Citrus Sinensis ID: 026620

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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-------180-------190-------200-------210-------220-------230------
Protein Sequence
MEDGNGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccEEcHHcccccHHHHHHHHccccccccEEEEEEccccccccEEEEEccccEEcHHHHHHHHHHHHHccccEEEEEEEcccccHHHHHHHcccccEEEEEEEcEEEEEccccccccccEEccHHHHHHHHHHccccccccccccccccHHHHcccccccEEEEEEcccccccEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEcccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccEccHHHHcccHHHHHHHHcccccccccEEEEEccccccccEEEEEccccEEcHHHHHHHHHHHHHccccEEEEEEccEEcHHHHcccccccccEEEEEEHHHHcccHHHcccccEEEEccHHHHHHHHHHccccHHHccEEccccHHHHHHccccccEEEEEccccccccccEEEEEc
Coil and Loop (DISEMBL)
medgngydssmemeggngyngeptesclsgfvdngsrdsLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAiygqdpdvdrlrisishqsdpskrILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKhvlkpkhqvlTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYsgeiteshvtyrcvw
Flexible Loop (DISEMBL)
medgngydssMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRIsishqsdpskriLVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVlkpkhqvltdqekekLLKKysieekqlprmlKKDAIAQYYGLERGQVVKVtysgeiteshvtyrcvw
Low Complexity Region (SEG)
MEDGNGYDSSmemeggngyngePTESCLSGFVDNGsrdslryylsrrTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Disordered region (IsUnstruct)
***************************LSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISH****SKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTD*****LLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCV*
Disordered Region (DISOPRED)
************************************RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Disordered Region (DISEMBL)
**************GGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Disordered Region (DISPRO)
******YDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEDGNGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW
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	236	2.2.26 [Sep-21-2011]
Q9N5K2	211	DNA-directed RNA polymera	yes	no	0.834	0.933	0.341	6e-31
A8XGH1	211	DNA-directed RNA polymera	N/A	no	0.834	0.933	0.336	1e-30
Q757H7	215	DNA-directed RNA polymera	yes	no	0.838	0.920	0.374	1e-29
Q5R587	210	DNA-directed RNA polymera	yes	no	0.851	0.957	0.311	5e-28
Q9P4B9	215	DNA-directed RNA polymera	N/A	no	0.809	0.888	0.372	1e-27
P20434	215	DNA-directed RNA polymera	yes	no	0.834	0.916	0.361	1e-27
B0BNE2	210	DNA-directed RNA polymera	yes	no	0.851	0.957	0.306	1e-27
Q80UW8	210	DNA-directed RNA polymera	yes	no	0.851	0.957	0.306	1e-27
Q6CJ62	215	DNA-directed RNA polymera	yes	no	0.826	0.906	0.365	2e-27
Q6FQA6	215	DNA-directed RNA polymera	yes	no	0.809	0.888	0.367	2e-27

>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 =  134 bits (337), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 70/205 (34%), Positives = 125/205 (60%), Gaps = 8/205 (3%)

Query: 38  DSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQ 92
           ++ R +  R+TVL+M+ DRGY VA  E++  ++ F+  YG  P   +     L I ++H 
Sbjct: 7   ETYRLWRIRKTVLQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLTILVAHN 66

Query: 93  SDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--Q 150
            DP+ ++ V F     + +  I++I  Q+  ++ ++  I+++Q  +T  A +++G    +
Sbjct: 67  DDPADQMFVFFPEDAKIGIKTIKAICQQMQEQN-ISRAIIVVQTGMTPSAKQSIGDMAPK 125

Query: 151 FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYG 210
           + +E F   +L+VNIT+H L P+H V+T +EK +LL +Y +++ QLPR+ + D +A+Y+G
Sbjct: 126 YMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPVARYFG 185

Query: 211 LERGQVVKVTYSGEITESHVTYRCV 235
           L RGQVVK+    E    ++TYR V
Sbjct: 186 LRRGQVVKIIRPSETAGRYITYRLV 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|A8XGH1|RPAB1_CAEBR DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis briggsae GN=rpb-5 PE=3 SV=1

 Score =  132 bits (333), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 125/205 (60%), Gaps = 8/205 (3%)

Query: 38  DSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQ 92
           ++ R +  R+TVL+M+ DRGY VA  E++  ++ F+  +G  P   +     L I ++H 
Sbjct: 7   ETYRLWRIRKTVLQMVHDRGYLVAQEELDQPLETFKETFGDRPSEKKPARSDLTILVAHN 66

Query: 93  SDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--Q 150
            DP+ ++ V F     + +  I++I  Q+  ++ ++  I+++Q  +T  A +++G    +
Sbjct: 67  DDPADQMFVFFPEDTKIGIKTIKAICQQMQEQN-ISRAIIVVQTGMTPSAKQSIGDMAPK 125

Query: 151 FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYG 210
           + +E F   +L+VNIT+H L P+H V+T +EK +LL +Y +++ QLPR+ + D +A+Y+G
Sbjct: 126 YMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPVARYFG 185

Query: 211 LERGQVVKVTYSGEITESHVTYRCV 235
           L RGQVVK+    E    ++TYR V
Sbjct: 186 LRRGQVVKIIRPSETAGRYITYRLV 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|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 =  129 bits (325), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 79/211 (37%), Positives = 122/211 (57%), Gaps = 13/211 (6%)

Query: 34  NGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQS 93
           +  R+  R + + RTV EM++DRGY +   E++LS++DF+A Y  D      R  +S QS
Sbjct: 4   DNERNVSRLWRAFRTVKEMVRDRGYFITQEEVDLSLEDFKAKYC-DSMGRPQRKMMSFQS 62

Query: 94  DPSKRIL----------VVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQAT 143
           +P++  L          V FC    V +  +++ +  I  ++  TG I I QN IT  A 
Sbjct: 63  NPTEETLKKSPNMGSVWVEFCDEPSVGIKTMKNFVIHIGEKNFQTG-IFIYQNGITPSAL 121

Query: 144 KAV-GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKK 202
           K +  +    +E F  T L+VNIT H L PKH  L+D+EK++LLK+Y ++E QLPR+ + 
Sbjct: 122 KLLPSVAPATIETFNETALVVNITHHELVPKHIKLSDEEKKELLKRYRLKESQLPRIQRM 181

Query: 203 DAIAQYYGLERGQVVKVTYSGEITESHVTYR 233
           D +A Y GL+RG+VVK+    E +  + +YR
Sbjct: 182 DPVALYLGLKRGEVVKIIRKSETSGRYASYR 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|Q5R587|RPAB1_PONAB DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Pongo abelii GN=POLR2E PE=2 SV=1

 Score =  124 bits (311), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 122/209 (58%), Gaps = 8/209 (3%)

Query: 34  NGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLR-----IS 88
           +   ++ R +  R+T++++  DRGY V   E++ ++++FRA +G  P   R R     + 
Sbjct: 2   DDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVL 61

Query: 89  ISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-- 146
           ++H  DP+ ++ V F     V +  I+ +  Q +  + +T  ++++Q  +T  A +++  
Sbjct: 62  VAHNDDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVD 120

Query: 147 GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 206
              ++ +E F   +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A
Sbjct: 121 MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA 180

Query: 207 QYYGLERGQVVKVTYSGEITESHVTYRCV 235
           +Y+G++RGQVVK+    E    ++TYR V
Sbjct: 181 RYFGIKRGQVVKIIRPSETAGRYITYRLV 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.

Pongo abelii (taxid: 9601)

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

 Score =  123 bits (309), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 76/204 (37%), Positives = 115/204 (56%), Gaps = 13/204 (6%)

Query: 41  RYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKR-- 98
           R + + RTV EM++DRGY +   EI+LS++DF+  Y  D      R  +S QS+P++   
Sbjct: 11  RLWRAFRTVKEMVRDRGYFITQEEIDLSLEDFKVKYC-DSMGKPQRKMMSFQSNPTEESI 69

Query: 99  --------ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ 150
                   + V FC    V V  +++ +  I  ++  TG I I Q+ IT  A K +    
Sbjct: 70  EKFPEMGSLWVEFCDEASVGVKTMKNFVVHITEKNFQTG-IFIYQSGITPSANKILPTAA 128

Query: 151 FKV-EMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYY 209
             V E F    L+VNIT H L PKH  L+D EK++LLK+Y ++E QLPR+ + D +A Y 
Sbjct: 129 PAVIETFPEASLVVNITHHELVPKHIRLSDAEKKELLKRYRLKESQLPRIQRMDPVALYL 188

Query: 210 GLERGQVVKVTYSGEITESHVTYR 233
           GL+RG+V+K+    E +  + +YR
Sbjct: 189 GLKRGEVIKIIRKSETSGRYASYR 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|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 =  123 bits (308), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 76/210 (36%), Positives = 115/210 (54%), Gaps = 13/210 (6%)

Query: 35  GSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSD 94
             R+  R + + RTV EM+KDRGY +   E+ L ++DF+A Y  D      R  +S Q++
Sbjct: 5   NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYC-DSMGRPQRKMMSFQAN 63

