESCLSGFVDNGSRDSLRYYLSRRTVL 50
           E+G G +       ++ME+E G+    +P       CL    DNGS +S RYYLSRRTVL
Sbjct: 4   ENGGGQNGTTETAITTMEIENGD-ITTQPQLQEQPQCLFTKKDNGSIESHRYYLSRRTVL 62

Query: 51  EMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRI----------- 99
           EMLKDRGY++   EI LS+ DFR I+GQ PDVDRLR++ +H ++PSKRI           
Sbjct: 63  EMLKDRGYSIPSDEIQLSLDDFRQIHGQSPDVDRLRLTATHATNPSKRILVVFSGPGIVK 122

Query: 100 -----------------TDLLV----NITKHVLK-------------------------- 112
                            T L++     IT   LK                          
Sbjct: 123 VNGVRDIAGQIVNRESLTGLILIVQNQITSQALKAVNLLSFKVEILQITDLLVNATKHVL 182

Query: 113 -PKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHV 171
            PKHQVLTD++K+ LLKKY I+EKQLPRML+ DAIA+YYGL+RGQVVKVTY+GEIT+ HV
Sbjct: 183 KPKHQVLTDKQKKNLLKKYDIQEKQLPRMLQTDAIARYYGLQRGQVVKVTYTGEITQMHV 242

Query: 172 TYRCVW 177
           TYRCVW
Sbjct: 243 TYRCVW 248

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357509489|ref|XP_003625033.1| DNA-directed RNA polymerases I, II, and III subunit RPABC1 [Medicago truncatula] gi|124359979|gb|ABN07995.1| RNA polymerase subunit, RPB5; RNA polymerase Rpb5, N-terminal [Medicago truncatula] gi|355500048|gb|AES81251.1| DNA-directed RNA polymerases I, II, and III subunit RPABC1 [Medicago truncatula]

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 114/246 (46%), Positives = 142/246 (57%), Gaps = 71/246 (28%)

Query: 2   EDGNGYD-------SSMEMEGGNGYNGEPT----ESCLSGFVDNGSRDSLRYYLSRRTVL 50
           E+G G +       ++ME+E G+    +P       CL    DNGS +S RYYLSRRTVL
Sbjct: 4   ENGGGQNGTTETAITTMEIENGD-ITTQPQLQEQPQCLFTKKDNGSIESHRYYLSRRTVL 62

Query: 51  EMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRI----------- 99
           EMLKDRGY++   EI LS+ DFR I+GQ PDVDRLR++ +H ++PSKRI           
Sbjct: 63  EMLKDRGYSIPSDEIQLSLDDFRQIHGQSPDVDRLRLTATHATNPSKRILVVFSGPGIVK 122

Query: 100 -----------------TDLLV----NITKHVLK-------------------------- 112
                            T L++     IT   LK                          
Sbjct: 123 VNGVRDIAGQIVNRESLTGLILIVQNQITSQALKAVNLLSFKVEIFQITDLLVNATKHVL 182

Query: 113 -PKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHV 171
            PKHQVLTD++K+ LLKKY I+EKQLPRML+ DAIA+YYGL+RGQVVKVTY+GEIT+ HV
Sbjct: 183 KPKHQVLTDKQKKNLLKKYDIQEKQLPRMLQTDAIARYYGLQRGQVVKVTYTGEITQMHV 242

Query: 172 TYRCVW 177
           TYRCVW
Sbjct: 243 TYRCVW 248

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739911|emb|CBI30093.3| unnamed protein product [Vitis vinifera]

 Score =  195 bits (496), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 107/231 (46%), Positives = 136/231 (58%), Gaps = 64/231 (27%)

Query: 11  MEMEGGNGYNGE-----PTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEI 65
           + M+GG  ++G+       + CLS FVD G  +S RYYL+RRT+LEML+DRGY++   +I
Sbjct: 100 VSMDGGGWFDGDLNGDFEVKRCLSSFVDEGRIESHRYYLARRTLLEMLRDRGYSIPALDI 159

Query: 66  NLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLV--------------------- 104
           ++S+QDFR+ Y Q PD DRLRIS + +SDPSK+I  +                       
Sbjct: 160 DISLQDFRSFYSQKPDPDRLRISAALRSDPSKKILVIFCGPDVVKVNAIRSIATQIVNKD 219

Query: 105 -----------NITKHVLK---------------------------PKHQVLTDQEKEKL 126
                      +IT   LK                           PKH+VLTDQEK KL
Sbjct: 220 SLSKLILVLQNHITSQALKAVDLFSFQVEKFQITDLLVNITKHVLKPKHRVLTDQEKNKL 279

Query: 127 LKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           LKKYS+ EKQLPRML++DAIA+YYGLE+GQVVKV Y+GEIT SHVTYRCVW
Sbjct: 280 LKKYSLNEKQLPRMLQQDAIARYYGLEKGQVVKVIYNGEITGSHVTYRCVW 330

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482221|ref|XP_003632734.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Vitis vinifera]

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 107/229 (46%), Positives = 135/229 (58%), Gaps = 64/229 (27%)

Query: 13  MEGGNGYNGE-----PTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINL 67
           M+GG  ++G+       + CLS FVD G  +S RYYL+RRT+LEML+DRGY++   +I++
Sbjct: 1   MDGGGWFDGDLNGDFEVKRCLSSFVDEGRIESHRYYLARRTLLEMLRDRGYSIPALDIDI 60

Query: 68  SVQDFRAIYGQDPDVDRLRISISHQSDPSKRITDLLV----------------------- 104
           S+QDFR+ Y Q PD DRLRIS + +SDPSK+I  +                         
Sbjct: 61  SLQDFRSFYSQKPDPDRLRISAALRSDPSKKILVIFCGPDVVKVNAIRSIATQIVNKDSL 120

Query: 105 ---------NITKHVLK---------------------------PKHQVLTDQEKEKLLK 128
                    +IT   LK                           PKH+VLTDQEK KLLK
Sbjct: 121 SKLILVLQNHITSQALKAVDLFSFQVEKFQITDLLVNITKHVLKPKHRVLTDQEKNKLLK 180

Query: 129 KYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           KYS+ EKQLPRML++DAIA+YYGLE+GQVVKV Y+GEIT SHVTYRCVW
Sbjct: 181 KYSLNEKQLPRMLQQDAIARYYGLEKGQVVKVIYNGEITGSHVTYRCVW 229

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224139746|ref|XP_002323257.1| predicted protein [Populus trichocarpa] gi|222867887|gb|EEF05018.1| predicted protein [Populus trichocarpa]

 Score =  193 bits (490), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 113/210 (53%), Positives = 134/210 (63%), Gaps = 59/210 (28%)

Query: 27  CLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFR------------- 73
           CLS FVD GS +S RYYLSRRTVLEMLKDRGY+V  SEI++S+QDFR             
Sbjct: 7   CLSSFVDEGSTESHRYYLSRRTVLEMLKDRGYSVPSSEIDISLQDFRGVYGQNPDIELLK 66

Query: 74  --AIYGQDPD-------------------------VDR---------LRISISHQS---- 93
             A +  DP                           DR         L+ +I++Q+    
Sbjct: 67  FSATHKSDPSKRMLVIFCGLGVVKVGMIRLITVQITDRDSLTGLILVLQNNITNQAMKAL 126

Query: 94  DPSK------RITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 147
           D  K      +ITDLLVNITKH+LKPKHQVL++Q K++LLKKYSIEEKQLPR+LKKDAI+
Sbjct: 127 DLFKFKIEIFQITDLLVNITKHILKPKHQVLSEQAKQRLLKKYSIEEKQLPRLLKKDAIS 186

