Citrus Sinensis ID: 032325

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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---
Protein Sequence
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHccccccccHHHHcccHHHHHHHHcccccccccEEEEcccccccccEEEEccccccccHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHcccccEEEEEEccEEEEEccccEEEcc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHHHHHHHHcccEccHHHHcccHHHHHHHHccccccccEEEEEcccccccccEEEEEccccEEcHHHHHHHHHHHHHccccEEEEEEccEEcHHHHcccccccccEEEEEEEHHHEEEEEccEEEEcc
Coil and Loop (DISEMBL)
MTLSDEEIKRLFRIRRTVMQMLRDrgyfvgdfeinMSKEQFIAKFGENMKREDLVINKAlrndssdqiyvffpdeqkvgVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
Flexible Loop (DISEMBL)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALrndssdqiyvffpdeqkvgVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
Low Complexity Region (SEG)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
Disordered region (IsUnstruct)
********KRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLF**
Disordered Region (DISOPRED)
****DEE*KRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKRED****************VFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
Disordered Region (DISEMBL)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
Disordered Region (DISPRO)
****DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFNC
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	143	2.2.26 [Sep-21-2011]
B0BNE2	210	DNA-directed RNA polymera	yes	no	0.860	0.585	0.437	4e-27
Q80UW8	210	DNA-directed RNA polymera	yes	no	0.860	0.585	0.437	4e-27
Q5R587	210	DNA-directed RNA polymera	yes	no	0.860	0.585	0.437	6e-27
P19388	210	DNA-directed RNA polymera	yes	no	0.860	0.585	0.429	4e-26
Q2T9T3	210	DNA-directed RNA polymera	yes	no	0.860	0.585	0.429	6e-26
Q9N5K2	211	DNA-directed RNA polymera	yes	no	0.867	0.587	0.404	2e-24
A8XGH1	211	DNA-directed RNA polymera	N/A	no	0.867	0.587	0.412	2e-24
Q54EH2	197	DNA-directed RNA polymera	yes	no	0.860	0.624	0.415	2e-22
Q09191	210	DNA-directed RNA polymera	yes	no	0.888	0.604	0.328	8e-15
Q6FQA6	215	DNA-directed RNA polymera	yes	no	0.888	0.590	0.321	3e-13

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

 Score =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 56/128 (43%), Positives = 88/128 (68%), Gaps = 5/128 (3%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINK 58
            +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  
Sbjct: 3   DEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLV 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 AKFHLEVF 126
            K+ LE F
Sbjct: 123 PKYVLEQF 130

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 =  119 bits (299), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 56/128 (43%), Positives = 88/128 (68%), Gaps = 5/128 (3%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINK 58
            +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+FG+       +R DL +  
Sbjct: 3   DEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLV 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 AKFHLEVF 126
            K+ LE F
Sbjct: 123 PKYVLEQF 130

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 =  119 bits (298), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 56/128 (43%), Positives = 88/128 (68%), Gaps = 5/128 (3%)

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 AKFHLEVF 126
            K+ LE F
Sbjct: 123 PKYILEQF 130

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

 Score =  116 bits (291), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 55/128 (42%), Positives = 87/128 (67%), Gaps = 5/128 (3%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINK 58
            +EE  RL++IR+T+MQ+  DRGY V   E++ + E+F A+ G+       +R DL +  
Sbjct: 3   DEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQSGDKPSEGRPRRTDLTVLV 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 AKFHLEVF 126
            K+ LE F
Sbjct: 123 PKYILEQF 130

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 =  115 bits (289), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 55/128 (42%), Positives = 86/128 (67%), Gaps = 5/128 (3%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-----KREDLVINK 58
            +EE  RL++IR+T+MQ+  DRGY V    ++ + E+F A+FG        +R DL +  
Sbjct: 3   DEEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLV 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 AKFHLEVF 126
            K+ LE F
Sbjct: 123 PKYILEQF 130

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

 Score =  111 bits (277), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 53/131 (40%), Positives = 87/131 (66%), Gaps = 7/131 (5%)

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 EISAKFHLEVF 126
           +++ K+ LE F
Sbjct: 121 DMAPKYMLEHF 131

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 =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 54/131 (41%), Positives = 86/131 (65%), Gaps = 7/131 (5%)

Query: 3   LSDEEIK--RLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE-----NMKREDLV 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 EISAKFHLEVF 126
           +++ K+ LE F
Sbjct: 121 DMAPKYMLEHF 131

