Citrus Sinensis ID: 030846

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170
Protein Sequence
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHccccccccHHHHcccHHHHHHHHcccccccccccEEcccccccccEEEEccccccccHHHHHHHHHHHHHccccEEEEEEEccccHHHHHHHHHcccccEEEEEEccHHHHcccccccccccccccHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHHHHHcccEccHHHHcccHHHHHHHHcccccccccEEEEcccccccccEEEEEccccEEcHHHHHHHHHHHHHccccEEEEEEccEEcHHHHccccccccccEEEEEEHHHHcccHHHcccccEEEEccHHHHHHHHHHccccHHHccccc
Coil and Loop (DISEMBL)
MTLSDEEIKRLFRIRRTVMQMLRDrgyfvgdfeinMSKEQFIAKFGENMKREDLVINKAlrndssdqiyvffpdeqkvgVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIkehvlvpehqvltnEEKKTLLKRytvketqvsdkf
Flexible Loop (DISEMBL)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALrndssdqiyvffpdeqkvgVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHvlvpehqvltneekktllkrytvketqvsdkf
Low Complexity Region (SEG)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF
Disordered region (IsUnstruct)
********KRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRY***********
Disordered Region (DISOPRED)
*****EE**RLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINK*****SSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS***
Disordered Region (DISEMBL)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF
Disordered Region (DISPRO)
****DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV***F
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF
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	170	2.2.26 [Sep-21-2011]
B0BNE2	210	DNA-directed RNA polymera	yes	no	0.958	0.776	0.464	2e-39
Q80UW8	210	DNA-directed RNA polymera	yes	no	0.958	0.776	0.464	2e-39
Q5R587	210	DNA-directed RNA polymera	yes	no	0.964	0.780	0.461	4e-39
Q9N5K2	211	DNA-directed RNA polymera	yes	no	0.970	0.781	0.453	9e-39
A8XGH1	211	DNA-directed RNA polymera	N/A	no	0.970	0.781	0.459	1e-38
P19388	210	DNA-directed RNA polymera	yes	no	0.958	0.776	0.458	3e-38
Q2T9T3	210	DNA-directed RNA polymera	yes	no	0.958	0.776	0.458	4e-38
Q54EH2	197	DNA-directed RNA polymera	yes	no	0.911	0.786	0.487	3e-35
Q09191	210	DNA-directed RNA polymera	yes	no	0.976	0.790	0.376	2e-27
P20434	215	DNA-directed RNA polymera	yes	no	0.935	0.739	0.396	2e-25

>sp|B0BNE2|RPAB1_RAT DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus GN=Polr2e PE=2 SV=1

 Score =  161 bits (408), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 78/168 (46%), Positives = 117/168 (69%), Gaps = 5/168 (2%)

Query: 5   DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
           +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct: 4   EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query: 60  LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
             +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct: 64  HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query: 120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E+Q+ 
Sbjct: 124 KYVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQLP 171

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 =  161 bits (408), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 78/168 (46%), Positives = 117/168 (69%), Gaps = 5/168 (2%)

Query: 5   DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
           +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct: 4   EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query: 60  LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
             +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct: 64  HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query: 120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E+Q+ 
Sbjct: 124 KYVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQLP 171

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|Q5R587|RPAB1_PONAB DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Pongo abelii GN=POLR2E PE=2 SV=1

 Score =  160 bits (405), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 78/169 (46%), Positives = 116/169 (68%), Gaps = 5/169 (2%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINK 58
            +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  
Sbjct: 3   DEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLV 62

Query: 59  ALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118
           A  +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++
Sbjct: 63  AHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMA 122

Query: 119 AKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
            K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+ 
Sbjct: 123 PKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLP 171

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

 Score =  159 bits (402), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 78/172 (45%), Positives = 118/172 (68%), Gaps = 7/172 (4%)

Query: 3   LSDEEIK--RLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE-----NMKREDLV 55
           ++D+E++  RL+RIR+TV+QM+ DRGY V   E++   E F  ++G+        R DL 
Sbjct: 1   MADDELETYRLWRIRKTVLQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLT 60

Query: 56  INKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQ 115
           I  A  +D +DQ++VFFP++ K+G+KT+K    +M+ +N+ RAI+VVQ  +TP A+  I 
Sbjct: 61  ILVAHNDDPADQMFVFFPEDAKIGIKTIKAICQQMQEQNISRAIIVVQTGMTPSAKQSIG 120

Query: 116 EISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           +++ K+ LE F EAEL+VNI EH LVPEH V+T EEK  LL RY +K++Q+ 
Sbjct: 121 DMAPKYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLP 172

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 =  158 bits (400), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/172 (45%), Positives = 117/172 (68%), Gaps = 7/172 (4%)

Query: 3   LSDEEIK--RLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMK-----REDLV 55
           ++D+E++  RL+RIR+TV+QM+ DRGY V   E++   E F   FG+        R DL 
Sbjct: 1   MADDELETYRLWRIRKTVLQMVHDRGYLVAQEELDQPLETFKETFGDRPSEKKPARSDLT 60

Query: 56  INKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQ 115
           I  A  +D +DQ++VFFP++ K+G+KT+K    +M+ +N+ RAI+VVQ  +TP A+  I 
Sbjct: 61  ILVAHNDDPADQMFVFFPEDTKIGIKTIKAICQQMQEQNISRAIIVVQTGMTPSAKQSIG 120

Query: 116 EISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           +++ K+ LE F EAEL+VNI EH LVPEH V+T EEK  LL RY +K++Q+ 
Sbjct: 121 DMAPKYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQLP 172

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|P19388|RPAB1_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Homo sapiens GN=POLR2E PE=1 SV=4

 Score =  157 bits (397), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 77/168 (45%), Positives = 115/168 (68%), Gaps = 5/168 (2%)

Query: 5   DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
           +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+ G+       +R DL +  A
Sbjct: 4   EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQSGDKPSEGRPRRTDLTVLVA 63

Query: 60  LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
             +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct: 64  HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query: 120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+ 
Sbjct: 124 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLP 171

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.

Homo sapiens (taxid: 9606)

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

 Score =  157 bits (396), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 77/168 (45%), Positives = 114/168 (67%), Gaps = 5/168 (2%)

Query: 5   DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
           +EE  RL++IR+T+MQ+  DRGY V    ++ + E+F A+FG        +R DL +  A
Sbjct: 4   EEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVA 63

Query: 60  LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
             +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct: 64  HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query: 120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+ 
Sbjct: 124 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLP 171

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

Bos taurus (taxid: 9913)

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

 Score =  147 bits (372), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 80/164 (48%), Positives = 105/164 (64%), Gaps = 9/164 (5%)

Query: 6   EEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSS 65
           E+I RL +IR+TV+QML DR Y +  +E    +E F++       RE+L +    ++D +
Sbjct: 2   EDINRLLQIRKTVLQMLSDREYIITAYEQEYPRESFVS-------RENLTMYCVKKDDPT 54

Query: 66  DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS--AKFHL 123
           D IYVFFPD  KVGV  +K Y + MK     RAI+VVQQN+TPFA+  + E S   K  L
Sbjct: 55  DSIYVFFPDTPKVGVTQIKKYVDIMKDRQANRAIIVVQQNITPFAKQALAEFSQEKKITL 114