Query: 148 QYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           +YYGLERGQVVKVTY G+IT SHVTYRCVW
Sbjct: 187 RYYGLERGQVVKVTYDGDITGSHVTYRCVW 216

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15230206|ref|NP_191267.1| rpb5 RNA polymerase subunit family protein [Arabidopsis thaliana] gi|6911878|emb|CAB72178.1| putative protein [Arabidopsis thaliana] gi|26452919|dbj|BAC43537.1| unknown protein [Arabidopsis thaliana] gi|28973011|gb|AAO63830.1| unknown protein [Arabidopsis thaliana] gi|332646091|gb|AEE79612.1| rpb5 RNA polymerase subunit family protein [Arabidopsis thaliana]

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 102/218 (46%), Positives = 127/218 (58%), Gaps = 61/218 (27%)

Query: 21  GEPTES--CLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ 78
           G+ T S  CLS +VD  S +S RYYL+RR  L+ML+DRGY V+  +INLS+ DFR +YG+
Sbjct: 5   GKETASVLCLSKYVDLSSEESHRYYLARRNGLQMLRDRGYEVSDEDINLSLHDFRTVYGE 64

Query: 79  DPDVDRLRISISHQSDPSKR----------------------------ITDLLVNITKHV 110
            PDVDRLRIS  H+SD +K+                            IT L++ +  HV
Sbjct: 65  RPDVDRLRISALHRSDSTKKVKIVFFGTSMVKVNAIRSVVADILSQETITGLILVLQNHV 124

Query: 111 -------------------------------LKPKHQVLTDQEKEKLLKKYSIEEKQLPR 139
                                          LKP+HQVL D+EK  LLKK+SIEEKQLPR
Sbjct: 125 TNQALKAIELFSFKVEIFQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQLPR 184

Query: 140 MLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           + KKDAI +YYGLE+GQVVKV Y GE+TESHV +RCVW
Sbjct: 185 ISKKDAIVRYYGLEKGQVVKVNYRGELTESHVAFRCVW 222

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21617912|gb|AAM66962.1| putative DNA-directed RNA polymerase 23kD subunit [Arabidopsis thaliana]

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 101/218 (46%), Positives = 127/218 (58%), Gaps = 61/218 (27%)

Query: 21  GEPTES--CLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ 78
           G+ T S  CLS +VD  S +S RYYL+RR  L++L+DRGY V+  +INLS+ DFR +YG+
Sbjct: 5   GKETASVLCLSKYVDLSSEESHRYYLARRNGLQILRDRGYEVSDEDINLSLHDFRTVYGE 64

Query: 79  DPDVDRLRISISHQSDPSKR----------------------------ITDLLVNITKHV 110
            PDVDRLRIS  H+SD +K+                            IT L++ +  HV
Sbjct: 65  RPDVDRLRISALHRSDSTKKVKIVFFGTSMVKVNAIRSVVADILSQETITGLILVLQNHV 124

Query: 111 -------------------------------LKPKHQVLTDQEKEKLLKKYSIEEKQLPR 139
                                          LKP+HQVL D+EK  LLKK+SIEEKQLPR
Sbjct: 125 TNQALKAIELFSFKVEIFQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQLPR 184

Query: 140 MLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           + KKDAI +YYGLE+GQVVKV Y GE+TESHV +RCVW
Sbjct: 185 ISKKDAIVRYYGLEKGQVVKVNYRGELTESHVAFRCVW 222

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817026|ref|XP_002876396.1| eukaryotic rpb5 RNA polymerase subunit family protein [Arabidopsis lyrata subsp. lyrata] gi|297322234|gb|EFH52655.1| eukaryotic rpb5 RNA polymerase subunit family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 98/210 (46%), Positives = 124/210 (59%), Gaps = 59/210 (28%)

Query: 27  CLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLR 86
           CLS +VD  S +S RYYL+R+  L+ML+DRGY V+  +INLS+ DFRA+YG+ PDVDRLR
Sbjct: 13  CLSKYVDPSSEESHRYYLARQNALQMLRDRGYQVSDEDINLSLHDFRAVYGERPDVDRLR 72

Query: 87  ISISHQSDPSKR----------------------------ITDLLV----NITKHVLK-- 112
           IS  H+SD SK+                            +T L++     +TK  +K  
Sbjct: 73  ISAQHRSDSSKKVKVVFFGTGMVKVNAIRSIAADVLSQETVTGLILVLQSQVTKQAMKAI 132

Query: 113 -------------------------PKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 147
                                    P+H+VL D+EK  LLKK+SIEEKQLPR+ KKDAI 
Sbjct: 133 ELFSFKVEIFQITDLLVNITKHALKPQHRVLNDKEKTTLLKKFSIEEKQLPRISKKDAIV 192

Query: 148 QYYGLERGQVVKVTYSGEITESHVTYRCVW 177
           +YYGLE+GQVVKV Y GE+TESHV YRCVW
Sbjct: 193 RYYGLEKGQVVKVNYRGELTESHVAYRCVW 222

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	177
TAIR|locus:2080650	222	NRPE5 [Arabidopsis thaliana (t	0.451	0.360	0.775	2.6e-47
TAIR|locus:2040257	218	RPB5D ""RNA polymerase II fift	0.440	0.357	0.756	1.4e-44
TAIR|locus:2096971	233	RPB5E ""RNA polymerase II fift	0.440	0.334	0.551	8.1e-35
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.429	0.361	0.460	2.1e-23
ZFIN|ZDB-GENE-040801-83	210	polr2eb "polymerase (RNA) II (	0.429	0.361	0.473	4.3e-23
UNIPROTKB|F2Z4J4	210	POLR2E "DNA-directed RNA polym	0.429	0.361	0.460	4.3e-23
UNIPROTKB|I3LSI7	210	POLR2E "Uncharacterized protei	0.429	0.361	0.460	4.3e-23
ASPGD|ASPL0000062840	235	AN0752 [Emericella nidulans (t	0.429	0.323	0.513	6.9e-23
UNIPROTKB|P19388	210	POLR2E "DNA-directed RNA polym	0.429	0.361	0.460	1.4e-22
UNIPROTKB|Q2T9T3	210	POLR2E "DNA-directed RNA polym	0.429	0.361	0.460	3.7e-22

TAIR|locus:2080650 NRPE5 [Arabidopsis thaliana (taxid:3702)]

 Score = 333 (122.3 bits), Expect = 2.6e-47, Sum P(2) = 2.6e-47
 Identities = 62/80 (77%), Positives = 71/80 (88%)

Query:    98 RITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQV 157
             +ITDLLVNITKH LKP+HQVL D+EK  LLKK+SIEEKQLPR+ KKDAI +YYGLE+GQV
Sbjct:   143 QITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQLPRISKKDAIVRYYGLEKGQV 202

Query:   158 VKVTYSGEITESHVTYRCVW 177
             VKV Y GE+TESHV +RCVW
Sbjct:   203 VKVNYRGELTESHVAFRCVW 222

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS

GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IPI

TAIR|locus:2040257 RPB5D ""RNA polymerase II fifth largest subunit, D"" [Arabidopsis thaliana (taxid:3702)]

 Score = 318 (117.0 bits), Expect = 1.4e-44, Sum P(2) = 1.4e-44
 Identities = 59/78 (75%), Positives = 69/78 (88%)

Query:    99 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVV 158
             ITDLLVN++KHVL+PKHQVL D+EKE LLKK+SIEEKQLPR+  KD I +YYGLE GQV+
Sbjct:   140 ITDLLVNVSKHVLRPKHQVLNDKEKESLLKKFSIEEKQLPRLSSKDPIVRYYGLETGQVM 199