Query: 95  PSKR----------ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATK 144
           P++           + V FC    V V  +++ +  I  ++  TG I + QN IT  A K
Sbjct: 64  PTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMK 122

Query: 145 AV-GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKD 203
            V  +    +E F    L+VNIT H L PKH  L+  EK +LLK+Y ++E QLPR+ + D
Sbjct: 123 LVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRAD 182

Query: 204 AIAQYYGLERGQVVKVTYSGEITESHVTYR 233
            +A Y GL+RG+VVK+    E +  + +YR
Sbjct: 183 PVALYLGLKRGEVVKIIRKSETSGRYASYR 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|B0BNE2|RPAB1_RAT DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus GN=Polr2e PE=2 SV=1

 Score =  123 bits (308), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/209 (30%), Positives = 122/209 (58%), Gaps = 8/209 (3%)

Query: 34  NGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLR-----IS 88
           +   ++ R +  R+T++++  DRGY V   E++ ++++F+A +G  P   R R     + 
Sbjct: 2   DDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVL 61

Query: 89  ISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-- 146
           ++H  DP+ ++ V F     V +  I+ +  Q +  + +T  ++++Q  +T  A +++  
Sbjct: 62  VAHNDDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVD 120

Query: 147 GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 206
              ++ +E F   +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A
Sbjct: 121 MAPKYVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQLPRIQAGDPVA 180

Query: 207 QYYGLERGQVVKVTYSGEITESHVTYRCV 235
           +Y+G++RGQVVK+    E    ++TYR V
Sbjct: 181 RYFGIKRGQVVKIIRPSETAGRYITYRLV 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.

Rattus norvegicus (taxid: 10116)

>sp|Q80UW8|RPAB1_MOUSE DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Mus musculus GN=Polr2e PE=2 SV=1

 Score =  123 bits (308), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/209 (30%), Positives = 122/209 (58%), Gaps = 8/209 (3%)

Query: 34  NGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLR-----IS 88
           +   ++ R +  R+T++++  DRGY V   E++ ++++F+A +G  P   R R     + 
Sbjct: 2   DDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVL 61

Query: 89  ISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-- 146
           ++H  DP+ ++ V F     V +  I+ +  Q +  + +T  ++++Q  +T  A +++  
Sbjct: 62  VAHNDDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVD 120

Query: 147 GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 206
              ++ +E F   +LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A
Sbjct: 121 MAPKYVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQLPRIQAGDPVA 180

Query: 207 QYYGLERGQVVKVTYSGEITESHVTYRCV 235
           +Y+G++RGQVVK+    E    ++TYR V
Sbjct: 181 RYFGIKRGQVVKIIRPSETAGRYITYRLV 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.

Mus musculus (taxid: 10090)

>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 =  122 bits (307), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 76/208 (36%), Positives = 118/208 (56%), Gaps = 13/208 (6%)

Query: 37  RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPS 96
           R+  R + + +TV EM++DRGY +   EI+LS++DF+A Y  D      R  +S QS+P+
Sbjct: 7   RNISRLWRAFKTVKEMVRDRGYFITQEEIDLSLEDFKAKYC-DSMGKPQRKMMSFQSNPT 65

Query: 97  KR----------ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV 146
           +           + V FC    V V  +++ +  I  ++  TG I I Q+ IT  A K +
Sbjct: 66  EESIEKFPEMGSLWVEFCDEASVGVKTMKNFVVHITEKNFQTG-IFIYQSGITPSANKIL 124

Query: 147 GLFQFKV-EMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
                 V E F    L+VNIT H L PKH  L++ EK++LLK+Y ++E QLPR+ + D +
Sbjct: 125 PTAAPAVIETFPEASLVVNITHHELVPKHIRLSEAEKKELLKRYRLKESQLPRIQRMDPV 184

Query: 206 AQYYGLERGQVVKVTYSGEITESHVTYR 233
           A Y GL+RG+V+K+    E +  + +YR
Sbjct: 185 ALYLGLKRGEVIKIIRKSETSGRYASYR 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|Q6FQA6|RPAB1_CANGA DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=RPB5 PE=3 SV=1

 Score =  122 bits (306), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 75/204 (36%), Positives = 114/204 (55%), Gaps = 13/204 (6%)

Query: 41  RYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKR-- 98
           R + + RTV EM++DRGY +A  E++L+++DF+  Y  D      R  +S Q++P++   
Sbjct: 11  RLWRTFRTVKEMVRDRGYFIAQEELDLTLEDFKVKYC-DSMGRAQRKMMSFQANPTEESM 69

Query: 99  --------ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-GLF 149
                   + V FC    V V  +++ +  I  +   TG I I QN IT  A K V  + 
Sbjct: 70  TKFPDMGTLWVEFCDEPSVGVKTMKTFVIHIQEKQFQTG-IFIYQNNITPSAMKLVPSIP 128

Query: 150 QFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYY 209
              +E F    L+VNIT H L PKH  L ++EK +LLK+Y ++E QLPR+ + D +A Y 
Sbjct: 129 PATIETFHEAALVVNITHHDLVPKHIRLNEEEKAELLKRYRLKESQLPRIQRADPVALYL 188

Query: 210 GLERGQVVKVTYSGEITESHVTYR 233
           GL+RG+VVK+    E    + +YR
Sbjct: 189 GLKRGEVVKIIRKSETAGRYASYR 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.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

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	236
255576548	238	DNA-directed RNA polymerase II, putative	0.966	0.957	0.713	1e-94
351723899	237	uncharacterized protein LOC100306033 [Gl	0.902	0.898	0.746	3e-90
224139746	216	predicted protein [Populus trichocarpa]	0.911	0.995	0.725	2e-89
297739911	330	unnamed protein product [Vitis vinifera]	0.957	0.684	0.683	4e-89
359482221	229	PREDICTED: DNA-directed RNA polymerases	0.949	0.978	0.689	1e-88
357509489	248	DNA-directed RNA polymerases I, II, and	0.991	0.943	0.670	2e-88
388510192	248	unknown [Medicago truncatula]	0.991	0.943	0.666	7e-88
449437743	227	PREDICTED: DNA-directed RNA polymerases	0.932	0.969	0.674	1e-87
297817026	222	eukaryotic rpb5 RNA polymerase subunit f	0.889	0.945	0.671	1e-80
15230206	222	rpb5 RNA polymerase subunit family prote	0.915	0.972	0.646	2e-79

>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 =  352 bits (902), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 167/234 (71%), Positives = 201/234 (85%), Gaps = 6/234 (2%)

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

Query: 63  SEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIV 122
           SEI+LS+Q+FRAI+G +PD+DRL+ S +H SDPSKR+LV+F GPGI+KV+ IR+I  QIV
Sbjct: 65  SEIDLSLQEFRAIHGPNPDIDRLKFSATHTSDPSKRMLVLFGGPGIIKVSTIRAIAGQIV 124

Query: 123 NRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEK 182
           N+D+LTGLIL+LQNQIT+QA KAV LF+FKVEMFQITDLLVNITKHVLKPKHQVLTD+EK
Sbjct: 125 NKDSLTGLILVLQNQITNQAMKAVDLFKFKVEMFQITDLLVNITKHVLKPKHQVLTDREK 184

Query: 183 EKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           +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|351723899|ref|NP_001236527.1| uncharacterized protein LOC100306033 [Glycine max] gi|255627335|gb|ACU14012.1| unknown [Glycine max]

 Score =  337 bits (863), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 159/213 (74%), Positives = 185/213 (86%)

Query: 24  TESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVD 83
            + CLS FVDNGS +S RYYLSRRT LEMLKDRGY++   EI+LS+ DFR I+GQ PD D
Sbjct: 25  AKGCLSKFVDNGSVESHRYYLSRRTTLEMLKDRGYSIPSHEIDLSLSDFRDIHGQFPDPD 84

Query: 84  RLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQAT 143
           RLR+S++H ++ SKRILV+FCGPG+VKV  IR+   QI+NRDTLTGLILI++N ITSQA 
Sbjct: 85  RLRLSLTHATNSSKRILVIFCGPGVVKVTAIRNTAGQIINRDTLTGLILIVENHITSQAL 144

Query: 144 KAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKD 203
           KAV LF FKVE+FQITDLLVNITKHVLKPKHQVLTD++K  LLKKY+IEEKQLPRML+ D
Sbjct: 145 KAVNLFSFKVEIFQITDLLVNITKHVLKPKHQVLTDKQKINLLKKYNIEEKQLPRMLQTD 204

Query: 204 AIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           AIA+YYGLERGQVVKVTYSGE+T+ HVTYRCVW
Sbjct: 205 AIARYYGLERGQVVKVTYSGEVTQMHVTYRCVW 237

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  334 bits (856), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 156/215 (72%), Positives = 189/215 (87%)

Query: 22  EPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPD 81
           E    CLS FVD GS +S RYYLSRRTVLEMLKDRGY+V  SEI++S+QDFR +YGQ+PD
Sbjct: 2   ESLGRCLSSFVDEGSTESHRYYLSRRTVLEMLKDRGYSVPSSEIDISLQDFRGVYGQNPD 61