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

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 54/130 (41%), Positives = 79/130 (60%), Gaps = 7/130 (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  DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEV 125
           D IYVFFPD  KVGV  +K Y + MK     RAI+VVQQN+TPFA+  + E S +  + +
Sbjct: 55  DSIYVFFPDTPKVGVTQIKKYVDIMKDRQANRAIIVVQQNITPFAKQALAEFSQEKKITL 114

Query: 126 FQVNVFSLMI 135
            Q N   L++
Sbjct: 115 EQFNEAELLV 124

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 = 79.0 bits (193), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 70/131 (53%), Gaps = 4/131 (3%)

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 ISAKFHLEVFQ 127
           ++ +F +E FQ
Sbjct: 121 VTGQFTIETFQ 131

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|Q6FQA6|RPAB1_CANGA DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=RPB5 PE=3 SV=1

 Score = 73.9 bits (180), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 45/140 (32%), Positives = 70/140 (50%), Gaps = 13/140 (9%)

Query: 4   SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRND 63
           +D  I RL+R  RTV +M+RDRGYF+   E++++ E F  K+ ++M R    +     N 
Sbjct: 5   NDRSISRLWRTFRTVKEMVRDRGYFIAQEELDLTLEDFKVKYCDSMGRAQRKMMSFQANP 64

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

Query: 115 QEISAK----FHLEVFQVNV 130
             I       FH     VN+
Sbjct: 125 PSIPPATIETFHEAALVVNI 144

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

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	143
225445170	206	PREDICTED: DNA-directed RNA polymerases	0.888	0.616	0.881	5e-61
224119828	206	predicted protein [Populus trichocarpa]	0.888	0.616	0.858	6e-59
351723363	206	uncharacterized protein LOC100499667 [Gl	0.888	0.616	0.787	2e-54
351722355	206	uncharacterized protein LOC100306098 [Gl	0.888	0.616	0.787	5e-54
449462431	207	PREDICTED: DNA-directed RNA polymerases	0.888	0.613	0.789	1e-53
15228724	205	DNA-directed RNA polymerase II subunit E	0.874	0.609	0.784	2e-53
297835232	205	ATRPABC24.3 [Arabidopsis lyrata subsp. l	0.874	0.609	0.768	2e-52
297738790	186	unnamed protein product [Vitis vinifera]	0.748	0.575	0.906	8e-52
449502080	208	PREDICTED: DNA-directed RNA polymerases	0.888	0.610	0.767	9e-52
388506474	206	unknown [Medicago truncatula]	0.888	0.616	0.740	2e-50

>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 =  238 bits (608), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 112/127 (88%), Positives = 120/127 (94%)

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 FHLEVFQ 127
           FHLEVFQ
Sbjct: 121 FHLEVFQ 127

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 =  231 bits (590), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 109/127 (85%), Positives = 118/127 (92%)

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 FHLEVFQ 127
           FHLEVFQ
Sbjct: 121 FHLEVFQ 127

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 =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 100/127 (78%), Positives = 115/127 (90%)

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 FHLEVFQ 127
           FHLEVFQ
Sbjct: 121 FHLEVFQ 127

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  215 bits (547), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 100/127 (78%), Positives = 114/127 (89%)

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 FHLEVFQ 127
           FHLEVFQ
Sbjct: 121 FHLEVFQ 127

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 =  214 bits (544), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 101/128 (78%), Positives = 115/128 (89%), Gaps = 1/128 (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 -FHLEVFQ 127
            FHLEVFQ
Sbjct: 121 SFHLEVFQ 128

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 =  213 bits (541), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 98/125 (78%), Positives = 114/125 (91%)

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 LEVFQ 127
           LEVFQ
Sbjct: 122 LEVFQ 126

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  209 bits (533), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 96/125 (76%), Positives = 113/125 (90%)

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 LEVFQ 127
           LEVFQ
Sbjct: 122 LEVFQ 126

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 =  207 bits (528), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 97/107 (90%), Positives = 102/107 (95%)

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

Query: 81  KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQ 127
           KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCI EIS KFHLEVFQ
Sbjct: 61  KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCINEISTKFHLEVFQ 107

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 =  207 bits (528), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 99/129 (76%), Positives = 115/129 (89%), Gaps = 2/129 (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-FHLEVFQ 127
           K FHLEVFQ
Sbjct: 121 KSFHLEVFQ 129