Query:   159 KVTYSGEITESHVTYRCV 176
             KVTY  E++ESHVTYRCV
Sbjct:   200 KVTYKDELSESHVTYRCV 217

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS

TAIR|locus:2096971 RPB5E ""RNA polymerase II fifth largest subunit, E"" [Arabidopsis thaliana (taxid:3702)]

 Score = 238 (88.8 bits), Expect = 8.1e-35, Sum P(2) = 8.1e-35
 Identities = 43/78 (55%), Positives = 62/78 (79%)

Query:    99 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVV 158
             I DLLVNITKH+ +PK ++L  +EKE+LL+K+++E+KQLP + +KD+  +YYGL++ QVV
Sbjct:   155 IEDLLVNITKHIQQPKIEILNKEEKEQLLRKHALEDKQLPYLQEKDSFVRYYGLKKKQVV 214

Query:   159 KVTYSGEITESHVTYRCV 176
             K+TYS E     VTYRC+
Sbjct:   215 KITYSKEPVGDFVTYRCI 232

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA;ISS

UNIPROTKB|Q5R587 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" [Pongo abelii (taxid:9601)]

 Score = 192 (72.6 bits), Expect = 2.1e-23, Sum P(2) = 2.1e-23
 Identities = 35/76 (46%), Positives = 53/76 (69%)

Query:   101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
             +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+
Sbjct:   134 ELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKI 193

Query:   161 TYSGEITESHVTYRCV 176
                 E    ++TYR V
Sbjct:   194 IRPSETAGRYITYRLV 209

GO:0005634 "nucleus" evidence=ISS

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

ZFIN|ZDB-GENE-040801-83 polr2eb "polymerase (RNA) II (DNA directed) polypeptide E, b" [Danio rerio (taxid:7955)]

 Score = 194 (73.4 bits), Expect = 4.3e-23, Sum P(2) = 4.3e-23
 Identities = 36/76 (47%), Positives = 54/76 (71%)

Query:   101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
             +LL+NIT+H L P+H V+T +E  +LL +Y ++E QLPR+   D +A+Y+GL+RGQVVK+
Sbjct:   134 ELLINITEHELVPEHIVMTKEEVTELLARYKLKESQLPRIQAGDPVARYFGLKRGQVVKI 193

Query:   161 TYSGEITESHVTYRCV 176
                 E    ++TYR V
Sbjct:   194 IRPSETAGRYITYRLV 209

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F2Z4J4 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" [Bos taurus (taxid:9913)]

 Score = 192 (72.6 bits), Expect = 4.3e-23, Sum P(2) = 4.3e-23
 Identities = 35/76 (46%), Positives = 53/76 (69%)

Query:   101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
             +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+
Sbjct:   134 ELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKI 193

Query:   161 TYSGEITESHVTYRCV 176
                 E    ++TYR V
Sbjct:   194 IRPSETAGRYITYRLV 209

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LSI7 POLR2E "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 192 (72.6 bits), Expect = 4.3e-23, Sum P(2) = 4.3e-23
 Identities = 35/76 (46%), Positives = 53/76 (69%)

Query:   101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
             +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+
Sbjct:   134 ELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKI 193

Query:   161 TYSGEITESHVTYRCV 176
                 E    ++TYR V
Sbjct:   194 IRPSETAGRYITYRLV 209

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

ASPGD|ASPL0000062840 AN0752 [Emericella nidulans (taxid:162425)]

 Score = 202 (76.2 bits), Expect = 6.9e-23, Sum P(2) = 6.9e-23
 Identities = 39/76 (51%), Positives = 53/76 (69%)

Query:   101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
             DLLVNIT+H L PKH +L+ +EK KLL++Y ++E QLPR+   D +A+Y GL RGQVVK+
Sbjct:   159 DLLVNITRHELVPKHVLLSPEEKSKLLQRYRLKESQLPRIQVSDPVARYLGLRRGQVVKI 218

Query:   161 TYSGEITESHVTYRCV 176
                 E    + +YR V
Sbjct:   219 IRKSETAGRYASYRWV 234

GO:0006360 "transcription from RNA polymerase I promoter" evidence=IEA

GO:0042797 "tRNA transcription from RNA polymerase III promoter" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0001055 "RNA polymerase II activity" evidence=IEA

GO:0001056 "RNA polymerase III activity" evidence=IEA

GO:0003968 "RNA-directed RNA polymerase activity" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=IEA

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P19388 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" [Homo sapiens (taxid:9606)]

 Score = 192 (72.6 bits), Expect = 1.4e-22, Sum P(2) = 1.4e-22
 Identities = 35/76 (46%), Positives = 53/76 (69%)

Query:   101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
             +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+
Sbjct:   134 ELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKI 193

Query:   161 TYSGEITESHVTYRCV 176
                 E    ++TYR V
Sbjct:   194 IRPSETAGRYITYRLV 209

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IDA;TAS

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=TAS

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0006468 "protein phosphorylation" evidence=IDA

UNIPROTKB|Q2T9T3 POLR2E "DNA-directed RNA polymerases I, II, and III subunit RPABC1" [Bos taurus (taxid:9913)]

 Score = 192 (72.6 bits), Expect = 3.7e-22, Sum P(2) = 3.7e-22
 Identities = 35/76 (46%), Positives = 53/76 (69%)

Query:   101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
             +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+
Sbjct:   134 ELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKI 193

Query:   161 TYSGEITESHVTYRCV 176
                 E    ++TYR V
Sbjct:   194 IRPSETAGRYITYRLV 209

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!
4th Layer	2.7.7.6	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00000682001	SubName- Full=Chromosome chr8 scaffold_106, whole genome shotgun sequence; (229 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00002744001	SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)				•	•	•	•		0.771
	GSVIVG00036639001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (318 aa)				•	•	•	•		0.694
	GSVIVG00024229001	SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (176 aa)					•	•	•		0.625
	GSVIVG00032808001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (116 aa)				•	•	•	•		0.590
	GSVIVG00033123001	SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_64, whole genome shotg [...] (114 aa)				•	•	•	•		0.584
	GSVIVG00033404001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (362 aa)				•	•	•	•		0.539
	GSVIVG00004487001	SubName- Full=Chromosome undetermined scaffold_712, whole genome shotgun sequence; (74 aa)					•	•	•		0.521
	GSVIVG00018575001	RecName- Full=DNA-directed RNA polymerase; EC=2.7.7.6; (1220 aa)	•				•	•	•		0.513
	GSVIVG00018813001	SubName- Full=Putative uncharacterized protein (Chromosome chr12 scaffold_18, whole genome shot [...] (138 aa)					•	•	•		0.499
	GSVIVG00002607001	SubName- Full=Chromosome undetermined scaffold_133, whole genome shotgun sequence; (114 aa)					•	•			0.498

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	177
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	7e-59
pfam01191	74	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-	7e-37
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	4e-24
COG2012	80	COG2012, RPB5, DNA-directed RNA polymerase, subuni	4e-20
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	4e-17
PRK09570	79	PRK09570, rpoH, DNA-directed RNA polymerase subuni	5e-15
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	2e-07

>gnl|CDD|215582 PLN03111, PLN03111, DNA-directed RNA polymerase II subunit family protein; Provisional

 Score =  182 bits (464), Expect = 7e-59
 Identities = 74/206 (35%), Positives = 102/206 (49%), Gaps = 60/206 (29%)

Query: 32  VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISH 91
           +D GS +S R YL RRTVLEML+DRGY V+ SE+NL++ +FR  +G+ P  + LRIS   
Sbjct: 1   MDTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPK 60