Query: 124 EVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           E F EAELLVNI  H LVP+H +LT EEK  LL RY +KE+Q+ 
Sbjct: 115 EQFNEAELLVNITHHQLVPKHILLTKEEKLELLTRYKMKESQLP 158

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

Dictyostelium discoideum (taxid: 44689)

>sp|Q09191|RPAB1_SCHPO DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb5 PE=1 SV=1

 Score =  122 bits (305), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/170 (37%), Positives = 101/170 (59%), Gaps = 4/170 (2%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIA---KFGENMKREDLVIN 57
           M+  ++ I R+FR  +T  Q++ DRGY V   E++++ +QF A     G N+ R  L   
Sbjct: 1   MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFY 60

Query: 58  KALRNDSS-DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQE 116
               NDS+   IY+ F  E  VG+K M+T+ + +   N    IL+   ++TP A   I  
Sbjct: 61  AKPSNDSNKGTIYIEFAKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIAT 120

Query: 117 ISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
           ++ +F +E FQE++L+VNI  H LVP+H +L+ +EKK LL RY ++ETQ+
Sbjct: 121 VTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQL 170

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.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>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 =  115 bits (288), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 67/169 (39%), Positives = 97/169 (57%), Gaps = 10/169 (5%)

Query: 8   IKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQ 67
           I RL+R  RTV +M++DRGYF+   E+ +  E F AK+ ++M R    +     N + + 
Sbjct: 9   ISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEES 68

Query: 68  I---------YVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118
           I         +V F DE  VGVKTMKT+   ++ +N    I V Q N+TP A   +  I 
Sbjct: 69  ISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIP 128

Query: 119 AKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
               +E F EA L+VNI  H LVP+H  L+++EK+ LLKRY +KE+Q+ 
Sbjct: 129 PA-TIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLP 176

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)

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	170
225445170	206	PREDICTED: DNA-directed RNA polymerases	0.976	0.805	0.891	3e-82
224119828	206	predicted protein [Populus trichocarpa]	0.982	0.810	0.868	3e-80
351723363	206	uncharacterized protein LOC100499667 [Gl	0.982	0.810	0.802	4e-74
449462431	207	PREDICTED: DNA-directed RNA polymerases	0.982	0.806	0.803	4e-74
15228724	205	DNA-directed RNA polymerase II subunit E	0.970	0.804	0.806	4e-74
351722355	206	uncharacterized protein LOC100306098 [Gl	0.982	0.810	0.802	1e-73
297835232	205	ATRPABC24.3 [Arabidopsis lyrata subsp. l	0.970	0.804	0.793	4e-73
297738790	186	unnamed protein product [Vitis vinifera]	0.864	0.790	0.904	5e-73
449502080	208	PREDICTED: DNA-directed RNA polymerases	0.982	0.802	0.786	2e-72
255546411	225	DNA-directed RNA polymerase II, putative	0.982	0.742	0.736	9e-72

>gi|225445170|ref|XP_002284107.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform 1 [Vitis vinifera] gi|225445172|ref|XP_002284110.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform 2 [Vitis vinifera]

 Score =  309 bits (791), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 148/166 (89%), Positives = 159/166 (95%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           M+ S+EEI RLFRIR+TVMQML+DRGYFVGDFEINM+K QF++KFGENMKREDLVINKA 
Sbjct: 1   MSASEEEISRLFRIRKTVMQMLKDRGYFVGDFEINMTKHQFVSKFGENMKREDLVINKAK 60

Query: 61  RNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK 120
           R DSSDQIYVFFP+EQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI EIS K
Sbjct: 61  RTDSSDQIYVFFPEEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISTK 120

Query: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
           FHLEVFQEAELLVNIKEHVLVPEHQVLT+EEKKTLL+RYTVKETQ+
Sbjct: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTSEEKKTLLERYTVKETQL 166

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119828|ref|XP_002331171.1| predicted protein [Populus trichocarpa] gi|222873254|gb|EEF10385.1| predicted protein [Populus trichocarpa]

 Score =  302 bits (774), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 145/167 (86%), Positives = 157/167 (94%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           MTL++EEIKRL RIR+TVMQML+DRGYFVGDFEI M++EQF +K+G NMKREDLVINK  
Sbjct: 1   MTLTEEEIKRLLRIRKTVMQMLKDRGYFVGDFEIKMTREQFESKYGNNMKREDLVINKTK 60

Query: 61  RNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK 120
           RNDSSDQIYVFFP+E KVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI EIS K
Sbjct: 61  RNDSSDQIYVFFPEEAKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISTK 120

Query: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           FHLEVFQEAELLVNIKEHVLVPEHQVL+NEEKKTLL+RYTVKETQ+ 
Sbjct: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLSNEEKKTLLERYTVKETQLP 167

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723363|ref|NP_001238044.1| uncharacterized protein LOC100499667 [Glycine max] gi|255625665|gb|ACU13177.1| unknown [Glycine max]

 Score =  282 bits (721), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 134/167 (80%), Positives = 152/167 (91%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           M LS+EE+ RL+RIR+TVMQMLRDRG+ VGDFEINMSK +F +K+GE+MKREDLVINK+ 
Sbjct: 1   MVLSEEEMGRLYRIRKTVMQMLRDRGFLVGDFEINMSKHEFKSKYGEHMKREDLVINKSK 60

Query: 61  RNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK 120
           +++S DQIYVFFPDE KVGVKTMKTYTNRM SENV+RAILV Q NLTPFARTCI EIS+K
Sbjct: 61  KDNSGDQIYVFFPDEPKVGVKTMKTYTNRMNSENVYRAILVTQTNLTPFARTCISEISSK 120

Query: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           FHLEVFQEAELLVNIKEH LVPEHQVLT+ EKKTLL+RYTVKETQ+ 
Sbjct: 121 FHLEVFQEAELLVNIKEHELVPEHQVLTDAEKKTLLERYTVKETQLP 167

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462431|ref|XP_004148944.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Cucumis sativus]

 Score =  282 bits (721), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 135/168 (80%), Positives = 153/168 (91%), Gaps = 1/168 (0%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           M LS+EEI RLFRIR+TV QMLRDRGYFVGDFEI+M++EQF  K+GENMKRED+VINK+ 
Sbjct: 1   MVLSEEEITRLFRIRKTVFQMLRDRGYFVGDFEIDMTREQFKQKYGENMKREDIVINKSK 60

Query: 61  RNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK 120
           RNDSSDQIYVFFP+E KVG+K +KTYT RMKSENVFRAILVVQQNLTPFAR C+ E ++K
Sbjct: 61  RNDSSDQIYVFFPEEAKVGIKPLKTYTTRMKSENVFRAILVVQQNLTPFARACMSEATSK 120

Query: 121 -FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
            FHLEVFQEAELLVNIK+HVLVPEHQ+L NEEKKTLL+RYTVKETQ+ 
Sbjct: 121 SFHLEVFQEAELLVNIKDHVLVPEHQLLNNEEKKTLLERYTVKETQLP 168