Query: 82  VDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQ 141
           ++ L+ S +H+SDPSKR+LV+FCG G+VKV +IR I  QI +RD+LTGLIL+LQN IT+Q
Sbjct: 62  IELLKFSATHKSDPSKRMLVIFCGLGVVKVGMIRLITVQITDRDSLTGLILVLQNNITNQ 121

Query: 142 ATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLK 201
           A KA+ LF+FK+E+FQITDLLVNITKH+LKPKHQVL++Q K++LLKKYSIEEKQLPR+LK
Sbjct: 122 AMKALDLFKFKIEIFQITDLLVNITKHILKPKHQVLSEQAKQRLLKKYSIEEKQLPRLLK 181

Query: 202 KDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           KDAI++YYGLERGQVVKVTY G+IT SHVTYRCVW
Sbjct: 182 KDAISRYYGLERGQVVKVTYDGDITGSHVTYRCVW 216

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  333 bits (854), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 158/231 (68%), Positives = 193/231 (83%), Gaps = 5/231 (2%)

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

Query: 66  NLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRD 125
           ++S+QDFR+ Y Q PD DRLRIS + +SDPSK+ILV+FCGP +VKVN IRSI +QIVN+D
Sbjct: 160 DISLQDFRSFYSQKPDPDRLRISAALRSDPSKKILVIFCGPDVVKVNAIRSIATQIVNKD 219

Query: 126 TLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL 185
           +L+ LIL+LQN ITSQA KAV LF F+VE FQITDLLVNITKHVLKPKH+VLTDQEK KL
Sbjct: 220 SLSKLILVLQNHITSQALKAVDLFSFQVEKFQITDLLVNITKHVLKPKHRVLTDQEKNKL 279

Query: 186 LKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           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 =  331 bits (849), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 158/229 (68%), Positives = 192/229 (83%), Gaps = 5/229 (2%)

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

Query: 68  SVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTL 127
           S+QDFR+ Y Q PD DRLRIS + +SDPSK+ILV+FCGP +VKVN IRSI +QIVN+D+L
Sbjct: 61  SLQDFRSFYSQKPDPDRLRISAALRSDPSKKILVIFCGPDVVKVNAIRSIATQIVNKDSL 120

Query: 128 TGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLK 187
           + LIL+LQN ITSQA KAV LF F+VE FQITDLLVNITKHVLKPKH+VLTDQEK KLLK
Sbjct: 121 SKLILVLQNHITSQALKAVDLFSFQVEKFQITDLLVNITKHVLKPKHRVLTDQEKNKLLK 180

Query: 188 KYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           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|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 =  331 bits (848), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 165/246 (67%), Positives = 196/246 (79%), Gaps = 12/246 (4%)

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

Query: 51  EMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVK 110
           EMLKDRGY++   EI LS+ DFR I+GQ PDVDRLR++ +H ++PSKRILVVF GPGIVK
Sbjct: 63  EMLKDRGYSIPSDEIQLSLDDFRQIHGQSPDVDRLRLTATHATNPSKRILVVFSGPGIVK 122

Query: 111 VNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVL 170
           VN +R I  QIVNR++LTGLILI+QNQITSQA KAV L  FKVE+FQITDLLVN TKHVL
Sbjct: 123 VNGVRDIAGQIVNRESLTGLILIVQNQITSQALKAVNLLSFKVEIFQITDLLVNATKHVL 182

Query: 171 KPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHV 230
           KPKHQVLTD++K+ LLKKY I+EKQLPRML+ DAIA+YYGL+RGQVVKVTY+GEIT+ HV
Sbjct: 183 KPKHQVLTDKQKKNLLKKYDIQEKQLPRMLQTDAIARYYGLQRGQVVKVTYTGEITQMHV 242

Query: 231 TYRCVW 236
           TYRCVW
Sbjct: 243 TYRCVW 248

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  329 bits (843), Expect = 7e-88,   Method: Compositional matrix adjust.
 Identities = 164/246 (66%), Positives = 195/246 (79%), Gaps = 12/246 (4%)

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

Query: 51  EMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVK 110
           EMLKDRGY++   EI LS+ DFR I+GQ PDVDRLR++ +H ++PSKRILVVF GPGIVK
Sbjct: 63  EMLKDRGYSIPSDEIQLSLDDFRQIHGQSPDVDRLRLTATHATNPSKRILVVFSGPGIVK 122

Query: 111 VNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVL 170
           VN +R I  QIVNR++LTGLILI+QNQITSQA KAV L  FKVE+ QITDLLVN TKHVL
Sbjct: 123 VNGVRDIAGQIVNRESLTGLILIVQNQITSQALKAVNLLSFKVEILQITDLLVNATKHVL 182

Query: 171 KPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHV 230
           KPKHQVLTD++K+ LLKKY I+EKQLPRML+ DAIA+YYGL+RGQVVKVTY+GEIT+ HV
Sbjct: 183 KPKHQVLTDKQKKNLLKKYDIQEKQLPRMLQTDAIARYYGLQRGQVVKVTYTGEITQMHV 242

Query: 231 TYRCVW 236
           TYRCVW
Sbjct: 243 TYRCVW 248

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449437743|ref|XP_004136650.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Cucumis sativus] gi|449524637|ref|XP_004169328.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Cucumis sativus]

 Score =  328 bits (840), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 151/224 (67%), Positives = 186/224 (83%), Gaps = 4/224 (1%)

Query: 17  NGYNGEPTE----SCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDF 72
           +G+  EP      +CLS ++D+G+ +S RY+LSRRTV+EMLKDRGY +    I+ S+Q F
Sbjct: 4   DGFEAEPNPVEFGTCLSSYIDDGTTESHRYFLSRRTVVEMLKDRGYTINSPNIDFSLQQF 63

Query: 73  RAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLIL 132
           R  +GQ PDVDRL++S +H SDPSKR+LVVFCG G VKVN IR+I  QI N+D+L GLIL
Sbjct: 64  RETFGQFPDVDRLKLSAAHHSDPSKRVLVVFCGTGAVKVNAIRNIAGQIANKDSLHGLIL 123

Query: 133 ILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE 192
           I+QNQIT+QA KAV LF FKVE+FQITDLLVNITKH LKP HQVLT++EK+KLLK+YSIE
Sbjct: 124 IVQNQITNQAMKAVELFSFKVEIFQITDLLVNITKHALKPNHQVLTEEEKQKLLKQYSIE 183

Query: 193 EKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           EKQLPRML+ DAIA+YYGLE+GQVVKVTY G++T +H+TYRCVW
Sbjct: 184 EKQLPRMLRTDAIARYYGLEKGQVVKVTYDGDMTRAHITYRCVW 227

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  305 bits (780), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 141/210 (67%), Positives = 176/210 (83%)

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

Query: 87  ISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV 146
           IS  H+SD SK++ VVF G G+VKVN IRSI + +++++T+TGLIL+LQ+Q+T QA KA+
Sbjct: 73  ISAQHRSDSSKKVKVVFFGTGMVKVNAIRSIAADVLSQETVTGLILVLQSQVTKQAMKAI 132

Query: 147 GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 206
            LF FKVE+FQITDLLVNITKH LKP+H+VL D+EK  LLKK+SIEEKQLPR+ KKDAI 
Sbjct: 133 ELFSFKVEIFQITDLLVNITKHALKPQHRVLNDKEKTTLLKKFSIEEKQLPRISKKDAIV 192

Query: 207 QYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           +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

>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 =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 141/218 (64%), Positives = 179/218 (82%), Gaps = 2/218 (0%)

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  DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQI 138
            PDVDRLRIS  H+SD +K++ +VF G  +VKVN IRS+++ I++++T+TGLIL+LQN +
Sbjct: 65  RPDVDRLRISALHRSDSTKKVKIVFFGTSMVKVNAIRSVVADILSQETITGLILVLQNHV 124

Query: 139 TSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPR 198
           T+QA KA+ LF FKVE+FQITDLLVNITKH LKP+HQVL D+EK  LLKK+SIEEKQLPR
Sbjct: 125 TNQALKAIELFSFKVEIFQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQLPR 184

Query: 199 MLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW 236
           + 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

---

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	236
TAIR|locus:2080650	222	NRPE5 [Arabidopsis thaliana (t	0.889	0.945	0.619	4.4e-68
TAIR|locus:2040257	218	RPB5D ""RNA polymerase II fift	0.796	0.862	0.670	1.5e-65
TAIR|locus:2096971	233	RPB5E ""RNA polymerase II fift	0.889	0.901	0.447	3.8e-46
WB|WBGene00019246	211	rpb-5 [Caenorhabditis elegans	0.792	0.886	0.348	2.1e-29
TAIR|locus:2087842	205	NRPB5 [Arabidopsis thaliana (t	0.792	0.912	0.357	2.4e-28
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.792	0.890	0.328	2.2e-27
MGI|MGI:1913670	210	Polr2e "polymerase (RNA) II (D	0.792	0.890	0.323	3.5e-27
RGD|1589817	210	Polr2e "polymerase (RNA) II (D	0.792	0.890	0.323	3.5e-27
UNIPROTKB|F2Z4J4	210	POLR2E "DNA-directed RNA polym	0.792	0.890	0.323	4.5e-27
UNIPROTKB|I3LSI7	210	POLR2E "Uncharacterized protei	0.792	0.890	0.323	4.5e-27