Query: 92  QSDPSKRI-----------------------TD-----LLV---NITKHVLK------PK 114
           +SDPSK+I                        +     +LV    +T    +       K
Sbjct: 61  RSDPSKKILVFFPEEEKVGVKTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSK 120

Query: 115 HQVLTDQEKE-----------------------KLLKKYSIEEKQLPRMLKKDAIAQYYG 151
            ++   QE E                        LLK+Y+++E QLPR+   D IA+YYG
Sbjct: 121 FKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRIQVSDPIARYYG 180

Query: 152 LERGQVVKVTYSGEITESHVTYRCVW 177
           L+RGQVVK+    E    +VTYRCV 
Sbjct: 181 LKRGQVVKIIRPSETAGRYVTYRCVV 206

Length = 206

>gnl|CDD|201651 pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-terminal domain

 Score =  121 bits (307), Expect = 7e-37
 Identities = 41/74 (55%), Positives = 55/74 (74%)

Query: 104 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 163
           VNITKH L PKH+VL+++EK+KLLK+Y I+E+QLPR+L  D +A+Y G + G VVK+T  
Sbjct: 1   VNITKHELVPKHEVLSEEEKKKLLKRYKIKEEQLPRILATDPVARYLGAKPGDVVKITRK 60

Query: 164 GEITESHVTYRCVW 177
            E    +VTYR V 
Sbjct: 61  SETAGEYVTYRLVV 74

The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. Length = 74

>gnl|CDD|173356 PTZ00061, PTZ00061, DNA-directed RNA polymerase; Provisional

 Score = 93.0 bits (231), Expect = 4e-24
 Identities = 42/77 (54%), Positives = 54/77 (70%)

Query: 100 TDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVK 159
           T+LLVNITKH L PKH  LTD EK  LL++Y ++E QLPR+   D +A+Y+GL +GQVVK
Sbjct: 128 TELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRIQSADPVARYFGLSKGQVVK 187

Query: 160 VTYSGEITESHVTYRCV 176
           +    E    +VTYR V
Sbjct: 188 IIRPSETAGRYVTYRLV 204

Length = 205

>gnl|CDD|224923 COG2012, RPB5, DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]

 Score = 79.3 bits (196), Expect = 4e-20
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 101 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 160
            L  N+  H L P+H+VL+++E +++LK+  IE +QLP++   D +A+  G + G VVK+
Sbjct: 4   MLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKALGAKPGDVVKI 63

Query: 161 TYSGEITESHVTYRCV 176
                     V YR V
Sbjct: 64  VRKSPTAGESVYYRLV 79

Length = 80

>gnl|CDD|217772 pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-terminal domain

 Score = 71.9 bits (177), Expect = 4e-17
 Identities = 29/66 (43%), Positives = 41/66 (62%), Gaps = 2/66 (3%)

Query: 36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIY--GQDPDVDRLRISISHQS 93
           R+  R +  RRTV+EML+DRGY V   E+NLS+++F+  Y    +PD  +L  S   + 
Sbjct: 4  ERELYRLWRVRRTVMEMLRDRGYLVTEEELNLSLEEFKEKYGDNGNPDRSKLTFSARPKD 63

Query: 94 DPSKRI 99
          DPS RI
Sbjct: 64 DPSGRI 69

Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure. This module is important for positioning the downstream DNA. Length = 92

>gnl|CDD|236575 PRK09570, rpoH, DNA-directed RNA polymerase subunit H; Reviewed

 Score = 66.0 bits (162), Expect = 5e-15
 Identities = 24/73 (32%), Positives = 43/73 (58%)

Query: 104 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 163
            ++  H L P+H++L+++E +KLLK+Y I+ +QLP++   D + +  G + G V+K+   
Sbjct: 4   FDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRK 63

Query: 164 GEITESHVTYRCV 176
                  V YR V
Sbjct: 64  SPTAGEAVYYRLV 76

Length = 79

>gnl|CDD|173356 PTZ00061, PTZ00061, DNA-directed RNA polymerase; Provisional

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 31/112 (27%), Positives = 59/112 (52%), Gaps = 3/112 (2%)

Query: 41  RYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDV-DRLRISISHQSDPSKRI 99
           R++  RRT  EML+DRGY +   E   +   F+  + ++  +  R+ +  SH++DP+ RI
Sbjct: 7   RFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRI 66

Query: 100 TDLLVNITKHV-LKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYY 150
                + TK   +KP  + LT++ +E  +++  +  + +     KDAI +  
Sbjct: 67  IVYFADETKKTGVKPIRE-LTEKMEEHDIQRAILVTQNVLTPFAKDAILEAA 117

Length = 205

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	177
KOG3218	208	consensus RNA polymerase, 25-kDa subunit (common t	100.0
PLN03111	206	DNA-directed RNA polymerase II subunit family prot	100.0
PTZ00061	205	DNA-directed RNA polymerase; Provisional	100.0
PF01191	74	RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal do	100.0
PRK09570	79	rpoH DNA-directed RNA polymerase subunit H; Review	100.0
COG2012	80	RPB5 DNA-directed RNA polymerase, subunit H, RpoH/	100.0
PF03871	93	RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal do	99.87

>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]

Probab=100.00  E-value=1.4e-64  Score=422.85  Aligned_cols=142  Identities=51%  Similarity=0.924  Sum_probs=140.2

Q ss_pred             hhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceeEeecCCCCCchh----------------
Q 030447           36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKR----------------   98 (177)
Q Consensus        36 ~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~-~~r~~L~~~~~~~~dp~~k----------------   98 (177)
                      +.|++|||++|||++||||||||.|+|+|++++|++|+++||+. |+|++|+|++.|++||++|                
T Consensus         6 e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~   85 (208)
T KOG3218|consen    6 EEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTM   85 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHH
Confidence            78999999999999999999999999999999999999999998 9999999999999999988                


Q ss_pred             --------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHHHhhcCCCc
Q 030447           99 --------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEE  134 (177)
Q Consensus        99 --------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~  134 (177)
                                                                  |+||+||||+|+|||||.+||+|||++||++|++++
T Consensus        86 k~~~~~~~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~e  165 (208)
T KOG3218|consen   86 KTYVIQMQSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLKE  165 (208)
T ss_pred             HHHHHHHHhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCCc
Confidence                                                        999999999999999999999999999999999999


Q ss_pred             CCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          135 KQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       135 ~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      +||||||.+||||||||||+||||||+|+|+|||+|+|||||+
T Consensus       166 ~qLPRIq~~DpvaRYyGLKrGqVVKI~r~setag~yitYR~v~  208 (208)
T KOG3218|consen  166 TQLPRIQKKDPVARYYGLKRGQVVKIIRRSETAGRYITYRCVV  208 (208)
T ss_pred             ccCCeeeccChHHhhhccccCcEEEEEecCccCcceEEEEEeC
Confidence            9999999999999999999999999999999999999999996

>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional

Probab=100.00  E-value=1.5e-63  Score=418.20  Aligned_cols=146  Identities=60%  Similarity=0.947  Sum_probs=142.8

Q ss_pred             CCCChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceeEeecCCCCCchh-------------
Q 030447           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKR-------------   98 (177)
Q Consensus        32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~k-------------   98 (177)
                      |+.++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|++.+++||+++             
T Consensus         1 ~~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgv   80 (206)
T PLN03111          1 MDTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPKRSDPSKKILVFFPEEEKVGV   80 (206)
T ss_pred             CCcchHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHHcCCcCHHHcEeeeecCCCCCCcEEEEeCCCCccCH
Confidence            4667889999999999999999999999999999999999999999999999999999999999988             