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15228724|ref|NP_188871.1| DNA-directed RNA polymerase II subunit E [Arabidopsis thaliana] gi|13899113|gb|AAK48978.1|AF370551_1 RNA polymerase I, II and III 24.3 kDa subunit [Arabidopsis thaliana] gi|15724322|gb|AAL06554.1|AF412101_1 AT3g22320/MCB17_5 [Arabidopsis thaliana] gi|3372233|gb|AAC28253.1| RNA polymerase I, II and III 24.3 kDa subunit [Arabidopsis thaliana] gi|9293866|dbj|BAB01769.1| RNA polymerase I, II and III 24.3 kDa subunit [Arabidopsis thaliana] gi|21554280|gb|AAM63355.1| RNA polymerase I, II and III 24.3 kDa subunit [Arabidopsis thaliana] gi|25083949|gb|AAN72141.1| RNA polymerase I, II and III 24.3 kDa subunit [Arabidopsis thaliana] gi|332643100|gb|AEE76621.1| DNA-directed RNA polymerase II subunit E [Arabidopsis thaliana]

 Score =  282 bits (721), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 133/165 (80%), Positives = 152/165 (92%)

Query: 3   LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRN 62
           L++EE+KRL+RI++T+MQMLRDRGYF+ D E+ M+K+QFI K G+NMKREDLV  KA RN
Sbjct: 2   LTEEELKRLYRIQKTLMQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKRN 61

Query: 63  DSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFH 122
           D+SDQ+Y+FFPDE KVGVKTMK YTNRMKSENVFRAILVVQQNLTPFARTCI EIS+KFH
Sbjct: 62  DNSDQLYIFFPDEAKVGVKTMKMYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFH 121

Query: 123 LEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           LEVFQEAE+LVNIKEHVLVPEHQVLT EEKKTLL+RYTVKETQ+ 
Sbjct: 122 LEVFQEAEMLVNIKEHVLVPEHQVLTTEEKKTLLERYTVKETQLP 166

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722355|ref|NP_001237497.1| uncharacterized protein LOC100306098 [Glycine max] gi|255627545|gb|ACU14117.1| unknown [Glycine max]

 Score =  280 bits (717), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 134/167 (80%), Positives = 151/167 (90%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           M LS+EEI RL+RIR+TVMQMLRDR + VGDFEINMSK +F +K+GE+MKREDLVINK+ 
Sbjct: 1   MVLSEEEIGRLYRIRKTVMQMLRDRNFLVGDFEINMSKHEFKSKYGEHMKREDLVINKSK 60

Query: 61  RNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK 120
           +++S DQIYVFFPDE KVGVKTMKTYTNRM SENV+RAILV Q NLTPFARTCI EIS+K
Sbjct: 61  KDNSGDQIYVFFPDEPKVGVKTMKTYTNRMNSENVYRAILVTQTNLTPFARTCISEISSK 120

Query: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           FHLEVFQEAELLVNIKEH LVPEHQVLT+ EKKTLL+RYTVKETQ+ 
Sbjct: 121 FHLEVFQEAELLVNIKEHELVPEHQVLTDAEKKTLLERYTVKETQLP 167

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297835232|ref|XP_002885498.1| ATRPABC24.3 [Arabidopsis lyrata subsp. lyrata] gi|297331338|gb|EFH61757.1| ATRPABC24.3 [Arabidopsis lyrata subsp. lyrata]

 Score =  279 bits (713), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 131/165 (79%), Positives = 151/165 (91%)

Query: 3   LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRN 62
           L++EEIKRL+RI++T+MQML+DRGYF+ D E+ M+K+QFI K G+NMKREDLV  K  RN
Sbjct: 2   LTEEEIKRLYRIQKTLMQMLKDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKVKRN 61

Query: 63  DSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFH 122
           D+SDQ+Y+FFPDE KVGVKTMK YTNRMKSENV+RAILVVQQNLTPFARTCI EIS+KFH
Sbjct: 62  DNSDQLYIFFPDEAKVGVKTMKMYTNRMKSENVYRAILVVQQNLTPFARTCISEISSKFH 121

Query: 123 LEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           LEVFQEAE+LVNIKEHVLVPEHQVLT EEKKTLL+RYTVKETQ+ 
Sbjct: 122 LEVFQEAEMLVNIKEHVLVPEHQVLTTEEKKTLLERYTVKETQLP 166

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738790|emb|CBI28035.3| unnamed protein product [Vitis vinifera]

 Score =  278 bits (711), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 133/147 (90%), Positives = 141/147 (95%)

Query: 21  MLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGV 80
           ML+DRGYFVGDFEINM+K QF++KFGENMKREDLVINKA R DSSDQIYVFFP+EQKVGV
Sbjct: 1   MLKDRGYFVGDFEINMTKHQFVSKFGENMKREDLVINKAKRTDSSDQIYVFFPEEQKVGV 60

Query: 81  KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVL 140
           KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI EIS KFHLEVFQEAELLVNIKEHVL
Sbjct: 61  KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISTKFHLEVFQEAELLVNIKEHVL 120

Query: 141 VPEHQVLTNEEKKTLLKRYTVKETQVS 167
           VPEHQVLT+EEKKTLL+RYTVKETQ+ 
Sbjct: 121 VPEHQVLTSEEKKTLLERYTVKETQLP 147

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449502080|ref|XP_004161536.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Cucumis sativus]

 Score =  276 bits (706), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 133/169 (78%), Positives = 153/169 (90%), Gaps = 2/169 (1%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           M LS+EEI RLFRIR+TV QMLRDRGYFVGDFEI+M++EQF  K+GENMKRED+VINK+ 
Sbjct: 1   MVLSEEEITRLFRIRKTVFQMLRDRGYFVGDFEIDMTREQFKQKYGENMKREDIVINKSK 60

Query: 61  RNDSSDQIYV-FFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
           RNDSSDQ+Y+ FFP+E KVG+K +KTYT RMKSENVFRAILVVQQNLTPFAR C+ E ++
Sbjct: 61  RNDSSDQVYICFFPEEAKVGIKPLKTYTTRMKSENVFRAILVVQQNLTPFARACMSEATS 120

Query: 120 K-FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
           K FHLEVFQEAELLVNIK+HVLVPEHQ+L NEEKKTLL+RYTVKETQ+ 
Sbjct: 121 KSFHLEVFQEAELLVNIKDHVLVPEHQLLNNEEKKTLLERYTVKETQLP 169

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546411|ref|XP_002514265.1| DNA-directed RNA polymerase II, putative [Ricinus communis] gi|223546721|gb|EEF48219.1| DNA-directed RNA polymerase II, putative [Ricinus communis]

 Score =  274 bits (700), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 137/186 (73%), Positives = 155/186 (83%), Gaps = 19/186 (10%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           MTLS++EIKRLFRIRRTVMQML+DR Y V D EIN++K QF +K+G+NMKREDLVI+K+ 
Sbjct: 1   MTLSEDEIKRLFRIRRTVMQMLKDRTYLVTDSEINITKHQFTSKYGDNMKREDLVIHKSK 60

Query: 61  RNDSSD-------------------QIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILV 101
           R+ S                     QIYVFFP+EQKVGVKTMKTYTNRMKSENVFRAILV
Sbjct: 61  RDGSDSFYPTKLLFLNQLEAWLPLYQIYVFFPEEQKVGVKTMKTYTNRMKSENVFRAILV 120