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

 Score = 691 (248.3 bits), Expect = 4.4e-68, P = 4.4e-68
 Identities = 130/210 (61%), Positives = 165/210 (78%)

Query:    27 CLSGFVDNGXXXXXXXXXXXXTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLR 86
             CLS +VD                L+ML+DRGY V+  +INLS+ DFR +YG+ PDVDRLR
Sbjct:    13 CLSKYVDLSSEESHRYYLARRNGLQMLRDRGYEVSDEDINLSLHDFRTVYGERPDVDRLR 72

Query:    87 ISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV 146
             IS  H+SD +K++ +VF G  +VKVN IRS+++ I++++T+TGLIL+LQN +T+QA KA+
Sbjct:    73 ISALHRSDSTKKVKIVFFGTSMVKVNAIRSVVADILSQETITGLILVLQNHVTNQALKAI 132

Query:   147 GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 206
              LF FKVE+FQITDLLVNITKH LKP+HQVL D+EK  LLKK+SIEEKQLPR+ KKDAI 
Sbjct:   133 ELFSFKVEIFQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQLPRISKKDAIV 192

Query:   207 QYYGLERGQVVKVTYSGEITESHVTYRCVW 236
             +YYGLE+GQVVKV Y GE+TESHV +RCVW
Sbjct:   193 RYYGLEKGQVVKVNYRGELTESHVAFRCVW 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 = 667 (239.9 bits), Expect = 1.5e-65, P = 1.5e-65
 Identities = 126/188 (67%), Positives = 157/188 (83%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPG 107
             T +EML+DRGY V+  +INLS+Q FRA+YG+ PDVD LRIS  H+ D SK+I VVFCG G
Sbjct:    30 TTMEMLRDRGYDVSDEDINLSLQQFRALYGEHPDVDLLRISAKHRFDSSKKISVVFCGTG 89

Query:   108 IVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITK 167
             IVKVN +R I + +++R+ +TGLIL+LQ+ IT+QA KAV LF FKVE+F+ITDLLVN++K
Sbjct:    90 IVKVNAMRVIAADVLSRENITGLILVLQSHITNQALKAVELFSFKVELFEITDLLVNVSK 149

Query:   168 HVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 227
             HVL+PKHQVL D+EKE LLKK+SIEEKQLPR+  KD I +YYGLE GQV+KVTY  E++E
Sbjct:   150 HVLRPKHQVLNDKEKESLLKKFSIEEKQLPRLSSKDPIVRYYGLETGQVMKVTYKDELSE 209

Query:   228 SHVTYRCV 235
             SHVTYRCV
Sbjct:   210 SHVTYRCV 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 = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 94/210 (44%), Positives = 142/210 (67%)

Query:    26 SCLSGFVDNGXXXXXXXXXXXXTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRL 85
             +C+S   D G            T  EML+DRGY V  +E++L++ +FR+++G+ P+++RL
Sbjct:    23 NCISKTEDTGGIESKRFYLARTTAFEMLRDRGYEVNEAELSLTLSEFRSVFGEKPELERL 82

Query:    86 RISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKA 145
             RI +  +SDP K+ILVVF G   + V  +R++  QI N   L  +IL+LQ+++   A KA
Sbjct:    83 RICVPLRSDPKKKILVVFMGTEPITVKSVRALHIQISNNVGLHAMILVLQSKMNHFAQKA 142

Query:   146 VGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
             +  F F VE F I DLLVNITKH+ +PK ++L  +EKE+LL+K+++E+KQLP + +KD+ 
Sbjct:   143 LTTFPFTVETFPIEDLLVNITKHIQQPKIEILNKEEKEQLLRKHALEDKQLPYLQEKDSF 202

Query:   206 AQYYGLERGQVVKVTYSGEITESHVTYRCV 235
              +YYGL++ QVVK+TYS E     VTYRC+
Sbjct:   203 VRYYGLKKKQVVKITYSKEPVGDFVTYRCI 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

WB|WBGene00019246 rpb-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 68/195 (34%), Positives = 119/195 (61%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQSDPSKRILVV 102
             TVL+M+ DRGY VA  E++  ++ F+  YG  P   +     L I ++H  DP+ ++ V 
Sbjct:    17 TVLQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLTILVAHNDDPADQMFVF 76

Query:   103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--QFKVEMFQITD 160
             F     + +  I++I  Q+  ++ ++  I+++Q  +T  A +++G    ++ +E F   +
Sbjct:    77 FPEDAKIGIKTIKAICQQMQEQN-ISRAIIVVQTGMTPSAKQSIGDMAPKYMLEHFLEAE 135

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
             L+VNIT+H L P+H V+T +EK +LL +Y +++ QLPR+ + D +A+Y+GL RGQVVK+ 
Sbjct:   136 LMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLPRIQQCDPVARYFGLRRGQVVKII 195

Query:   221 YSGEITESHVTYRCV 235
                E    ++TYR V
Sbjct:   196 RPSETAGRYITYRLV 210

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

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0032502 "developmental process" evidence=IMP

TAIR|locus:2087842 NRPB5 [Arabidopsis thaliana (taxid:3702)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 68/190 (35%), Positives = 118/190 (62%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPG 107
             T+++ML+DRGY +A SE+ ++ Q F   +G +   + L    + ++D S ++ + F    
Sbjct:    16 TLMQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKRNDNSDQLYIFFPDEA 75

Query:   108 IVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--QFKVEMFQITDLLVNI 165
              V V  ++   +++ + +    ++++ QN +T  A   +     +F +E+FQ  ++LVNI
Sbjct:    76 KVGVKTMKMYTNRMKSENVFRAILVVQQN-LTPFARTCISEISSKFHLEVFQEAEMLVNI 134

Query:   166 TKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEI 225
              +HVL P+HQVLT +EK+ LL++Y+++E QLPR+   D IA+Y+GL+RGQVVK+    E 
Sbjct:   135 KEHVLVPEHQVLTTEEKKTLLERYTVKETQLPRIQVTDPIARYFGLKRGQVVKIIRPSET 194

Query:   226 TESHVTYRCV 235
                +VTYR V
Sbjct:   195 AGRYVTYRYV 204

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

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0000418 "DNA-directed RNA polymerase IV complex" evidence=IPI

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

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

GO:0051604 "protein maturation" evidence=RCA

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

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 64/195 (32%), Positives = 116/195 (59%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQSDPSKRILVV 102
             T++++  DRGY V   E++ ++++FRA +G  P   R     L + ++H  DP+ ++ V 
Sbjct:    16 TIMQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVF 75

Query:   103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKA-VGLF-QFKVEMFQITD 160
             F     V +  I+ +  Q +  + +T  ++++Q  +T  A ++ V +  ++ +E F   +
Sbjct:    76 FPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQE 134

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
             LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+ 
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKII 194

Query:   221 YSGEITESHVTYRCV 235
                E    ++TYR V
Sbjct:   195 RPSETAGRYITYRLV 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

MGI|MGI:1913670 Polr2e "polymerase (RNA) II (DNA directed) polypeptide E" [Mus musculus (taxid:10090)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 63/195 (32%), Positives = 116/195 (59%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQSDPSKRILVV 102
             T++++  DRGY V   E++ ++++F+A +G  P   R     L + ++H  DP+ ++ V 
Sbjct:    16 TIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVF 75

Query:   103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKA-VGLF-QFKVEMFQITD 160
             F     V +  I+ +  Q +  + +T  ++++Q  +T  A ++ V +  ++ +E F   +
Sbjct:    76 FPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQE 134

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
             LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+ 
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRESQLPRIQAGDPVARYFGIKRGQVVKII 194

Query:   221 YSGEITESHVTYRCV 235
                E    ++TYR V
Sbjct:   195 RPSETAGRYITYRLV 209

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

RGD|1589817 Polr2e "polymerase (RNA) II (DNA directed) polypeptide E" [Rattus norvegicus (taxid:10116)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 63/195 (32%), Positives = 116/195 (59%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQSDPSKRILVV 102
             T++++  DRGY V   E++ ++++F+A +G  P   R     L + ++H  DP+ ++ V 
Sbjct:    16 TIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVF 75

Query:   103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKA-VGLF-QFKVEMFQITD 160
             F     V +  I+ +  Q +  + +T  ++++Q  +T  A ++ V +  ++ +E F   +
Sbjct:    76 FPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQE 134

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
             LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+ 
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRESQLPRIQAGDPVARYFGIKRGQVVKII 194

Query:   221 YSGEITESHVTYRCV 235
                E    ++TYR V
Sbjct:   195 RPSETAGRYITYRLV 209

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=ISO;ISS

GO:0005634 "nucleus" evidence=IEA;ISO;ISS

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

 Score = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 63/195 (32%), Positives = 116/195 (59%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQSDPSKRILVV 102
             T++++  DRGY V   E++ ++++F+A +G  P   R     L + ++H  DP+ ++ V 
Sbjct:    16 TIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVF 75