Q ss_pred             -----------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHHHhhcC
Q 030447           99 -----------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYS  131 (177)
Q Consensus        99 -----------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~  131 (177)
                                                                     |+||+||||+|+|||||++||+|||++||++|+
T Consensus        81 k~ir~~~~~~~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~  160 (206)
T PLN03111         81 KTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYT  160 (206)
T ss_pred             HHHHHHHHHHhhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcC
Confidence                                                           999999999999999999999999999999999


Q ss_pred             CCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          132 IEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       132 i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      ++++|||||+.+||||||||||+||||||+|+|+|||+||+||+|+
T Consensus       161 i~~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~taG~~v~YR~vv  206 (206)
T PLN03111        161 VKETQLPRIQVSDPIARYYGLKRGQVVKIIRPSETAGRYVTYRCVV  206 (206)
T ss_pred             CCHHHCCcccccChhhHhcCCCCCCEEEEEECCCCCCCceEEEEeC
Confidence            9999999999999999999999999999999999999999999996

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=7.7e-62  Score=407.65  Aligned_cols=142  Identities=43%  Similarity=0.686  Sum_probs=137.6

Q ss_pred             hhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceeEeecCCCCCchh----------------
Q 030447           36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKR----------------   98 (177)
Q Consensus        36 ~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~-~~r~~L~~~~~~~~dp~~k----------------   98 (177)
                      ++++.||||+|||++|||+||||.|+++|+++|+++|+++||++ +.|++|+|++++.+||+++                
T Consensus         2 ~~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~   81 (205)
T PTZ00061          2 DDSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKP   81 (205)
T ss_pred             cHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHH
Confidence            47889999999999999999999999999999999999999987 4689999999999999766                


Q ss_pred             ---------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHHHhhcCCC
Q 030447           99 ---------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE  133 (177)
Q Consensus        99 ---------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~  133 (177)
                                                                   |+||+||||+|+|||||++||+|||++||++|+++
T Consensus        82 ir~~~~~~~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~  161 (205)
T PTZ00061         82 IRELTEKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVK  161 (205)
T ss_pred             HHHHHHHHhhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCC
Confidence                                                         99999999999999999999999999999999999


Q ss_pred             cCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          134 EKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       134 ~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      ++|||||+.+||||||||||+||||||+|+|+|||+||+||+|+
T Consensus       162 ~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~taG~~v~YR~vv  205 (205)
T PTZ00061        162 ESQLPRIQSADPVARYFGLSKGQVVKIIRPSETAGRYVTYRLVV  205 (205)
T ss_pred             HHHCCcccccChhhHhcCCCCCCEEEEEECCCCCCcceEEEEeC
Confidence            99999999999999999999999999999999999999999996

>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2

Probab=100.00  E-value=3.2e-40  Score=239.39  Aligned_cols=74  Identities=49%  Similarity=0.793  Sum_probs=66.2

Q ss_pred             hcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          104 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       104 vNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      ||||+|+|||||++||+||+++||++|+++++|||||+.+||+|||||+|+||||||+|+|+|||+|++||+||
T Consensus         1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~Vv   74 (74)
T PF01191_consen    1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSSDPVARYLGAKPGDVVKIIRKSETAGEYVTYRLVV   74 (74)
T ss_dssp             S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHHHHHTT--TTSEEEEEEEETTTSEEEEEEEEE
T ss_pred             CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCcccccChhhhhcCCCCCCEEEEEecCCCCCCcEEEEEeC
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999996

7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....

>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed

Probab=100.00  E-value=4.2e-40  Score=241.53  Aligned_cols=75  Identities=32%  Similarity=0.589  Sum_probs=73.9

Q ss_pred             hhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          103 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       103 lvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      .||||+|+|||+|++||+||+++||++|+++++|||||+.+||+|+||||++||||||+|+|+|||+|++||+|+
T Consensus         3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR~Vv   77 (79)
T PRK09570          3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRKSPTAGEAVYYRLVV   77 (79)
T ss_pred             ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEEEECCCCCCccEEEEEEe
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999996

>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]

Probab=100.00  E-value=3.4e-37  Score=226.25  Aligned_cols=79  Identities=34%  Similarity=0.543  Sum_probs=76.9

Q ss_pred             hhhhhhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447           99 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus        99 e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      ++.+.||+++|+|||+|++||+||++++|++|+|+++|||||+.+||||+++|+|+||||||+|+|+|||++++||+|+
T Consensus         2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPva~~lgak~GdvVkIvRkS~TaGe~v~YR~Vv   80 (80)
T COG2012           2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKALGAKPGDVVKIVRKSPTAGESVYYRLVV   80 (80)
T ss_pred             ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcccccChhHHHccCCCCcEEEEEecCCCCCceEEEEEeC
Confidence            4578899999999999999999999999999999999999999999999999999999999999999999999999996

>PF03871 RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal domain; InterPro: IPR005571 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2

Probab=99.87  E-value=7.6e-24  Score=157.51  Aligned_cols=64  Identities=45%  Similarity=0.835  Sum_probs=52.7

Q ss_pred             ChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCC---CCCCCceeEeecCCCCCchh
Q 030447           35 GSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKR   98 (177)
Q Consensus        35 ~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~---~~~r~~L~~~~~~~~dp~~k   98 (177)
                      +++|++|||||||||+|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++.+.+||+++
T Consensus         3 ~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~   69 (93)
T PF03871_consen    3 DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDK   69 (93)
T ss_dssp             TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--E
T ss_pred             cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCe
Confidence            34899999999999999999999999999999999999999998   79999999999999999877

7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) (IPR000783 from INTERPRO) [, , , ]. This entry represents the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers alpha/beta/alpha []. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure []. This module is important for positioning the downstream DNA.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3H0G_Q 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E 1I50_E ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	177
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		8e-16
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		5e-14
1hmj_A	78	Solution Structure Of Rna Polymerase Subunit H Leng		2e-08
1eik_A	77	Solution Structure Of Rna Polymerase Subunit Rpb5 F		6e-08
2waq_H	84	The Complete Structure Of The Archaeal 13-Subunit D		3e-05
2pmz_H	84	Archaeal Rna Polymerase From Sulfolobus Solfataricu		4e-05

>pdb|1DZF|A Chain A, Rpb5 From S.Cerevisiae Length = 215

Iteration: 1
 Score = 79.7 bits (195), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 51/152 (33%), Positives = 74/152 (48%), Gaps = 3/152 (1%)
Query: 23  PTESCLSGFVDNGXXXXXXXXXXXXTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDV 82
           PTE  +S F D G             V  M   + + + + E N     F       P  
Sbjct: 64  PTEESISKFPDMGSLWVEFCDEPSVGVKTM---KTFVIHIQEKNFQTGIFVYQNNITPSA 120
Query: 83  DRLRISISHQSDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLK 142
            +L  SI   +  +     L+VNIT H L PKH  L+  EK +LLK+Y ++E QLPR+ +
Sbjct: 121 MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR 180
Query: 143 KDAIAQYYGLERGQVVKVTYSGEITESHVTYR 174
            D +A Y GL+RG+VVK+    E +  + +YR
Sbjct: 181 ADPVALYLGLKRGEVVKIIRKSETSGRYASYR 212

>pdb|3H0G|E Chain E, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 210

Iteration: 1
 Score = 73.9 bits (180), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 35/75 (46%), Positives = 52/75 (69%)
Query: 100 TDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVK 159
           +DL+VNIT H L PKH +L+  EK++LL +Y + E QLPR+   D +A+Y GL+RG+VVK
Sbjct: 133 SDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQLPRIQLADPVARYLGLKRGEVVK 192
Query: 160 VTYSGEITESHVTYR 174
           +    E +  + +YR
Sbjct: 193 IVRRSETSGRYNSYR 207