Query: 102 VQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTV 161
           VQQ+LTPFARTCI EI++KFHLEVFQE+ELLVNIKEHVLVPEHQVLTNEEKKTLL+RYTV
Sbjct: 121 VQQSLTPFARTCIAEIASKFHLEVFQESELLVNIKEHVLVPEHQVLTNEEKKTLLERYTV 180

Query: 162 KETQVS 167
           KETQ+ 
Sbjct: 181 KETQLP 186

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	170
TAIR|locus:2087842	205	NRPB5 [Arabidopsis thaliana (t	0.964	0.8	0.810	6.3e-69
FB|FBgn0033571	210	Rpb5 "Rpb5" [Drosophila melano	0.964	0.780	0.476	2.4e-37
MGI|MGI:1913670	210	Polr2e "polymerase (RNA) II (D	0.952	0.771	0.467	3.9e-37
RGD|1589817	210	Polr2e "polymerase (RNA) II (D	0.952	0.771	0.467	3.9e-37
UNIPROTKB|F2Z4J4	210	POLR2E "DNA-directed RNA polym	0.952	0.771	0.467	4.9e-37
UNIPROTKB|E2R2E8	212	POLR2E "Uncharacterized protei	0.952	0.764	0.467	4.9e-37
UNIPROTKB|F6X571	210	POLR2E "Uncharacterized protei	0.952	0.771	0.467	4.9e-37
UNIPROTKB|I3LSI7	210	POLR2E "Uncharacterized protei	0.952	0.771	0.467	4.9e-37
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.952	0.771	0.467	4.9e-37
UNIPROTKB|F1NHV9	215	POLR2E "Uncharacterized protei	0.952	0.753	0.467	6.3e-37

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

 Score = 699 (251.1 bits), Expect = 6.3e-69, P = 6.3e-69
 Identities = 133/164 (81%), Positives = 152/164 (92%)

Query:     3 LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRN 62
             L++EE+KRL+RI++T+MQMLRDRGYF+ D E+ M+K+QFI K G+NMKREDLV  KA RN
Sbjct:     2 LTEEELKRLYRIQKTLMQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDLVTLKAKRN 61

Query:    63 DSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFH 122
             D+SDQ+Y+FFPDE KVGVKTMK YTNRMKSENVFRAILVVQQNLTPFARTCI EIS+KFH
Sbjct:    62 DNSDQLYIFFPDEAKVGVKTMKMYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFH 121

Query:   123 LEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             LEVFQEAE+LVNIKEHVLVPEHQVLT EEKKTLL+RYTVKETQ+
Sbjct:   122 LEVFQEAEMLVNIKEHVLVPEHQVLTTEEKKTLLERYTVKETQL 165

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

FB|FBgn0033571 Rpb5 "Rpb5" [Drosophila melanogaster (taxid:7227)]

 Score = 401 (146.2 bits), Expect = 2.4e-37, P = 2.4e-37
 Identities = 81/170 (47%), Positives = 117/170 (68%)

Query:     3 LSDE-EIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMK-----REDLVI 56
             + DE E  +L+RIR+T+MQ+  DRGY V   E++ + EQF   FG+        R DL++
Sbjct:     1 MDDEAETYKLWRIRKTIMQLSHDRGYLVTQDELDQTLEQFKEMFGDKPSEKRPARSDLIV 60

Query:    57 NKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQE 116
               A  +D +DQ++VFFP+E K+G+KT+KTY  RM+ EN+ RAI+VVQ  +TP A+  + +
Sbjct:    61 LVAHNDDPTDQMFVFFPEEPKIGIKTIKTYCTRMQEENIHRAIVVVQGGMTPSAKQSLVD 120

Query:   117 ISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             ++ K+ LE F E+ELL+NI EH LVPEH V+T EEK+ LL RY +KE  +
Sbjct:   121 MAPKYILEQFLESELLINITEHELVPEHVVMTVEEKQELLSRYKLKENML 170

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

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

 Score = 399 (145.5 bits), Expect = 3.9e-37, P = 3.9e-37
 Identities = 78/167 (46%), Positives = 117/167 (70%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     4 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    64 HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E+Q+
Sbjct:   124 KYVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQL 170

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 = 399 (145.5 bits), Expect = 3.9e-37, P = 3.9e-37
 Identities = 78/167 (46%), Positives = 117/167 (70%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     4 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    64 HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E+Q+
Sbjct:   124 KYVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQL 170

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 = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 78/167 (46%), Positives = 116/167 (69%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     4 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    64 HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+
Sbjct:   124 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 170

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|E2R2E8 POLR2E "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 78/167 (46%), Positives = 116/167 (69%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     4 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    64 HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+
Sbjct:   124 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 170

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F6X571 POLR2E "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 78/167 (46%), Positives = 116/167 (69%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     4 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    64 HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+
Sbjct:   124 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 170

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

GO:0005634 "nucleus" 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 = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 78/167 (46%), Positives = 116/167 (69%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     4 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 63

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    64 HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+
Sbjct:   124 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 170

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

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 78/167 (46%), Positives = 116/167 (69%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     4 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLVA 63

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    64 HNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 123

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+
Sbjct:   124 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 170

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

UNIPROTKB|F1NHV9 POLR2E "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 78/167 (46%), Positives = 116/167 (69%)

Query:     5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINKA 59
             +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  A
Sbjct:     9 EEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVA 68

Query:    60 LRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISA 119
               +D +DQ++VFFP+E KVG+KT+K Y  RM+ EN+ RA++VVQQ +TP A+  + +++ 
Sbjct:    69 HNDDPTDQMFVFFPEEPKVGIKTIKMYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAP 128

Query:   120 KFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             K+ LE F + ELL+NI EH LVPEH V+T EE   LL RY ++E Q+
Sbjct:   129 KYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 175

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	170
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	7e-97
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	7e-50
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	3e-36
pfam01191	74	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-	7e-12
COG2012	80	COG2012, RPB5, DNA-directed RNA polymerase, subuni	1e-08
PRK09570	79	PRK09570, rpoH, DNA-directed RNA polymerase subuni	5e-08

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

 Score =  278 bits (713), Expect = 7e-97
 Identities = 106/165 (64%), Positives = 129/165 (78%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           M    EE  RL+ +RRTV++MLRDRGY V D E+N++  +F  KFGE  KREDL I+   
Sbjct: 1   MDTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPK 60

Query: 61  RNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK 120
           R+D S +I VFFP+E+KVGVKT+KTY  RMK ENV RAILV+Q  LTPFA+  + E ++K
Sbjct: 61  RSDPSKKILVFFPEEEKVGVKTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSK 120

Query: 121 FHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
           F +EVFQE ELLVNI +HVLVP+HQVLT+EEKKTLLKRYTVKETQ
Sbjct: 121 FKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQ 165

Length = 206

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

 Score =  159 bits (403), Expect = 7e-50
 Identities = 70/164 (42%), Positives = 103/164 (62%), Gaps = 2/164 (1%)

Query: 5   DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMK-REDLVINKALRND 63
           D+   R FR RRT  +ML DRGY +   E   +   F  +F EN + R  +++  + + D
Sbjct: 2   DDSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTD 61

Query: 64  SSDQIYVFFPDE-QKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFH 122
            +++I V+F DE +K GVK ++  T +M+  ++ RAILV Q  LTPFA+  I E + +  
Sbjct: 62  PTNRIIVYFADETKKTGVKPIRELTEKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHI 121