Query:   103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKA-VGLF-QFKVEMFQITD 160
             F     V +  I+ +  Q +  + +T  ++++Q  +T  A ++ V +  ++ +E F   +
Sbjct:    76 FPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQE 134

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
             LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+ 
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKII 194

Query:   221 YSGEITESHVTYRCV 235
                E    ++TYR V
Sbjct:   195 RPSETAGRYITYRLV 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 = 304 (112.1 bits), Expect = 4.5e-27, P = 4.5e-27
 Identities = 63/195 (32%), Positives = 116/195 (59%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRISISHQSDPSKRILVV 102
             T++++  DRGY V   E++ ++++F+A +G  P   R     L + ++H  DP+ ++ V 
Sbjct:    16 TIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVF 75

Query:   103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKA-VGLF-QFKVEMFQITD 160
             F     V +  I+ +  Q +  + +T  ++++Q  +T  A ++ V +  ++ +E F   +
Sbjct:    76 FPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQE 134

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
             LL+NIT+H L P+H V+T +E  +LL +Y + E QLPR+   D +A+Y+G++RGQVVK+ 
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKII 194

Query:   221 YSGEITESHVTYRCV 235
                E    ++TYR V
Sbjct:   195 RPSETAGRYITYRLV 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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5R587	RPAB1_PONAB	No assigned EC number	0.3110	0.8516	0.9571	yes	no
Q2T9T3	RPAB1_BOVIN	No assigned EC number	0.3014	0.8516	0.9571	yes	no
B0BNE2	RPAB1_RAT	No assigned EC number	0.3062	0.8516	0.9571	yes	no
Q757H7	RPAB1_ASHGO	No assigned EC number	0.3744	0.8389	0.9209	yes	no
Q09191	RPAB1_SCHPO	No assigned EC number	0.3448	0.8305	0.9333	yes	no
Q6CJ62	RPAB1_KLULA	No assigned EC number	0.3653	0.8262	0.9069	yes	no
Q80UW8	RPAB1_MOUSE	No assigned EC number	0.3062	0.8516	0.9571	yes	no
P20434	RPAB1_YEAST	No assigned EC number	0.3619	0.8347	0.9162	yes	no
Q6CA26	RPAB1_YARLI	No assigned EC number	0.3523	0.8347	0.9292	yes	no
Q6FQA6	RPAB1_CANGA	No assigned EC number	0.3676	0.8093	0.8883	yes	no
P19388	RPAB1_HUMAN	No assigned EC number	0.3062	0.8516	0.9571	yes	no
Q6BIJ0	RPAB1_DEBHA	No assigned EC number	0.3380	0.8474	0.9345	yes	no
Q9N5K2	RPAB1_CAEEL	No assigned EC number	0.3414	0.8347	0.9336	yes	no

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

Fail to connect to STRING server

---

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	236
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	1e-115
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	1e-42
pfam01191	74	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-	3e-36
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	3e-24
COG2012	80	COG2012, RPB5, DNA-directed RNA polymerase, subuni	8e-20
PRK09570	79	PRK09570, rpoH, DNA-directed RNA polymerase subuni	1e-14

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

 Score =  327 bits (840), Expect = e-115
 Identities = 107/207 (51%), Positives = 146/207 (70%), Gaps = 3/207 (1%)

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

Query: 92  QSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ- 150
           +SDPSK+ILV F     V V  I++     +  + ++  IL+LQ+++T  A +A+  F  
Sbjct: 61  RSDPSKKILVFFPEEEKVGVKTIKTYAE-RMKDENVSRAILVLQSKLTPFAKQALSEFNS 119

Query: 151 -FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYY 209
            FK+E+FQ T+LLVNITKHVL PKHQVLTD+EK+ LLK+Y+++E QLPR+   D IA+YY
Sbjct: 120 KFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRIQVSDPIARYY 179

Query: 210 GLERGQVVKVTYSGEITESHVTYRCVW 236
           GL+RGQVVK+    E    +VTYRCV 
Sbjct: 180 GLKRGQVVKIIRPSETAGRYVTYRCVV 206

Length = 206

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

 Score =  143 bits (361), Expect = 1e-42
 Identities = 78/200 (39%), Positives = 115/200 (57%), Gaps = 7/200 (3%)

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

Query: 100 LVVFCGPGIVKVNV--IRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--QFKVEM 155
           +V F      K  V  IR +  ++   D +   IL+ QN +T  A  A+     +  +E 
Sbjct: 67  IVYFADE-TKKTGVKPIRELTEKMEEHD-IQRAILVTQNVLTPFAKDAILEAAPRHIIEN 124

Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQ 215
           F  T+LLVNITKH L PKH  LTD EK  LL++Y ++E QLPR+   D +A+Y+GL +GQ
Sbjct: 125 FLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRIQSADPVARYFGLSKGQ 184

Query: 216 VVKVTYSGEITESHVTYRCV 235
           VVK+    E    +VTYR V
Sbjct: 185 VVKIIRPSETAGRYVTYRLV 204

Length = 205

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

 Score =  122 bits (308), Expect = 3e-36
 Identities = 41/74 (55%), Positives = 55/74 (74%)

Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222
           VNITKH L PKH+VL+++EK+KLLK+Y I+E+QLPR+L  D +A+Y G + G VVK+T  
Sbjct: 1   VNITKHELVPKHEVLSEEEKKKLLKRYKIKEEQLPRILATDPVARYLGAKPGDVVKITRK 60

Query: 223 GEITESHVTYRCVW 236
            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|217772 pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-terminal domain

 Score = 91.9 bits (229), Expect = 3e-24
 Identities = 36/88 (40%), Positives = 52/88 (59%), Gaps = 2/88 (2%)

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

Query: 94  DPSKRILVVFCGPGIVKVNVIRSIISQI 121
           DPS RI V FC    V V  IR+ + ++
Sbjct: 64  DPSGRIYVFFCEEEKVGVKTIRTFVERM 91

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

 Score = 80.1 bits (198), Expect = 8e-20
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 160 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKV 219
            L  N+  H L P+H+VL+++E +++LK+  IE +QLP++   D +A+  G + G VVK+
Sbjct: 4   MLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKALGAKPGDVVKI 63

Query: 220 TYSGEITESHVTYRCV 235
                     V YR V
Sbjct: 64  VRKSPTAGESVYYRLV 79

Length = 80

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

 Score = 66.4 bits (163), Expect = 1e-14
 Identities = 24/73 (32%), Positives = 43/73 (58%)

Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222
            ++  H L P+H++L+++E +KLLK+Y I+ +QLP++   D + +  G + G V+K+   
Sbjct: 4   FDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRK 63

Query: 223 GEITESHVTYRCV 235
                  V YR V
Sbjct: 64  SPTAGEAVYYRLV 76

Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	236
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
PRK09570	79	rpoH DNA-directed RNA polymerase subunit H; Review	100.0
PF01191	74	RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal do	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	99.96
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	95.86

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

Probab=100.00  E-value=1.6e-79  Score=529.06  Aligned_cols=200  Identities=46%  Similarity=0.796  Sum_probs=197.7

Q ss_pred             chhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecCCCccchhhH
Q 026620           36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVI  114 (236)
Q Consensus        36 ~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~-~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgvk~I  114 (236)
                      +.|++|||++|||++|||+||||.|+++|++++|++|+++||+. |+|++|+|+|.|++||+++|+|||+++++||+|+|
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            68999999999999999999999999999999999999999997 99999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeeceeeeecccccccCceeecChHHHHHHHhhhcCC
Q 026620          115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE  192 (236)
Q Consensus       115 r~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~  192 (236)
                      |.++.+| .++|++++|+|+|+.+||+|++++..++  +.||+|+|+||+||||+|+|||||.+||+|||++||++|+++
T Consensus        86 k~~~~~~-~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~  164 (208)
T KOG3218|consen   86 KTYVIQM-QSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLK  164 (208)
T ss_pred             HHHHHHH-HhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCC
Confidence            9999999 8899999999999999999999999999  999999999999999999999999999999999999999999


Q ss_pred             cccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          193 EKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       193 ~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      ++|||||+.+||+|||||||+||||||+|+|+|||+|++||+|+
T Consensus       165 e~qLPRIq~~DpvaRYyGLKrGqVVKI~r~setag~yitYR~v~  208 (208)
T KOG3218|consen  165 ETQLPRIQKKDPVARYYGLKRGQVVKIIRRSETAGRYITYRCVV  208 (208)
T ss_pred             cccCCeeeccChHHhhhccccCcEEEEEecCccCcceEEEEEeC
Confidence            99999999999999999999999999999999999999999996

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

Probab=100.00  E-value=1.6e-78  Score=528.09  Aligned_cols=204  Identities=52%  Similarity=0.839  Sum_probs=200.3