>pdb|1HMJ|A Chain A, Solution Structure Of Rna Polymerase Subunit H Length = 78

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 45/73 (61%)
Query: 104 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 163
           + +T H+L PKH+++  +E E++LK+Y+I+ +QLP++ + D + Q  G + G VV+V   
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRK 60
Query: 164 GEITESHVTYRCV 176
                  + YR V
Sbjct: 61  SPTAGVSIAYRLV 73

>pdb|1EIK|A Chain A, Solution Structure Of Rna Polymerase Subunit Rpb5 From Methanobacterium Thermoautotrophicum Length = 77

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 41/71 (57%)
Query: 106 ITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGE 165
           I KH L P+H +L + E +++LK+     +QLP++   D +A+  G +RG +VK+     
Sbjct: 5   ILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKIIRKSP 64
Query: 166 ITESHVTYRCV 176
             E  VTYR V
Sbjct: 65  TAEEFVTYRLV 75

>pdb|2WAQ|H Chain H, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 84

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 38/68 (55%)
Query: 109 HVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 168
           H L PKH+VL+  E  K+LK+  I  +QLP +   D +A+    + G ++++    ++  
Sbjct: 14  HYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYG 73
Query: 169 SHVTYRCV 176
             V+YR V
Sbjct: 74  EVVSYRYV 81

>pdb|2PMZ|H Chain H, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 84

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 37/68 (54%)
Query: 109 HVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 168
           H L PKH+VL   E  K+LK+  I  +QLP +   D +A+    + G ++++    ++  
Sbjct: 14  HYLVPKHEVLNIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYG 73
Query: 169 SHVTYRCV 176
             V+YR V
Sbjct: 74  EVVSYRYV 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	177
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	5e-30
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	2e-29
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	9e-29
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	2e-26
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	4e-24
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	4e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-07

>4ayb_H DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_H 2y0s_H 2waq_H 4b1o_H 4b1p_Z 2pmz_H 3hkz_H Length = 84

 Score =  104 bits (260), Expect = 5e-30
 Identities = 22/78 (28%), Positives = 42/78 (53%)

Query: 99  ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVV 158
            ++  ++   H L PKH+VL+  E  K+LK+  I  +QLP +   D +A+    + G ++
Sbjct: 4   SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDII 63

Query: 159 KVTYSGEITESHVTYRCV 176
           ++    ++    V+YR V
Sbjct: 64  RIIRKSQLYGEVVSYRYV 81

>1eik_A RNA polymerase subunit RPB5; RPBH, OCSP, NESG, protein structure initiative, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.78.1.1 Length = 77

 Score =  102 bits (256), Expect = 2e-29
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 102 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 161
           +   I KH L P+H +L + E +++LK+     +QLP++   D +A+  G +RG +VK+ 
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKII 60

Query: 162 YSGEITESHVTYRCV 176
                 E  VTYR V
Sbjct: 61  RKSPTAEEFVTYRLV 75

>1hmj_A RPB5, protein (subunit H); RNA polymerase, archaea; NMR {Methanocaldococcus jannaschii} SCOP: d.78.1.1 Length = 78

 Score =  100 bits (252), Expect = 9e-29
 Identities = 25/73 (34%), Positives = 45/73 (61%)

Query: 104 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 163
           + +T H+L PKH+++  +E E++LK+Y+I+ +QLP++ + D + Q  G + G VV+V   
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRK 60

Query: 164 GEITESHVTYRCV 176
                  + YR V
Sbjct: 61  SPTAGVSIAYRLV 73

>3h0g_E DNA-directed RNA polymerases I, II, and III subunit rpabc1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 210

 Score = 99.0 bits (246), Expect = 2e-26
 Identities = 35/79 (44%), Positives = 53/79 (67%)

Query: 98  RITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQV 157
           + +DL+VNIT H L PKH +L+  EK++LL +Y + E QLPR+   D +A+Y GL+RG+V
Sbjct: 131 QESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQLPRIQLADPVARYLGLKRGEV 190

Query: 158 VKVTYSGEITESHVTYRCV 176
           VK+    E +  + +YR  
Sbjct: 191 VKIVRRSETSGRYNSYRIC 209

>1dzf_A DNA-directed RNA polymerases I, II, and III 27 KD polypeptide; RNA polymerase subunit; 1.9A {Saccharomyces cerevisiae} SCOP: c.52.3.1 d.78.1.1 PDB: 1i3q_E 1i50_E 1i6h_E 1k83_E* 1nik_E 1nt9_E 1pqv_E 1r5u_E 1r9s_E* 1r9t_E* 1sfo_E* 1twa_E* 1twc_E* 1twf_E* 1twg_E* 1twh_E* 1wcm_E 1y1v_E 1y1w_E 1y1y_E ... Length = 215

 Score = 92.9 bits (230), Expect = 4e-24
 Identities = 35/79 (44%), Positives = 50/79 (63%)

Query: 98  RITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQV 157
               L+VNIT H L PKH  L+  EK +LLK+Y ++E QLPR+ + D +A Y GL+RG+V
Sbjct: 136 NEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEV 195

Query: 158 VKVTYSGEITESHVTYRCV 176
           VK+    E +  + +YR  
Sbjct: 196 VKIIRKSETSGRYASYRIC 214

>1dzf_A DNA-directed RNA polymerases I, II, and III 27 KD polypeptide; RNA polymerase subunit; 1.9A {Saccharomyces cerevisiae} SCOP: c.52.3.1 d.78.1.1 PDB: 1i3q_E 1i50_E 1i6h_E 1k83_E* 1nik_E 1nt9_E 1pqv_E 1r5u_E 1r9s_E* 1r9t_E* 1sfo_E* 1twa_E* 1twc_E* 1twf_E* 1twg_E* 1twh_E* 1wcm_E 1y1v_E 1y1w_E 1y1y_E ... Length = 215

 Score = 66.3 bits (161), Expect = 4e-14
 Identities = 21/104 (20%), Positives = 42/104 (40%)

Query: 33  DNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQ 92
               R+  R + + RTV EM+KDRGY +   E+ L ++DF+A Y       + ++     
Sbjct: 3   QENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQA 62

Query: 93  SDPSKRITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 136
           +   + I+      +  V       +  +  +  +     +  Q
Sbjct: 63  NPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQ 106

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.2 bits (111), Expect = 8e-07
 Identities = 32/177 (18%), Positives = 53/177 (29%), Gaps = 56/177 (31%)

Query: 13  MEGGNGYNGEPTESCLSGFVDNGSRD--------------SLRYYLSRRTVLEMLKDRGY 58
           +  G+G      ++ ++  V                    +L+   S  TVLEML+   Y
Sbjct: 158 V-LGSG------KTWVALDV---CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY 207

Query: 59  AVALSEINLSVQDFRAIYGQDPDVDRLRISISHQS------------DPS---------- 96
            +  +  + S                LR  +  +             +            
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCK 267

Query: 97  -------KRITDLL-VNITKHV-LKPKHQVLTDQEKEKLLKKY-SIEEKQLPRMLKK 143
                  K++TD L    T H+ L      LT  E + LL KY     + LPR +  
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	177
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	100.0
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	100.0
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	100.0
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	100.0
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	100.0

>3h0g_E DNA-directed RNA polymerases I, II, and III subunit rpabc1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=5.4e-62  Score=408.37  Aligned_cols=146  Identities=34%  Similarity=0.575  Sum_probs=139.3