Query: 123 LEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
           +E F E ELLVNI +H LVP+H  LT++EK  LL+RY VKE+Q+
Sbjct: 122 IENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQL 165

Length = 205

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

 Score =  120 bits (304), Expect = 3e-36
 Identities = 44/90 (48%), Positives = 63/90 (70%), Gaps = 2/90 (2%)

Query: 4  SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKF--GENMKREDLVINKALR 61
           + E+ RL+R+RRTVM+MLRDRGY V + E+N+S E+F  K+    N  R  L  +   +
Sbjct: 3  DERELYRLWRVRRTVMEMLRDRGYLVTEEELNLSLEEFKEKYGDNGNPDRSKLTFSARPK 62

Query: 62 NDSSDQIYVFFPDEQKVGVKTMKTYTNRMK 91
          +D S +IYVFF +E+KVGVKT++T+  RMK
Sbjct: 63 DDPSGRIYVFFCEEEKVGVKTIRTFVERMK 92

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

 Score = 57.5 bits (140), Expect = 7e-12
 Identities = 22/33 (66%), Positives = 27/33 (81%)

Query: 133 VNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
           VNI +H LVP+H+VL+ EEKK LLKRY +KE Q
Sbjct: 1   VNITKHELVPKHEVLSEEEKKKLLKRYKIKEEQ 33

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

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 127 QEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
            E+ L  N+ +H LVPEH+VL+ EE K +LK   ++  Q
Sbjct: 1   MESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQ 39

Length = 80

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

 Score = 47.5 bits (114), Expect = 5e-08
 Identities = 16/33 (48%), Positives = 23/33 (69%)

Query: 133 VNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
            ++ +H LVPEH++L+ EE K LLK Y +K  Q
Sbjct: 4   FDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQ 36

Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	170
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
PF03871	93	RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal do	99.98
PRK09570	79	rpoH DNA-directed RNA polymerase subunit H; Review	99.59
PF01191	74	RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal do	99.56
COG2012	80	RPB5 DNA-directed RNA polymerase, subunit H, RpoH/	99.55
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	96.86

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

Probab=100.00  E-value=5.5e-66  Score=419.27  Aligned_cols=167  Identities=58%  Similarity=0.890  Sum_probs=164.4

Q ss_pred             CcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCC-CCCcceEEEeecCCCCCCcEEEEeCCCCccchh
Q 030846            3 LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN-MKREDLVINKALRNDSSDQIYVFFPDEQKVGVK   81 (170)
Q Consensus         3 ~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk   81 (170)
                      +++.|++||||+|||++||||||||.|+++|+++++++|+++||+. ++|++|+|++.|++||+++||||||++++||+|
T Consensus         4 ~~e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk   83 (208)
T KOG3218|consen    4 SKEEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVK   83 (208)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHH
Confidence            4578999999999999999999999999999999999999999998 889999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHHHHHhhcCC
Q 030846           82 TMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTV  161 (170)
Q Consensus        82 ~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~~  161 (170)
                      +||.|+.+|.++|+++||+|+|++|||+|++++..++|.|+||+|+|+||+||||+|+|||+|++||+|||++||++|++
T Consensus        84 ~~k~~~~~~~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l  163 (208)
T KOG3218|consen   84 TMKTYVIQMQSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKL  163 (208)
T ss_pred             HHHHHHHHHHhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCC
Q 030846          162 KETQVSDK  169 (170)
Q Consensus       162 ~~~qlP~~  169 (170)
                      +++|||+|
T Consensus       164 ~e~qLPRI  171 (208)
T KOG3218|consen  164 KETQLPRI  171 (208)
T ss_pred             CcccCCee
Confidence            99999998

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

Probab=100.00  E-value=4.9e-65  Score=418.35  Aligned_cols=170  Identities=62%  Similarity=0.940  Sum_probs=166.7

Q ss_pred             CCCcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccch
Q 030846            1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGV   80 (170)
Q Consensus         1 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgv   80 (170)
                      |++++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||++++|++|+|++++.+||+++|||||+++++||+
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            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHHHHHhhcC
Q 030846           81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYT  160 (170)
Q Consensus        81 k~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~  160 (170)
                      |+||.|+++|+++|+++||||+|+++||+|++++.++++.++||+|+|+||+||||+|+|||+|++||+|||++||++|+
T Consensus        81 k~ir~~~~~~~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~  160 (206)
T PLN03111         81 KTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYT  160 (206)
T ss_pred             HHHHHHHHHHhhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcC
Confidence            99999999999999999999999999999999999998889999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCC
Q 030846          161 VKETQVSDKF  170 (170)
Q Consensus       161 ~~~~qlP~~~  170 (170)
                      ++++|||+|.
T Consensus       161 i~~~qLPrI~  170 (206)
T PLN03111        161 VKETQLPRIQ  170 (206)
T ss_pred             CCHHHCCccc
Confidence            9999999984

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=1.6e-63  Score=408.89  Aligned_cols=166  Identities=42%  Similarity=0.659  Sum_probs=160.6

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCC-CCcceEEEeecCCCCCCcEEEEeCC-CCccchhH
Q 030846            5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-KREDLVINKALRNDSSDQIYVFFPD-EQKVGVKT   82 (170)
Q Consensus         5 ~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~-~r~~L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~   82 (170)
                      ++++.||||+|||++|||+||||.|+++|+++|+++|+++||+++ .|++|+|++++.+||+++|||||++ +++||+|+
T Consensus         2 ~~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~   81 (205)
T PTZ00061          2 DDSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKP   81 (205)
T ss_pred             cHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHH
Confidence            367899999999999999999999999999999999999999985 5899999999999999999999999 46999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHHHHHhhcCCC
Q 030846           83 MKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVK  162 (170)
Q Consensus        83 Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~  162 (170)
                      ||.|+++|+++|++|||||+|+++||+|++++.++++.|+||+|+|+||+||||+|+|||+|++||+|||++||++|+++
T Consensus        82 ir~~~~~~~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~  161 (205)
T PTZ00061         82 IRELTEKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVK  161 (205)
T ss_pred             HHHHHHHHhhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCC
Confidence            99999999999999999999999999999999999988999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCC
Q 030846          163 ETQVSDKF  170 (170)
Q Consensus       163 ~~qlP~~~  170 (170)
                      ++|||+|.
T Consensus       162 ~~qLPrI~  169 (205)
T PTZ00061        162 ESQLPRIQ  169 (205)
T ss_pred             HHHCCccc
Confidence            99999984

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

Probab=99.98  E-value=1.6e-34  Score=211.63  Aligned_cols=90  Identities=62%  Similarity=1.022  Sum_probs=74.6

Q ss_pred             CCCcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcC---CCCCcceEEEeecCCCCCCcEEEEeCCCCc
Q 030846            1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE---NMKREDLVINKALRNDSSDQIYVFFPDEQK   77 (170)
Q Consensus         1 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~---~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~   77 (170)
                      |+ +++|++||||||||++|||+||||.|+++|+++|+++|+++||+   .++|++|+|++.+.+||+++|+|||+++++
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            55 45999999999999999999999999999999999999999999   677999999999999999999999999999


Q ss_pred             cchhHHHHHHHHHh
Q 030846           78 VGVKTMKTYTNRMK   91 (170)
Q Consensus        78 vgvk~Ir~~~~~~~   91 (170)
                      ||+|+||.|+++|+
T Consensus        80 vgvk~Ir~~~~~m~   93 (93)
T PF03871_consen   80 VGVKTIRKYCERMK   93 (93)
T ss_dssp             ESCCCCHHHCHHH-
T ss_pred             cCHHHHHHHHHhcC
Confidence            99999999999984

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 ....