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388506474|gb|AFK41303.1| unknown [Medicago truncatula]

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/127 (74%), Positives = 109/127 (85%)

Query: 1   MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKAL 60
           M  S+EEI RL+RIR+TVMQML+DR Y VGDFE+NMSK  F  K+GENMKREDLVINK  
Sbjct: 1   MVFSEEEITRLYRIRKTVMQMLKDRNYLVGDFELNMSKHDFKDKYGENMKREDLVINKTK 60

Query: 61  RNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAK 120
           ++  SDQIYVFFP+E KVGVKTMKTYTNRM SENV+RAILV Q +LTPFA+TC+ EI++K
Sbjct: 61  KDKPSDQIYVFFPEEAKVGVKTMKTYTNRMNSENVYRAILVCQTSLTPFAKTCVSEIASK 120

Query: 121 FHLEVFQ 127
           FHLEVFQ
Sbjct: 121 FHLEVFQ 127

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	143
TAIR|locus:2087842	205	NRPB5 [Arabidopsis thaliana (t	0.874	0.609	0.784	4.6e-50
UNIPROTKB|F2Z4J4	210	POLR2E "DNA-directed RNA polym	0.853	0.580	0.440	2.2e-25
UNIPROTKB|E2R2E8	212	POLR2E "Uncharacterized protei	0.853	0.575	0.440	2.2e-25
UNIPROTKB|F6X571	210	POLR2E "Uncharacterized protei	0.853	0.580	0.440	2.2e-25
UNIPROTKB|I3LSI7	210	POLR2E "Uncharacterized protei	0.853	0.580	0.440	2.2e-25
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.853	0.580	0.440	2.2e-25
MGI|MGI:1913670	210	Polr2e "polymerase (RNA) II (D	0.853	0.580	0.440	2.2e-25
RGD|1589817	210	Polr2e "polymerase (RNA) II (D	0.853	0.580	0.440	2.2e-25
UNIPROTKB|F1NHV9	215	POLR2E "Uncharacterized protei	0.853	0.567	0.440	2.9e-25
FB|FBgn0033571	210	Rpb5 "Rpb5" [Drosophila melano	0.867	0.590	0.438	1.2e-24

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

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 98/125 (78%), Positives = 114/125 (91%)

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 LEVFQ 127
             LEVFQ
Sbjct:   122 LEVFQ 126

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

GO:0051604 "protein maturation" evidence=RCA

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

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   124 KYILEQF 130

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 = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   124 KYILEQF 130

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 = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   124 KYILEQF 130

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 = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   124 KYILEQF 130

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 = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   124 KYILEQF 130

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

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

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   124 KYVLEQF 130

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 = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   124 KYVLEQF 130

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

 Score = 287 (106.1 bits), Expect = 2.9e-25, P = 2.9e-25
 Identities = 56/127 (44%), Positives = 88/127 (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 KFHLEVF 126
             K+ LE F
Sbjct:   129 KYILEQF 135

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

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

 Score = 281 (104.0 bits), Expect = 1.2e-24, P = 1.2e-24
 Identities = 57/130 (43%), Positives = 87/130 (66%)

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 ISAKFHLEVF 126
             ++ K+ LE F
Sbjct:   121 MAPKYILEQF 130

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

---

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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00016705001	SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (206 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00002744001	SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)	•			•	•	•	•		0.983
	GSVIVG00018575001	RecName- Full=DNA-directed RNA polymerase; EC=2.7.7.6; (1220 aa)	•			•	•	•	•		0.957
	GSVIVG00033123001	SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_64, whole genome shotg [...] (114 aa)			•	•	•	•	•		0.952
	GSVIVG00036639001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (318 aa)	•			•	•	•	•		0.924
	GSVIVG00024229001	SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (176 aa)				•	•	•	•		0.924
	GSVIVG00032808001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (116 aa)				•	•	•	•		0.921
	GSVIVG00020457001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (208 aa)				•		•			0.917
	GSVIVG00018833001	SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (141 aa)			•	•	•	•	•		0.910
	GSVIVG00028076001	SubName- Full=Chromosome chr7 scaffold_42, whole genome shotgun sequence; (533 aa)				•		•			0.909
	GSVIVG00002140001	SubName- Full=Chromosome chr19 scaffold_126, whole genome shotgun sequence; (528 aa)				•		•			0.908

---

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	143
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	3e-70
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	2e-36
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	1e-31