Q ss_pred             CCCCchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccch
Q 026620           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKV  111 (236)
Q Consensus        32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~vgv  111 (236)
                      |+.++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|++++.+||+++|+|||+++++||+
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            46678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeeceeeeecccccccCceeecChHHHHHHHhhh
Q 026620          112 NVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKY  189 (236)
Q Consensus       112 k~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y  189 (236)
                      |+||.|+++| +++|++++|||+|+++||+|++++.+++  ++||+|+|+||++|||+|+|||||++||+|||++||++|
T Consensus        81 k~ir~~~~~~-~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y  159 (206)
T PLN03111         81 KTIKTYAERM-KDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRY  159 (206)
T ss_pred             HHHHHHHHHH-hhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHc
Confidence            9999999999 9999999999999999999999999995  899999999999999999999999999999999999999


Q ss_pred             cCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          190 SIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       190 ~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      +++++|||||+.+||+||||||++||||||+|+|+|||+|++||+|+
T Consensus       160 ~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R~S~taG~~v~YR~vv  206 (206)
T PLN03111        160 TVKETQLPRIQVSDPIARYYGLKRGQVVKIIRPSETAGRYVTYRCVV  206 (206)
T ss_pred             CCCHHHCCcccccChhhHhcCCCCCCEEEEEECCCCCCCceEEEEeC
Confidence            99999999999999999999999999999999999999999999996

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=6.9e-77  Score=517.29  Aligned_cols=199  Identities=38%  Similarity=0.584  Sum_probs=194.0

Q ss_pred             hhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecC-CCccchhhH
Q 026620           37 RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCG-PGIVKVNVI  114 (236)
Q Consensus        37 ~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~-~~r~~L~~~~~~~~~p~~~I~VfF~~-~~~vgvk~I  114 (236)
                      +++.||||+|||++|||+||||.|+++|+++|+++|+++||+. +.|++|+|++++.+||+++|+|||++ +++||+|+|
T Consensus         3 ~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~i   82 (205)
T PTZ00061          3 DSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKPI   82 (205)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHHH
Confidence            6789999999999999999999999999999999999999887 47899999999999999999999998 579999999


Q ss_pred             HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeeceeeeecccccccCceeecChHHHHHHHhhhcCC
Q 026620          115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE  192 (236)
Q Consensus       115 r~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~  192 (236)
                      |.|+++| +++|++++|||+|+++||+|++++.+++  ++||+|+|+||++|||+|+|||+|++||+|||++||++|+++
T Consensus        83 r~~~~~~-~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~  161 (205)
T PTZ00061         83 RELTEKM-EEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVK  161 (205)
T ss_pred             HHHHHHH-hhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCC
Confidence            9999999 9999999999999999999999998886  899999999999999999999999999999999999999999


Q ss_pred             cccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          193 EKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       193 ~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      ++|||||+.+||+||||||++||||||+|+|+|||+|++||+|+
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

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

Probab=100.00  E-value=5.7e-38  Score=237.78  Aligned_cols=75  Identities=32%  Similarity=0.589  Sum_probs=73.9

Q ss_pred             eeecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       162 l~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      .||||+|+|||+|++||+||+++||++|+++++|||||+.+||+|+||||++||||||+|+|+|||++++||+|+
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

>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=4.1e-38  Score=236.05  Aligned_cols=74  Identities=49%  Similarity=0.793  Sum_probs=66.2

Q ss_pred             eecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       163 ~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      ||||+|+|||+|++||+||+++||++|+++++|||||+.+||+|||||+++||||||+|+|+|||++++||+||
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            69999999999999999999999999999999999999999999999999999999999999999999999996

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 ....

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

Probab=100.00  E-value=3.1e-35  Score=221.41  Aligned_cols=79  Identities=34%  Similarity=0.543  Sum_probs=77.0

Q ss_pred             eceeeeecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       158 e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      ++.+.||+++|+|||+|++||+||++++|++|+++++|||||+.+||+|+++|+++||||||+|+|+|||++++||+|+
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            5678899999999999999999999999999999999999999999999999999999999999999999999999996

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

Probab=99.96  E-value=3e-30  Score=200.11  Aligned_cols=89  Identities=42%  Similarity=0.722  Sum_probs=74.6

Q ss_pred             CCCCchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCC---CCCCCceEEEeecCCCCCCcEEEEecCCCc
Q 026620           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKRILVVFCGPGI  108 (236)
Q Consensus        32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~---~~~r~~L~~~~~~~~~p~~~I~VfF~~~~~  108 (236)
                      || +++|++||||||||++|||+||||.|++.|+++|+++|+++|++   .|+|++|+|++.+.+||+++|+|||+++++
T Consensus         1 m~-~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~k   79 (93)
T PF03871_consen    1 MD-DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPK   79 (93)
T ss_dssp             ---TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSC
T ss_pred             Cc-cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCC
Confidence            45 44899999999999999999999999999999999999999988   799999999999999999999999999999


Q ss_pred             cchhhHHHHHHHH
Q 026620          109 VKVNVIRSIISQI  121 (236)
Q Consensus       109 vgvk~Ir~~~~~~  121 (236)
                      ||+|+||+|+++|
T Consensus        80 vgvk~Ir~~~~~m   92 (93)
T PF03871_consen   80 VGVKTIRKYCERM   92 (93)
T ss_dssp             ESCCCCHHHCHHH
T ss_pred             cCHHHHHHHHHhc
Confidence            9999999999988

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 ....

>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV

Probab=95.86  E-value=0.024  Score=42.75  Aligned_cols=76  Identities=21%  Similarity=0.270  Sum_probs=41.5

Q ss_pred             eEEEeecCCCCCCcEEEEecC-CCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhccceEeeeeeceee
Q 026620           85 LRISISHQSDPSKRILVVFCG-PGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLL  162 (236)
Q Consensus        85 L~~~~~~~~~p~~~I~VfF~~-~~~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~~~IEiF~e~eLl  162 (236)
                      ..+.+.........++|.+.. ..+++.+.|++++..+ ...+...++||+.+.+|+.|++.+.... .|+++.-++|+
T Consensus        36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~-~~~~~~~~iivt~~~~t~~a~~~~~~~~-~I~l~d~~~L~  112 (115)
T PF04471_consen   36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKA-KKYGADKGIIVTSSGFTPEAKEFAEKFK-NIELIDGEDLQ  112 (115)
T ss_dssp             EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHH-GGGT-SEEEEE-SSEE-HHHHHHHH---------------
T ss_pred             EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhh-hccCCCEEEEEECCcCCHHHHHHHHhhc-ccccccccccc
Confidence            344444433232456666644 3689999999999999 8889999999999999999999887643 67777766653

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	236
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		1e-27
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		2e-27
1hmj_A	78	Solution Structure Of Rna Polymerase Subunit H Leng		3e-08
1eik_A	77	Solution Structure Of Rna Polymerase Subunit Rpb5 F		1e-07
2waq_H	84	The Complete Structure Of The Archaeal 13-Subunit D		5e-05
2pmz_H	84	Archaeal Rna Polymerase From Sulfolobus Solfataricu		8e-05

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

Iteration: 1
 Score =  119 bits (298), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 73/197 (37%), Positives = 109/197 (55%), Gaps = 13/197 (6%)
Query: 48  TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKR--------- 98
           TV EM+KDRGY +   E+ L ++DF+A Y  D      R  +S Q++P++          
Sbjct: 18  TVKEMVKDRGYFITQEEVELPLEDFKAKYC-DSMGRPQRKMMSFQANPTEESISKFPDMG 76
Query: 99  -ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-GLFQFKVEMF 156
            + V FC    V V  +++ +  I  ++  TG I + QN IT  A K V  +    +E F
Sbjct: 77  SLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLVPSIPPATIETF 135
Query: 157 QITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQV 216
               L+VNIT H L PKH  L+  EK +LLK+Y ++E QLPR+ + D +A Y GL+RG+V
Sbjct: 136 NEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEV 195
Query: 217 VKVTYSGEITESHVTYR 233
           VK+    E +  + +YR
Sbjct: 196 VKIIRKSETSGRYASYR 212

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

Iteration: 1
 Score =  119 bits (297), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 69/192 (35%), Positives = 115/192 (59%), Gaps = 7/192 (3%)
Query: 48  TVLEMLKDRGYAVALSEINLSVQDFRAIY-GQDPDVDRLRISI-SHQSDPSKR--ILVVF 103
           T  +++ DRGY V+ +E++L++  F+A++ G   ++DR  +S  +  S+ S +  I + F
Sbjct: 17  TAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEF 76
Query: 104 CGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--QFKVEMFQITDL 161
                V +  +R+ +  + + +  TG ILI  N +T  A K +     QF +E FQ +DL
Sbjct: 77  AKEPSVGIKEMRTFVHTLGDHNHKTG-ILIYANSMTPSAAKIIATVTGQFTIETFQESDL 135
Query: 162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTY 221
           +VNIT H L PKH +L+  EK++LL +Y + E QLPR+   D +A+Y GL+RG+VVK+  
Sbjct: 136 IVNITHHELVPKHILLSPDEKKELLDRYKLRETQLPRIQLADPVARYLGLKRGEVVKIVR 195
Query: 222 SGEITESHVTYR 233
             E +  + +YR
Sbjct: 196 RSETSGRYNSYR 207