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

Probab=99.59  E-value=3.7e-16  Score=111.77  Aligned_cols=39  Identities=41%  Similarity=0.666  Sum_probs=37.6

Q ss_pred             ccccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          132 LVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       132 l~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      .||||+|+|||+|++||+||+++||++|+++++|||||.
T Consensus         3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~   41 (79)
T PRK09570          3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIK   41 (79)
T ss_pred             ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCcee
Confidence            589999999999999999999999999999999999984

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

Probab=99.56  E-value=9.6e-16  Score=108.45  Aligned_cols=38  Identities=47%  Similarity=0.819  Sum_probs=31.8

Q ss_pred             cccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          133 VNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       133 ~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      ||||+|+|||+|++||+||++++|++|+++++|||+|.
T Consensus         1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~   38 (74)
T PF01191_consen    1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKIL   38 (74)
T ss_dssp             S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEE
T ss_pred             CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCccc
Confidence            79999999999999999999999999999999999973

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=99.55  E-value=1.4e-15  Score=108.09  Aligned_cols=42  Identities=40%  Similarity=0.616  Sum_probs=40.5

Q ss_pred             ccccccccccccccccccccCHHHHHHHHhhcCCCCCCCCCC
Q 030846          128 EAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDK  169 (170)
Q Consensus       128 e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~  169 (170)
                      ++.+.||+++|+|||+|++||+||++++|++|+|+++|||||
T Consensus         2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI   43 (80)
T COG2012           2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKI   43 (80)
T ss_pred             ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcc
Confidence            567899999999999999999999999999999999999998

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

Probab=96.86  E-value=0.0034  Score=44.91  Aligned_cols=64  Identities=22%  Similarity=0.376  Sum_probs=38.3

Q ss_pred             CcEEEEeCC-CCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccc
Q 030846           66 DQIYVFFPD-EQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELL  132 (170)
Q Consensus        66 ~~i~VfF~~-~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl  132 (170)
                      ..++|.+-. ..+++.+.|+.++..+...+...++||+.+++|+.|++.+....   .|+++.-++|.
T Consensus        48 ~~~~vqcK~~~~~v~~~~v~~~~~~~~~~~~~~~iivt~~~~t~~a~~~~~~~~---~I~l~d~~~L~  112 (115)
T PF04471_consen   48 ERILVQCKRYKKKVDVKAVRQLIGKAKKYGADKGIIVTSSGFTPEAKEFAEKFK---NIELIDGEDLQ  112 (115)
T ss_dssp             EEEEEEE---S-EE-HHHHHHHHHHHGGGT-SEEEEE-SSEE-HHHHHHHH-----------------
T ss_pred             eEEEEEEEEeccccchHHHHHHhhhhhccCCCEEEEEECCcCCHHHHHHHHhhc---ccccccccccc
Confidence            466666633 35899999999999999999999999999999999999887653   47777766663

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	170
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		1e-28
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		1e-26

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

Iteration: 1
 Score =  122 bits (305), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 64/170 (37%), Positives = 101/170 (59%), Gaps = 4/170 (2%)
Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIA---KFGENMKREDLVIN 57
           M+  ++ I R+FR  +T  Q++ DRGY V   E++++ +QF A     G N+ R  L   
Sbjct: 1   MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFY 60
Query: 58  KALRNDSS-DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQE 116
               NDS+   IY+ F  E  VG+K M+T+ + +   N    IL+   ++TP A   I  
Sbjct: 61  AKPSNDSNKGTIYIEFAKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIAT 120
Query: 117 ISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
           ++ +F +E FQE++L+VNI  H LVP+H +L+ +EKK LL RY ++ETQ+
Sbjct: 121 VTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQL 170

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

Iteration: 1
 Score =  115 bits (288), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 67/169 (39%), Positives = 97/169 (57%), Gaps = 10/169 (5%)
Query: 8   IKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQ 67
           I RL+R  RTV +M++DRGYF+   E+ +  E F AK+ ++M R    +     N + + 
Sbjct: 9   ISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEES 68
Query: 68  I---------YVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118
           I         +V F DE  VGVKTMKT+   ++ +N    I V Q N+TP A   +  I 
Sbjct: 69  ISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIP 128
Query: 119 AKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
               +E F EA L+VNI  H LVP+H  L+++EK+ LLKRY +KE+Q+ 
Sbjct: 129 PA-TIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLP 176

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	170
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	9e-52
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	8e-47
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	2e-10
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	5e-09
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	6e-09

>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 =  163 bits (414), Expect = 9e-52
 Identities = 64/170 (37%), Positives = 101/170 (59%), Gaps = 4/170 (2%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKF---GENMKREDLVIN 57
           M+  ++ I R+FR  +T  Q++ DRGY V   E++++ +QF A     G N+ R  L   
Sbjct: 1   MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFY 60

Query: 58  KALRNDSSDQ-IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQE 116
               NDS+   IY+ F  E  VG+K M+T+ + +   N    IL+   ++TP A   I  
Sbjct: 61  AKPSNDSNKGTIYIEFAKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIAT 120

Query: 117 ISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
           ++ +F +E FQE++L+VNI  H LVP+H +L+ +EKK LL RY ++ETQ+
Sbjct: 121 VTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQL 170

>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 =  151 bits (381), Expect = 8e-47
 Identities = 66/172 (38%), Positives = 99/172 (57%), Gaps = 10/172 (5%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRND 63
           ++  I RL+R  RTV +M++DRGYF+   E+ +  E F AK+ ++M R    +     N 
Sbjct: 5   NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANP 64

Query: 64  SSDQ---------IYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI 114
           + +          ++V F DE  VGVKTMKT+   ++ +N    I V Q N+TP A   +
Sbjct: 65  TEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLV 124

Query: 115 QEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
             I     +E F EA L+VNI  H LVP+H  L+++EK+ LLKRY +KE+Q+
Sbjct: 125 PSIP-PATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQL 175

>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 = 53.6 bits (129), Expect = 2e-10
 Identities = 11/38 (28%), Positives = 22/38 (57%)

Query: 128 EAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
            +   ++ + H LVP+H+VL+ +E   +LK   ++  Q
Sbjct: 4   SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQ 41

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

 Score = 49.7 bits (119), Expect = 5e-09
 Identities = 13/33 (39%), Positives = 24/33 (72%)

Query: 133 VNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
           + + +H+LVP+H+++  EE + +LKRY +K  Q
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQ 33

>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 = 49.7 bits (119), Expect = 6e-09
 Identities = 13/35 (37%), Positives = 17/35 (48%)

Query: 131 LLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
           +   I +H LVPEH +L   E K +LK       Q
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQ 35

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	170
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	99.7
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	99.62
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	99.61