Q ss_pred             CCCChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC---CCCCceeEeecCCCCC-chh---------
Q 030447           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD---PDVDRLRISISHQSDP-SKR---------   98 (177)
Q Consensus        32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~---~~r~~L~~~~~~~~dp-~~k---------   98 (177)
                      |+++++|++||||+|||++|||+||||.|+++|+++|+++|+++||+.   |+|++|+|++.+.+|| +++         
T Consensus         1 m~~~~~e~~rl~rirrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~~~~~r~~l~~~~~~~~dp~~~~i~VfF~~~~   80 (210)
T 3h0g_E            1 MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEFAKEP   80 (210)
T ss_dssp             ---CTHHHHHHHGGGSSSSSTTTTTTEECCTTTTSCCHHHHHHHSCCSSSSCCCSSCCCEEEESSCSSCCCEEEECCCSS
T ss_pred             CCcchHHHHHHHHHHHHHHHHhcCCCCccCHHHHhCCHHHHHHHhcccCCCCCchheEEEEEcCCCCccCeEEEEECCCC
Confidence            567789999999999999999999999999999999999999999875   8899999999999999 655         


Q ss_pred             ---------------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHHH
Q 030447           99 ---------------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKLL  127 (177)
Q Consensus        99 ---------------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~lL  127 (177)
                                                                         |+||+||||+|+|||||++||+|||++||
T Consensus        81 ~vgvk~Ir~~~~~~~~en~~~~IiV~q~~~t~~A~~~l~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eE~~~lL  160 (210)
T 3h0g_E           81 SVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELL  160 (210)
T ss_dssp             SCCTTTTGGGTHHHHHTTCSEEEECCSSCCCSHHHHTTTTTCTTCEECCCCSSSSCSCTTSBTTBCCEECCCHHHHHHHH
T ss_pred             ccChHHHHHHHHHHHHcCCceEEEEECCCCCHHHHHHHHHhCcCcEEEEEeehHeeEecccccccCcEEEcCHHHHHHHH
Confidence                                                               99999999999999999999999999999


Q ss_pred             hhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          128 KKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       128 ~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      ++|+++++|||||+.+||||+||||++||||||+|+|+|||+||+||+|+
T Consensus       161 ~~y~i~~~qLP~I~~~DPv~~~~g~k~GdVvkI~R~s~tag~~v~YR~V~  210 (210)
T 3h0g_E          161 DRYKLRETQLPRIQLADPVARYLGLKRGEVVKIVRRSETSGRYNSYRICA  210 (210)
T ss_dssp             HHTCCCTTTSCCCCTTCHHHHHHTCCTTCEEEEECCCCTTSCCEEEEECC
T ss_pred             HHcCCCHHHCCcccccCcchhhhCCCCCCEEEEEeCCCCCCCceEEEEeC
Confidence            99999999999999999999999999999999999999999999999996

>1dzf_A DNA-directed RNA polymerases I, II, and III 27 KD polypeptide; RNA polymerase subunit; 1.9A {Saccharomyces cerevisiae} SCOP: c.52.3.1 d.78.1.1 PDB: 1i3q_E 1i50_E 1i6h_E 1k83_E* 1nik_E 1nt9_E 1pqv_E 1r5u_E 1r9s_E* 1r9t_E* 1sfo_E* 1twa_E* 1twc_E* 1twf_E* 1twg_E* 1twh_E* 1wcm_E 1y1v_E 1y1w_E 1y1y_E ...

Probab=100.00  E-value=1.1e-60  Score=401.76  Aligned_cols=143  Identities=38%  Similarity=0.634  Sum_probs=137.9

Q ss_pred             ChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCC---CCCCCceeEeecCCCCCchh-------------
Q 030447           35 GSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKR-------------   98 (177)
Q Consensus        35 ~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~---~~~r~~L~~~~~~~~dp~~k-------------   98 (177)
                      ++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++.+.+||++|             
T Consensus         5 ~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~g~p~r~~L~~~~~~~~d~~~k~~~~~~~~VfF~~   84 (215)
T 1dzf_A            5 NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCD   84 (215)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECS
T ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCccCHhHhcCCHHHHHHHHccccCCCchhheEEEecCCCChhhhhccCCceEEEecC
Confidence            45889999999999999999999999999999999999999987   79999999999998877664             


Q ss_pred             ----------------------------------------------------hhhhhhcCCcccccCCceecCHHHHHHH
Q 030447           99 ----------------------------------------------------ITDLLVNITKHVLKPKHQVLTDQEKEKL  126 (177)
Q Consensus        99 ----------------------------------------------------e~eLlvNIt~H~LVPkH~vLs~eEk~~l  126 (177)
                                                                          |+||+||||+|+|||||++||+|||++|
T Consensus        85 ~~~vgvk~ir~~~~~~~~e~~~~~IlV~q~~itp~Ak~~l~~~~~~~iE~F~e~eL~vni~~H~lVP~H~~l~~eE~~~l  164 (215)
T 1dzf_A           85 EPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKREL  164 (215)
T ss_dssp             SSEECHHHHHHHHHHHHHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEEHHHHSSCGGGSTTSCEEEECCHHHHHHH
T ss_pred             CCccchHHHHHHHHHHHhcCCceEEEEECCCCChHHHHHHHHhcCceEEEeehHHheeccccceeccceEEccHHHHHHH
Confidence                                                                9999999999999999999999999999


Q ss_pred             HhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          127 LKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       127 L~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      |++|+|+++|||||+.+||||||||||+||||||+|+|+|||+||+||+|+
T Consensus       165 L~~y~i~~~qLP~I~~~DPvar~~g~k~G~vvkI~R~s~tag~~v~YR~vv  215 (215)
T 1dzf_A          165 LKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM  215 (215)
T ss_dssp             HHHTTCCGGGSCEECTTCHHHHHHTCCTTCEEEEECTTCSSSTTCEEEEEC
T ss_pred             HHHcCCCHHHCCceeccChhhHHhCCcCCCEEEEEECCCCCCCceEEEEeC
Confidence            999999999999999999999999999999999999999999999999996

>1eik_A RNA polymerase subunit RPB5; RPBH, OCSP, NESG, protein structure initiative, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.78.1.1

Probab=100.00  E-value=2.8e-42  Score=250.95  Aligned_cols=76  Identities=34%  Similarity=0.577  Sum_probs=74.9

Q ss_pred             hhhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          102 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       102 LlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      |+||||+|+|||||++||+|||++||++|+++++|||||+.+||+|||||+++||||||+|+|+|||+||+||+|+
T Consensus         1 l~vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLP~I~~~DPvar~~G~k~GdVvkI~R~S~taG~~v~YR~Vv   76 (77)
T 1eik_A            1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKIIRKSPTAEEFVTYRLVQ   76 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTTSHHHHGGGCCTTCEEEEEEEETTTEEEEEEEECB
T ss_pred             CcccCccceecCCEEEcCHHHHHHHHHHcCCCHHHCCeeeCcCHhhHHhCCCCCCEEEEEECCCCCCCcEEEEEEE
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999996

>1hmj_A RPB5, protein (subunit H); RNA polymerase, archaea; NMR {Methanocaldococcus jannaschii} SCOP: d.78.1.1

Probab=100.00  E-value=4.8e-41  Score=245.00  Aligned_cols=74  Identities=34%  Similarity=0.653  Sum_probs=73.1

Q ss_pred             hcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          104 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       104 vNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      ||||+|+|||||++||+|||++||++|+++++|||||+.+||+|||||+++||||||+|+|+|||+|++||+|+
T Consensus         1 vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLPrI~~~DPvar~~G~k~GdVvkI~R~S~taG~~v~YR~Vv   74 (78)
T 1hmj_A            1 MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRKSPTAGVSIAYRLVI   74 (78)
T ss_pred             CCccceeeCCCeEECCHHHHHHHHHHcCCCHHHCCeeeCcCHhhHHhCCCCCCEEEEEECCCCCCCcEEEEEEE
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999996