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 45/73 (61%)
Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222
           + +T H+L PKH+++  +E E++LK+Y+I+ +QLP++ + D + Q  G + G VV+V   
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRK 60
Query: 223 GEITESHVTYRCV 235
                  + 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 = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 41/72 (56%)
Query: 164 NITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSG 223
            I KH L P+H +L + E +++LK+     +QLP++   D +A+  G +RG +VK+    
Sbjct: 4   EILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKIIRKS 63
Query: 224 EITESHVTYRCV 235
              E  VTYR V
Sbjct: 64  PTAEEFVTYRLV 75

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 38/68 (55%)
Query: 168 HVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 227
           H L PKH+VL+  E  K+LK+  I  +QLP +   D +A+    + G ++++    ++  
Sbjct: 14  HYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYG 73
Query: 228 SHVTYRCV 235
             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 = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 37/68 (54%)
Query: 168 HVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 227
           H L PKH+VL   E  K+LK+  I  +QLP +   D +A+    + G ++++    ++  
Sbjct: 14  HYLVPKHEVLNIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYG 73
Query: 228 SHVTYRCV 235
             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	236
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	2e-59
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	1e-55
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	2e-29
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	1e-28
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	6e-28
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-05

>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 =  185 bits (471), Expect = 2e-59
 Identities = 67/209 (32%), Positives = 115/209 (55%), Gaps = 7/209 (3%)

Query: 33  DNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIY---GQDPDVDRLRISI 89
               ++ +R + + +T  +++ DRGY V+ +E++L++  F+A++   G++ D   L    
Sbjct: 2   SAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYA 61

Query: 90  SHQSDPSKR-ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGL 148
              +D +K  I + F     V +  +R+ +  +         ILI  N +T  A K +  
Sbjct: 62  KPSNDSNKGTIYIEFAKEPSVGIKEMRTFVHTL-GDHNHKTGILIYANSMTPSAAKIIAT 120

Query: 149 F--QFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIA 206
              QF +E FQ +DL+VNIT H L PKH +L+  EK++LL +Y + E QLPR+   D +A
Sbjct: 121 VTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQLPRIQLADPVA 180

Query: 207 QYYGLERGQVVKVTYSGEITESHVTYRCV 235
           +Y GL+RG+VVK+    E +  + +YR  
Sbjct: 181 RYLGLKRGEVVKIVRRSETSGRYNSYRIC 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 =  176 bits (446), Expect = 1e-55
 Identities = 71/213 (33%), Positives = 108/213 (50%), Gaps = 11/213 (5%)

Query: 33  DNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD---PDVDRLRISI 89
               R+  R + + RTV EM+KDRGY +   E+ L ++DF+A Y      P    +    
Sbjct: 3   QENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQA 62

Query: 90  SHQSDPS------KRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQAT 143
           +   +          + V FC    V V  +++ +  I  ++  T  I + QN IT  A 
Sbjct: 63  NPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQT-GIFVYQNNITPSAM 121

Query: 144 KAVG-LFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKK 202
           K V  +    +E F    L+VNIT H L PKH  L+  EK +LLK+Y ++E QLPR+ + 
Sbjct: 122 KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRA 181

Query: 203 DAIAQYYGLERGQVVKVTYSGEITESHVTYRCV 235
           D +A Y GL+RG+VVK+    E +  + +YR  
Sbjct: 182 DPVALYLGLKRGEVVKIIRKSETSGRYASYRIC 214

>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 (261), Expect = 2e-29
 Identities = 23/81 (28%), Positives = 43/81 (53%)

Query: 155 MFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERG 214
           M   ++  ++   H L PKH+VL+  E  K+LK+  I  +QLP +   D +A+    + G
Sbjct: 1   MRGSSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPG 60

Query: 215 QVVKVTYSGEITESHVTYRCV 235
            ++++    ++    V+YR V
Sbjct: 61  DIIRIIRKSQLYGEVVSYRYV 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 = 1e-28
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
           +   I KH L P+H +L + E +++LK+     +QLP++   D +A+  G +RG +VK+ 
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKII 60

Query: 221 YSGEITESHVTYRCV 235
                 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 (251), Expect = 6e-28
 Identities = 25/73 (34%), Positives = 45/73 (61%)

Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222
           + +T H+L PKH+++  +E E++LK+Y+I+ +QLP++ + D + Q  G + G VV+V   
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRK 60

Query: 223 GEITESHVTYRCV 235
                  + YR V
Sbjct: 61  SPTAGVSIAYRLV 73

>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 = 51.4 bits (122), Expect = 9e-08
 Identities = 40/213 (18%), Positives = 65/213 (30%), Gaps = 69/213 (32%)

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

Query: 59  AVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSII 118
            +  +  + S                LR  +  +  P +  L                  
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK--PYENCL------------------ 247

Query: 119 SQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMF------QITDLL-VNITKHV-L 170
                        L+L N   ++A  A   F    ++       Q+TD L    T H+ L
Sbjct: 248 -------------LVLLNVQNAKAWNA---FNLSCKILLTTRFKQVTDFLSAATTTHISL 291

Query: 171 KPKHQVLTDQEKEKLLKKY-SIEEKQLPRMLKK 202
                 LT  E + LL KY     + LPR +  
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324

>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 = 42.1 bits (98), Expect = 8e-05
 Identities = 37/222 (16%), Positives = 70/222 (31%), Gaps = 60/222 (27%)

Query: 10  SMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSV 69
           S++         +  +S L  ++D   +D     L R    E+L        LS I  S+
Sbjct: 290 SLD-HHSMTLTPDEVKSLLLKYLDCRPQD-----LPR----EVLT--TNPRRLSIIAESI 337

Query: 70  QDF--RAIYGQDPDVDRL----RISISHQSDPSKR----ILVVFCGPGIVKV-------- 111
           +D        +  + D+L      S++       R     L VF  P    +        
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF--PPSAHIPTILLSLI 395

Query: 112 --NVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHV 169
             +VI+S +  +VN   L    L+ +                K     I  + + +   +
Sbjct: 396 WFDVIKSDVMVVVN--KLHKYSLVEKQP--------------KESTISIPSIYLELKVKL 439

Query: 170 --LKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYY 209
                 H+         ++  Y+I +      L    + QY+
Sbjct: 440 ENEYALHR--------SIVDHYNIPKTFDSDDLIPPYLDQYF 473

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	236
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=6.7e-77  Score=518.90  Aligned_cols=204  Identities=31%  Similarity=0.531  Sum_probs=197.4

Q ss_pred             CCCCchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCC---CCCCceEEEeecCCCC-CCcEEEEecCCC
Q 026620           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD---PDVDRLRISISHQSDP-SKRILVVFCGPG  107 (236)
Q Consensus        32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~---~~r~~L~~~~~~~~~p-~~~I~VfF~~~~  107 (236)
                      |+.++.|++||||+|||++|||+||||.|+++|+++|+++|+++|++.   |+|++|+|++.+.+|| +++|+|||++++
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            566788999999999999999999999999999999999999999875   8899999999999999 999999999999


Q ss_pred             ccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc--ceEeeeeeceeeeecccccccCceeecChHHHHHH
Q 026620          108 IVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL  185 (236)
Q Consensus       108 ~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~--~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eEk~~l  185 (236)
                      +||+|+||.|++++ .++|++++|||+|+++||+|++++.+++  ++||+|+++||+||||+|+|||+|++||+|||++|
T Consensus        81 ~vgvk~Ir~~~~~~-~~en~~~~IiV~q~~~t~~A~~~l~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eE~~~l  159 (210)
T 3h0g_E           81 SVGIKEMRTFVHTL-GDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKEL  159 (210)
T ss_dssp             SCCTTTTGGGTHHH-HHTTCSEEEECCSSCCCSHHHHTTTTTCTTCEECCCCSSSSCSCTTSBTTBCCEECCCHHHHHHH
T ss_pred             ccChHHHHHHHHHH-HHcCCceEEEEECCCCCHHHHHHHHHhCcCcEEEEEeehHeeEecccccccCcEEEcCHHHHHHH
Confidence            99999999999999 9999999999999999999999999997  79999999999999999999999999999999999


Q ss_pred             HhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          186 LKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       186 l~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      |++|+++++|||||+.+||+|+||||++||||||+|+|+|||+|++||+|+
T Consensus       160 L~~y~i~~~qLP~I~~~DPv~~~~g~k~GdVvkI~R~s~tag~~v~YR~V~  210 (210)
T 3h0g_E          160 LDRYKLRETQLPRIQLADPVARYLGLKRGEVVKIVRRSETSGRYNSYRICA  210 (210)
T ss_dssp             HHHTCCCTTTSCCCCTTCHHHHHHTCCTTCEEEEECCCCTTSCCEEEEECC
T ss_pred             HHHcCCCHHHCCcccccCcchhhhCCCCCCEEEEEeCCCCCCCceEEEEeC
Confidence            999999999999999999999999999999999999999999999999996

>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=1.3e-75  Score=512.13  Aligned_cols=203  Identities=34%  Similarity=0.573  Sum_probs=196.1