>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=1.8e-63  Score=409.80  Aligned_cols=170  Identities=36%  Similarity=0.603  Sum_probs=163.5

Q ss_pred             CCCcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCC---CCCcceEEEeecCCCC-CCcEEEEeCCCC
Q 030846            1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN---MKREDLVINKALRNDS-SDQIYVFFPDEQ   76 (170)
Q Consensus         1 m~~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~---~~r~~L~~~~~~~~dp-~~~i~VfF~~~~   76 (170)
                      |+++++|++||||+|||++|||+||||.|+++|+++|+++|+++||++   ++|++|+|++++.+|| +++|+|||++++
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            788889999999999999999999999999999999999999999987   5699999999999999 999999999999


Q ss_pred             ccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHHHHH
Q 030846           77 KVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLL  156 (170)
Q Consensus        77 ~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~~ll  156 (170)
                      +||+|+||.|+++|.++|+++||||+|+++||+|++++.+++++++||+|+|+||+||||+|+|||+|++||+||+++||
T Consensus        81 ~vgvk~Ir~~~~~~~~en~~~~IiV~q~~~t~~A~~~l~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eE~~~lL  160 (210)
T 3h0g_E           81 SVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELL  160 (210)
T ss_dssp             SCCTTTTGGGTHHHHHTTCSEEEECCSSCCCSHHHHTTTTTCTTCEECCCCSSSSCSCTTSBTTBCCEECCCHHHHHHHH
T ss_pred             ccChHHHHHHHHHHHHcCCceEEEEECCCCCHHHHHHHHHhCcCcEEEEEeehHeeEecccccccCcEEEcCHHHHHHHH
Confidence            99999999999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCCCCCC
Q 030846          157 KRYTVKETQVSDKF  170 (170)
Q Consensus       157 ~~y~~~~~qlP~~~  170 (170)
                      ++|+++++|||+|.
T Consensus       161 ~~y~i~~~qLP~I~  174 (210)
T 3h0g_E          161 DRYKLRETQLPRIQ  174 (210)
T ss_dssp             HHTCCCTTTSCCCC
T ss_pred             HHcCCCHHHCCccc
Confidence            99999999999984

>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=6.5e-62  Score=401.61  Aligned_cols=167  Identities=39%  Similarity=0.608  Sum_probs=161.2

Q ss_pred             CcHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcC---CCCCcceEEEeecCCCCCCcE------EEEeC
Q 030846            3 LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE---NMKREDLVINKALRNDSSDQI------YVFFP   73 (170)
Q Consensus         3 ~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~---~~~r~~L~~~~~~~~dp~~~i------~VfF~   73 (170)
                      +++.++.||||+|||++|||+||||.|+++|+++|+++|+++||+   .++|++|+|++++++||++++      +||||
T Consensus         4 ~~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~g~p~r~~L~~~~~~~~d~~~k~~~~~~~~VfF~   83 (215)
T 1dzf_A            4 ENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFC   83 (215)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEEEC
T ss_pred             chHHHHHHHHHHHHHHHHHHhcCCCccCHhHhcCCHHHHHHHHccccCCCchhheEEEecCCCChhhhhccCCceEEEec
Confidence            467899999999999999999999999999999999999999998   567999999999999999998      99999


Q ss_pred             CCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccccccccccccccccCHHHHH
Q 030846           74 DEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKK  153 (170)
Q Consensus        74 ~~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~ni~~H~lVP~h~~l~~eE~~  153 (170)
                      ++++||+|+||+|+++|+++|+++||||+|+++||+|++++.++++ ++||+|+|+||+||||+|+|||+|++||+|||+
T Consensus        84 ~~~~vgvk~ir~~~~~~~~e~~~~~IlV~q~~itp~Ak~~l~~~~~-~~iE~F~e~eL~vni~~H~lVP~H~~l~~eE~~  162 (215)
T 1dzf_A           84 DEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPP-ATIETFNEAALVVNITHHELVPKHIRLSSDEKR  162 (215)
T ss_dssp             SSSEECHHHHHHHHHHHHHTTCSEEEEEESSEECHHHHTTTTSSTT-CEEEEEEHHHHSSCGGGSTTSCEEEECCHHHHH
T ss_pred             CCCccchHHHHHHHHHHHhcCCceEEEEECCCCChHHHHHHHHhcC-ceEEEeehHHheeccccceeccceEEccHHHHH
Confidence            9999999999999999999999999999999999999999999998 899999999999999999999999999999999


Q ss_pred             HHHhhcCCCCCCCCCCC
Q 030846          154 TLLKRYTVKETQVSDKF  170 (170)
Q Consensus       154 ~ll~~y~~~~~qlP~~~  170 (170)
                      +||++|+++++|||+|.
T Consensus       163 ~lL~~y~i~~~qLP~I~  179 (215)
T 1dzf_A          163 ELLKRYRLKESQLPRIQ  179 (215)
T ss_dssp             HHHHHTTCCGGGSCEEC
T ss_pred             HHHHHcCCCHHHCCcee
Confidence            99999999999999984

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

Probab=99.70  E-value=5.9e-18  Score=119.45  Aligned_cols=40  Identities=33%  Similarity=0.457  Sum_probs=38.7

Q ss_pred             cccccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          131 LLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       131 Ll~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      |+||||+|+|||+|++||+|||++||++|+++++|||+|.
T Consensus         1 l~vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLP~I~   40 (77)
T 1eik_A            1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIK   40 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCB
T ss_pred             CcccCccceecCCEEEcCHHHHHHHHHHcCCCHHHCCeee
Confidence            7899999999999999999999999999999999999984

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

Probab=99.62  E-value=6.4e-17  Score=114.39  Aligned_cols=38  Identities=34%  Similarity=0.778  Sum_probs=36.9

Q ss_pred             cccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          133 VNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       133 ~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      ||||+|+|||+|++||+|||++||++|+++++|||+|.
T Consensus         1 vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLPrI~   38 (78)
T 1hmj_A            1 MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIY   38 (78)
T ss_pred             CCccceeeCCCeEECCHHHHHHHHHHcCCCHHHCCeee
Confidence            79999999999999999999999999999999999984

>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=99.61  E-value=1.4e-16  Score=114.16  Aligned_cols=43  Identities=26%  Similarity=0.376  Sum_probs=37.9

Q ss_pred             ccccccccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          128 EAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       128 e~ELl~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      .++++||||+|+|||+|++||+||+++||++|+++++|||+|.
T Consensus         4 ~~~~~~Ni~~H~LVPkH~vLs~eE~~~ll~~y~i~~~qLP~I~   46 (84)
T 4ayb_H            4 SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIR   46 (84)
T ss_dssp             ----CCCCSSSSSCCEEEECCHHHHHHHHHHHTCCGGGSCCEE
T ss_pred             cccceecccccccCCCeEECCHHHHHHHHHHhcCCHhHCCeec
Confidence            4679999999999999999999999999999999999999973

---

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	170
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	2e-49
d1dzfa2	72	d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal do	5e-09
d1eika_	77	d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA pol	7e-09

>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 =  154 bits (390), Expect = 2e-49
 Identities = 49/140 (35%), Positives = 74/140 (52%), Gaps = 10/140 (7%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRND 63
           ++  I RL+R  RTV +M++DRGYF+   E+ +  E F AK+ ++M R    +     N 
Sbjct: 1   NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANP 60