>4ayb_H DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_H 2y0s_H 2waq_H 4b1o_H 4b1p_Z 2pmz_H 3hkz_H

Probab=100.00  E-value=1.4e-39  Score=239.57  Aligned_cols=79  Identities=28%  Similarity=0.456  Sum_probs=74.4

Q ss_pred             hhhhhhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447           99 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus        99 e~eLlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      .+.++||||+|+|||+|++||+||+++||++|+++++|||+|+.+||||+|||+++||||||+|+|+|||++++||+|+
T Consensus         4 ~~~~~~Ni~~H~LVPkH~vLs~eE~~~ll~~y~i~~~qLP~I~~~DPva~~~g~k~GdVvkI~R~S~tag~~~~YR~vv   82 (84)
T 4ayb_H            4 SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYGEVVSYRYVI   82 (84)
T ss_dssp             ----CCCCSSSSSCCEEEECCHHHHHHHHHHHTCCGGGSCCEESSSHHHHHHTCCTTCEEEEEEEETTTEEEEEEEEEE
T ss_pred             cccceecccccccCCCeEECCHHHHHHHHHHhcCCHhHCCeecccCHhHHhhCCCCCCEEEEEEcCCCCCccEEEEEEe
Confidence            3678999999999999999999999999999999999999999999999999999999999999999999999999996

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	177
d1eika_	77	d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA pol	2e-29
d1dzfa2	72	d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal do	7e-29
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	8e-17

>d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 77

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score =  101 bits (254), Expect = 2e-29
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 102 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 161
           +   I KH L P+H +L + E +++LK+     +QLP++   D +A+  G +RG +VK+ 
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKII 60

Query: 162 YSGEITESHVTYRCV 176
                 E  VTYR V
Sbjct: 61  RKSPTAEEFVTYRLV 75

>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 72

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: Eukaryotic RPB5 C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 99.8 bits (249), Expect = 7e-29
 Identities = 32/71 (45%), Positives = 46/71 (64%)

Query: 106 ITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGE 165
           IT H L PKH  L+  EK +LLK+Y ++E QLPR+ + D +A Y GL+RG+VVK+    E
Sbjct: 1   ITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSE 60

Query: 166 ITESHVTYRCV 176
            +  + +YR  
Sbjct: 61  TSGRYASYRIC 71

>d1dzfa1 c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 139

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Eukaryotic RPB5 N-terminal domain
family: Eukaryotic RPB5 N-terminal domain
domain: Eukaryotic RPB5 N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 70.6 bits (173), Expect = 8e-17
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 3/81 (3%)

Query: 37  RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYG---QDPDVDRLRISISHQS 93
           R+  R + + RTV EM+KDRGY +   E+ L ++DF+A Y      P    +    +   
Sbjct: 3   RNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTE 62

Query: 94  DPSKRITDLLVNITKHVLKPK 114
           +   +  D+     +   +P 
Sbjct: 63  ESISKFPDMGSLWVEFCDEPS 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	177
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	100.0
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	100.0
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	99.97
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	99.86

>d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=100.00  E-value=8.4e-38  Score=224.54  Aligned_cols=76  Identities=34%  Similarity=0.577  Sum_probs=74.7

Q ss_pred             hhhcCCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          102 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       102 LlvNIt~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      |.+||++|+|||+|++||+||++++|++|+++.+|||+|+.+||+|+|||+++||||||+|+|+|||.+++||+|+
T Consensus         1 l~~NI~~H~lVPkH~il~~ee~~~~l~~~~i~~~qLP~I~~~DPva~~~g~k~GdvvkI~R~S~tag~~~~YR~vv   76 (77)
T d1eika_           1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKIIRKSPTAEEFVTYRLVQ   76 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTTSHHHHGGGCCTTCEEEEEEEETTTEEEEEEEECB
T ss_pred             CCccccccccCCCeEEcCHHHHHHHHHHhcCCHHHCCeecccCHhhhhhCCcCCcEEEEEEcCCCCCCceEEEEEe
Confidence            6799999999999999999999999999999999999999999999999999999999999999999999999996

>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: Eukaryotic RPB5 C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.1e-35  Score=211.17  Aligned_cols=72  Identities=44%  Similarity=0.737  Sum_probs=71.1

Q ss_pred             CCcccccCCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          106 ITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       106 It~H~LVPkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      ||+|+|||+|++|++||++++|++|+++.+|||+|+.+||+|+|||+++||||||+|+|+|||.+++||+|+
T Consensus         1 It~H~lVPkH~~l~~eE~~~il~~y~i~~~qLP~I~~~DPva~~~g~~~GdvikI~R~s~tag~~~~YR~~V   72 (72)
T d1dzfa2           1 ITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM   72 (72)
T ss_dssp             GGGSTTSCEEEECCHHHHHHHHHHTTCCGGGSCEECTTCHHHHHHTCCTTCEEEEECTTCSSSTTCEEEEEC
T ss_pred             CCcCccCCCeEEcCHHHHHHHHHHhCCCHhHCCeecccCHhhhhcCCCCCCEEEEEEcCCCCCceeEEEEeC
Confidence            799999999999999999999999999999999999999999999999999999999999999999999996

>d1hmja_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.97  E-value=2.3e-31  Score=186.97  Aligned_cols=65  Identities=34%  Similarity=0.641  Sum_probs=64.3

Q ss_pred             CCceecCHHHHHHHHhhcCCCcCCCCCcccCChhhhhhCCCCCCEEEEEecCCCCccceEEEEeC
Q 030447          113 PKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  177 (177)
Q Consensus       113 PkH~vLs~eEk~~lL~~y~i~~~QLPrI~~sDPvary~Glk~GdVVKI~R~SetaG~~v~YR~V~  177 (177)
                      |+|++||+||+++||++|+++.+|||+|+.+||+|+|||+++||||||+|+|+|||.+++||+|+
T Consensus         1 PkH~il~~eE~~~ll~~y~i~~~qLP~I~~~DPva~~~g~k~GdvvkI~R~S~tag~~i~YR~vv   65 (68)
T d1hmja_           1 PKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRKSPTAGVSIAYRLVI   65 (68)
T ss_pred             CCCEECCHHHHHHHHHHhCCCHHHCCcccccCHHHHHhCCCCCcEEEEEEcCCCCCCceEEEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999996

>d1dzfa1 c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Eukaryotic RPB5 N-terminal domain
family: Eukaryotic RPB5 N-terminal domain
domain: Eukaryotic RPB5 N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=3.4e-23  Score=160.87  Aligned_cols=64  Identities=30%  Similarity=0.538  Sum_probs=59.0

Q ss_pred             ChhhhHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC---CCCCceeEeecCCCCCchh
Q 030447           35 GSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD---PDVDRLRISISHQSDPSKR   98 (177)
Q Consensus        35 ~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~sl~~F~~~y~~~---~~r~~L~~~~~~~~dp~~k   98 (177)
                      +++|++||||+||||+|||+||||.|+++|+++|+++|+++||++   |+|+.|+|++.+.+++.++
T Consensus         1 ~d~e~~rlfr~rrTv~EMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~p~r~~l~~~~~~~~~~~~k   67 (139)
T d1dzfa1           1 NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISK   67 (139)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHhcCCCcCCHHHHcCCHHHHHHHHccccCCcCHHHhcccCCCchhhhhc
Confidence            468999999999999999999999999999999999999999875   8999999999998876544