Q ss_pred             CCCCchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCC---CCCCCceEEEeecCCCCCCcE------EEE
Q 026620           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKRI------LVV  102 (236)
Q Consensus        32 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~---~~~r~~L~~~~~~~~~p~~~I------~Vf  102 (236)
                      |+ ++.++.||||+|||++|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++++.+||++++      +||
T Consensus         3 m~-~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~g~p~r~~L~~~~~~~~d~~~k~~~~~~~~Vf   81 (215)
T 1dzf_A            3 QE-NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVE   81 (215)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEE
T ss_pred             cc-hHHHHHHHHHHHHHHHHHHhcCCCccCHhHhcCCHHHHHHHHccccCCCchhheEEEecCCCChhhhhccCCceEEE
Confidence            44 45889999999999999999999999999999999999999987   789999999999999999888      999


Q ss_pred             ecCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc-ceEeeeeeceeeeecccccccCceeecChHH
Q 026620          103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ-FKVEMFQITDLLVNITKHVLKPKHQVLTDQE  181 (236)
Q Consensus       103 F~~~~~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~-~~IEiF~e~eLl~nit~H~lVPkH~~Ls~eE  181 (236)
                      |+++++||+|+||+|+++| +++|++++|||+|+++||+|++++++++ ++||+|+|+||+||||+|+|||+|++||+||
T Consensus        82 F~~~~~vgvk~ir~~~~~~-~~e~~~~~IlV~q~~itp~Ak~~l~~~~~~~iE~F~e~eL~vni~~H~lVP~H~~l~~eE  160 (215)
T 1dzf_A           82 FCDEPSVGVKTMKTFVIHI-QEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE  160 (215)
T ss_dssp             ECSSSEECHHHHHHHHHHH-HHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEEHHHHSSCGGGSTTSCEEEECCHHH
T ss_pred             ecCCCccchHHHHHHHHHH-HhcCCceEEEEECCCCChHHHHHHHHhcCceEEEeehHHheeccccceeccceEEccHHH
Confidence            9999999999999999999 9999999999999999999999999988 8999999999999999999999999999999


Q ss_pred             HHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          182 KEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       182 k~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      |++||++|+++++|||||+.+||+||||||++||||||+|+|+|||+|++||+|+
T Consensus       161 ~~~lL~~y~i~~~qLP~I~~~DPvar~~g~k~G~vvkI~R~s~tag~~v~YR~vv  215 (215)
T 1dzf_A          161 KRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM  215 (215)
T ss_dssp             HHHHHHHTTCCGGGSCEECTTCHHHHHHTCCTTCEEEEECTTCSSSTTCEEEEEC
T ss_pred             HHHHHHHcCCCHHHCCceeccChhhHHhCCcCCCEEEEEECCCCCCCceEEEEeC
Confidence            9999999999999999999999999999999999999999999999999999996

>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=4.7e-40  Score=247.01  Aligned_cols=76  Identities=34%  Similarity=0.577  Sum_probs=75.0

Q ss_pred             eeeecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       161 Ll~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      |+||||+|+|||+|++||+|||++||++|+++++|||||+.+||+|||||+++||||||+|+|+|||+|++||+|+
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=6.3e-39  Score=241.33  Aligned_cols=74  Identities=34%  Similarity=0.653  Sum_probs=73.1

Q ss_pred             eecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       163 ~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      ||||+|+|||+|++||+|||++||++|+++++|||||+.+||+|||||+++||||||+|+|+|||+|++||+|+
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            69999999999999999999999999999999999999999999999999999999999999999999999996

>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=1.6e-37  Score=236.82  Aligned_cols=79  Identities=28%  Similarity=0.456  Sum_probs=74.4

Q ss_pred             eceeeeecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       158 e~eLl~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      .+.++||||+|+|||+|++||+||+++||++|+++++|||+|+.+||+|+|||++|||||||+|+|+|||++++||+|+
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            4689999999999999999999999999999999999999999999999999999999999999999999999999996

---

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	236
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	2e-37
d1eika_	77	d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA pol	6e-29
d1dzfa2	72	d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal do	3e-28

>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 =  125 bits (316), Expect = 2e-37
 Identities = 40/138 (28%), Positives = 64/138 (46%), Gaps = 11/138 (7%)

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

Query: 94  DPSKR------ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV- 146
           +   +      + V FC    V V  +++ +  I  ++  TG I + QN IT  A K V 
Sbjct: 63  ESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLVP 121

Query: 147 GLFQFKVEMFQITDLLVN 164
            +    +E F    L+VN
Sbjct: 122 SIPPATIETFNEAALVVN 139

>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 =  102 bits (255), Expect = 6e-29
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
           +   I KH L P+H +L + E +++LK+     +QLP++   D +A+  G +RG +VK+ 
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKII 60

Query: 221 YSGEITESHVTYRCV 235
                 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 =  100 bits (250), Expect = 3e-28
 Identities = 32/71 (45%), Positives = 46/71 (64%)

Query: 165 ITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGE 224
           IT H L PKH  L+  EK +LLK+Y ++E QLPR+ + D +A Y GL+RG+VVK+    E
Sbjct: 1   ITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSE 60

Query: 225 ITESHVTYRCV 235
            +  + +YR  
Sbjct: 61  TSGRYASYRIC 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	236
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	100.0
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	99.96

>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=100.00  E-value=5.1e-41  Score=274.14  Aligned_cols=129  Identities=29%  Similarity=0.481  Sum_probs=121.5

Q ss_pred             CchhhHHHHHHHHHHHHHhcCCCcccCccccccCHHHHHHHhCCC---CCCCceEEEeecCCC------CCCcEEEEecC
Q 026620           35 GSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD---PDVDRLRISISHQSD------PSKRILVVFCG  105 (236)
Q Consensus        35 ~~~e~~rl~r~rrTv~eMl~DRGY~v~~~el~~sl~eF~~~y~~~---~~r~~L~~~~~~~~~------p~~~I~VfF~~  105 (236)
                      +++|++||||+||||+|||+||||.|+++|+++|+++|+++||++   |+|+.|++.+.+.++      +.++|+|||++
T Consensus         1 ~d~e~~rlfr~rrTv~EMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~p~r~~l~~~~~~~~~~~~k~~~~~~I~V~F~~   80 (139)
T d1dzfa1           1 NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCD   80 (139)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECS
T ss_pred             ChHHHHHHHHHHHHHHHHHhcCCCcCCHHHHcCCHHHHHHHHccccCCcCHHHhcccCCCchhhhhccCCCCeEEEEECC
Confidence            468999999999999999999999999999999999999999875   899999999987654      45679999999


Q ss_pred             CCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHhhhcc-ceEeeeeeceeeee
Q 026620          106 PGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ-FKVEMFQITDLLVN  164 (236)
Q Consensus       106 ~~~vgvk~Ir~~~~~~~~~en~~~~IiV~q~~lt~~Ark~l~~~~-~~IEiF~e~eLl~n  164 (236)
                      +++||+|+||.++++| +++|+++||||+|+++||+|++++.+++ ++||+|+++|||||
T Consensus        81 ~~kvgvk~ir~~~~~m-~~~~~~r~IlV~q~~iTp~Ak~~i~~~~~~~iE~F~e~eLLVN  139 (139)
T d1dzfa1          81 EPSVGVKTMKTFVIHI-QEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVN  139 (139)
T ss_dssp             SSEECHHHHHHHHHHH-HHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEEHHHHSSC
T ss_pred             CCccCHHHHHHHHHHH-HhcCCceEEEEECCCCCHHHHHHHHhccCceEEEechhhcccC
Confidence            9999999999999999 9999999999999999999999999887 89999999999998

>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=6.9e-36  Score=222.55  Aligned_cols=76  Identities=34%  Similarity=0.577  Sum_probs=74.8

Q ss_pred             eeeecccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       161 Ll~nit~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      |.+||++|+|||+|++||+||++++|++|+++.+|||+|+.+||+|+|||+++||||||+|+|+|||.+++||+|+
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            6899999999999999999999999999999999999999999999999999999999999999999999999996

>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=6.5e-34  Score=209.39  Aligned_cols=72  Identities=44%  Similarity=0.737  Sum_probs=71.1

Q ss_pred             cccccccCceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          165 ITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       165 it~H~lVPkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      ||+|+|||+|++|++||++++|++|+++.+|||+|+.+||+|+|||+++||||||+|+|+|||.+++||+||
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=99.96  E-value=7.8e-30  Score=185.58  Aligned_cols=65  Identities=34%  Similarity=0.641  Sum_probs=64.3

Q ss_pred             CceeecChHHHHHHHhhhcCCcccCCccccCCchhhhcCCCCCCEEEEEecCCCCcceeEEEEeC
Q 026620          172 PKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITESHVTYRCVW  236 (236)
Q Consensus       172 PkH~~Ls~eEk~~ll~~y~i~~~qLP~I~~~DPvary~g~~~GdVvkI~R~s~tag~~v~YR~V~  236 (236)
                      |+|++||+||+++||++|+++.+|||+|+.+||+|+|||+++||||||+|+|+|||.+++||+|+
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