Query: 64  SSD---------QIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI 114
           + +          ++V F DE  VGVKTMKT+   ++ +N    I V Q N+TP A   +
Sbjct: 61  TEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLV 120

Query: 115 QEISAKFHLEVFQEAELLVN 134
             I     +E F EA L+VN
Sbjct: 121 PSIP-PATIETFNEAALVVN 139

>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 = 48.2 bits (115), Expect = 5e-09
 Identities = 17/31 (54%), Positives = 24/31 (77%)

Query: 135 IKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
           I  H LVP+H  L+++EK+ LLKRY +KE+Q
Sbjct: 1   ITHHELVPKHIRLSSDEKRELLKRYRLKESQ 31

>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 = 48.2 bits (115), Expect = 7e-09
 Identities = 13/35 (37%), Positives = 17/35 (48%)

Query: 131 LLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQ 165
           +   I +H LVPEH +L   E K +LK       Q
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQ 35

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	170
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	100.0
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	99.5
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	99.3
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	98.48
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	82.87

>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-47  Score=292.87  Aligned_cols=130  Identities=36%  Similarity=0.585  Sum_probs=122.2

Q ss_pred             cHHHHHHHHHHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCC---CCCcceEEEeecCCC------CCCcEEEEeCC
Q 030846            4 SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN---MKREDLVINKALRND------SSDQIYVFFPD   74 (170)
Q Consensus         4 ~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~---~~r~~L~~~~~~~~d------p~~~i~VfF~~   74 (170)
                      +++|++||||+||||+|||+||||.|+++|+++|+++|+++||++   ++|+.|++.+.+.++      ++++||||||+
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            478999999999999999999999999999999999999999987   568999999987765      45679999999


Q ss_pred             CCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhcccccceeeeeccccccc
Q 030846           75 EQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVN  134 (170)
Q Consensus        75 ~~~vgvk~Ir~~~~~~~~e~~~~~IiV~q~~lt~~Ar~~~~~~~~~~~iE~F~e~ELl~n  134 (170)
                      +++||+|+||.|+++|+++|++|||||+|++|||+|++++.++++ ++||+|+|+|||||
T Consensus        81 ~~kvgvk~ir~~~~~m~~~~~~r~IlV~q~~iTp~Ak~~i~~~~~-~~iE~F~e~eLLVN  139 (139)
T d1dzfa1          81 EPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPP-ATIETFNEAALVVN  139 (139)
T ss_dssp             SSEECHHHHHHHHHHHHHTTCSEEEEEESSEECHHHHTTTTSSTT-CEEEEEEHHHHSSC
T ss_pred             CCccCHHHHHHHHHHHHhcCCceEEEEECCCCCHHHHHHHHhccC-ceEEEechhhcccC
Confidence            999999999999999999999999999999999999999998875 79999999999998

>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=99.50  E-value=3.4e-15  Score=103.60  Aligned_cols=40  Identities=33%  Similarity=0.457  Sum_probs=38.5

Q ss_pred             cccccccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          131 LLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       131 Ll~ni~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      |.+||++|+|||+|++||+||++++|++|+++.+|||+|.
T Consensus         1 l~~NI~~H~lVPkH~il~~ee~~~~l~~~~i~~~qLP~I~   40 (77)
T d1eika_           1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIK   40 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCB
T ss_pred             CCccccccccCCCeEEcCHHHHHHHHHHhcCCHHHCCeec
Confidence            6799999999999999999999999999999999999984

>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=99.30  E-value=2.8e-13  Score=92.68  Aligned_cols=36  Identities=47%  Similarity=0.731  Sum_probs=34.7

Q ss_pred             cccccccccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          135 IKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       135 i~~H~lVP~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      ||+|+|||+|++||+||++++|++|+++.+|||.|.
T Consensus         1 It~H~lVPkH~~l~~eE~~~il~~y~i~~~qLP~I~   36 (72)
T d1dzfa2           1 ITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQ   36 (72)
T ss_dssp             GGGSTTSCEEEECCHHHHHHHHHHTTCCGGGSCEEC
T ss_pred             CCcCccCCCeEEcCHHHHHHHHHHhCCCHhHCCeec
Confidence            799999999999999999999999999999999874

>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=98.48  E-value=1.9e-08  Score=67.47  Aligned_cols=29  Identities=34%  Similarity=0.735  Sum_probs=28.0

Q ss_pred             ccccccCHHHHHHHHhhcCCCCCCCCCCC
Q 030846          142 PEHQVLTNEEKKTLLKRYTVKETQVSDKF  170 (170)
Q Consensus       142 P~h~~l~~eE~~~ll~~y~~~~~qlP~~~  170 (170)
                      |+|++||+||++++|++|+++.+|||+|.
T Consensus         1 PkH~il~~eE~~~ll~~y~i~~~qLP~I~   29 (68)
T d1hmja_           1 PKHEIVPKEEVEEILKRYNIKIQQLPKIY   29 (68)
T ss_pred             CCCEECCHHHHHHHHHHhCCCHHHCCccc
Confidence            99999999999999999999999999984

>d7reqa2 c.23.6.1 (A:561-728) Methylmalonyl-CoA mutase alpha subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methylmalonyl-CoA mutase alpha subunit, C-terminal domain
species: Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]

Probab=82.87  E-value=0.98  Score=33.23  Aligned_cols=88  Identities=8%  Similarity=-0.007  Sum_probs=63.4

Q ss_pred             HHHHHHHHHhcCCCCCCChhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEeCCCCccchhHHHHHHHHHhh
Q 030846           13 RIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKS   92 (170)
Q Consensus        13 r~rrTv~eMl~DRGY~v~~~e~~~s~~~F~~~~~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~Ir~~~~~~~~   92 (170)
                      +-++.+..++++.||.|..--...|.++|.+..-+. +-+-+.++.                -....+..++.+++.+.+
T Consensus        52 ~G~~~va~~l~~~G~eVi~lg~~~~~e~iv~aa~~~-~advI~iSs----------------~~~~~~~~~~~l~~~L~~  114 (168)
T d7reqa2          52 RGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEA-DVHVVGVSS----------------LAGGHLTLVPALRKELDK  114 (168)
T ss_dssp             HHHHHHHHHHHHTTCEEEECCTTBCHHHHHHHHHHH-TCSEEEEEE----------------CSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcceecCCCcCcHHHHHHHHHcc-CCCEEEEec----------------CcccchHHHHHHHHHHHh
Confidence            456788899999999998877888999999876443 122233322                223577889999999999


Q ss_pred             cCCCeEEEEEcCCCCHHHHHHHHhc
Q 030846           93 ENVFRAILVVQQNLTPFARTCIQEI  117 (170)
Q Consensus        93 e~~~~~IiV~q~~lt~~Ar~~~~~~  117 (170)
                      .+....++++.+.+.+.-...+.+.
T Consensus       115 ~g~~~v~VivGG~ip~~d~~~l~~~  139 (168)
T d7reqa2         115 LGRPDILITVGGVIPEQDFDELRKD  139 (168)
T ss_dssp             TTCTTSEEEEEESCCGGGHHHHHHH
T ss_pred             cCCCCeEEEEeCCCCHHHHHHHHhC
Confidence            9988887787777666555555544