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

 Score =  209 bits (534), Expect = 3e-70
 Identities = 73/127 (57%), Positives = 93/127 (73%)

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 FHLEVFQ 127
           F +EVFQ
Sbjct: 121 FKIEVFQ 127

Length = 206

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

 Score =  120 bits (303), Expect = 2e-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|173356 PTZ00061, PTZ00061, DNA-directed RNA polymerase; Provisional

 Score =  111 bits (279), Expect = 1e-31
 Identities = 46/124 (37%), Positives = 72/124 (58%), Gaps = 2/124 (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 LEVF 126
           +E F
Sbjct: 122 IENF 125

Length = 205

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	143
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	100.0
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	97.4
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	80.85

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

Probab=100.00  E-value=1.7e-60  Score=371.98  Aligned_cols=140  Identities=50%  Similarity=0.773  Sum_probs=138.0

Q ss_pred             CcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCC-CCCcceEEEeecCCCCCCcEEEEcCCCCccchh
Q 032325            3 LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN-MKREDLVINKALRNDSSDQIYVFFPDEQKVGVK   81 (143)
Q Consensus         3 ~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk   81 (143)
                      +++.|++||||+|||++||||||||.|+|+|++++|++|+++||+. |+|++|+|+|.|++||+++||||||++++||+|
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            5689999999999999999999999999999999999999999998 999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325           82 TMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN  142 (143)
Q Consensus        82 ~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~  142 (143)
                      +||.|+.+|+++|+++||+|+|++|||+|++++..++|+|+||+|+|+|||||||||+|||
T Consensus        84 ~~k~~~~~~~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvP  144 (208)
T KOG3218|consen   84 TMKTYVIQMQSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVP  144 (208)
T ss_pred             HHHHHHHHHHhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecC
Confidence            9999999999999999999999999999999999999999999999999999999999999

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

Probab=100.00  E-value=1.4e-58  Score=365.47  Aligned_cols=142  Identities=53%  Similarity=0.818  Sum_probs=139.6

Q ss_pred             CCCcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccch
Q 032325            1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGV   80 (143)
Q Consensus         1 m~~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgv   80 (143)
                      |+++++|+.||||+|||++|||+||||.|+++|+++|+++|+++||++++|++|+|+|.+++||+++||||||++++||+
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             hHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325           81 KTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN  142 (143)
Q Consensus        81 k~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~  142 (143)
                      |+||+|+++|+++|++|||||+|++|||+|+++++++++.|+||+|+|+|||||||+|+|||
T Consensus        81 k~ir~~~~~~~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVP  142 (206)
T PLN03111         81 KTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVP  142 (206)
T ss_pred             HHHHHHHHHHhhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecC
Confidence            99999999999999999999999999999999999998889999999999999999999999

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=5.4e-57  Score=355.97  Aligned_cols=138  Identities=34%  Similarity=0.552  Sum_probs=133.6

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCC-CCcceEEEeecCCCCCCcEEEEcCC-CCccchhH
Q 032325            5 DEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENM-KREDLVINKALRNDSSDQIYVFFPD-EQKVGVKT   82 (143)
Q Consensus         5 ~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~-~r~~L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~   82 (143)
                      ++++.||||+|||++|||+||||.|+++|+++|+++|+++||+++ .|++|+|+|++++||+++||||||+ +++||+|+
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            378899999999999999999999999999999999999999985 5899999999999999999999999 57999999


Q ss_pred             HHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325           83 MKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN  142 (143)
Q Consensus        83 ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~  142 (143)
                      ||+|+++|+++|++|||||+|++|||+|+++++++++.|+||+|+|+|||||||+|+|||
T Consensus        82 ir~~~~~~~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVP  141 (205)
T PTZ00061         82 IRELTEKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVP  141 (205)
T ss_pred             HHHHHHHHhhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecC
Confidence            999999999999999999999999999999999999889999999999999999999999

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

Probab=100.00  E-value=1.2e-38  Score=224.98  Aligned_cols=90  Identities=62%  Similarity=1.022  Sum_probs=75.0

Q ss_pred             CCCcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcC---CCCCcceEEEeecCCCCCCcEEEEcCCCCc
Q 032325            1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE---NMKREDLVINKALRNDSSDQIYVFFPDEQK   77 (143)
Q Consensus         1 m~~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~---~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~   77 (143)
                      |+ +++|++||||||||++|||+||||.|+++|+++|+++|+++||+   .++|++|+|+|.+++||+++|+||||++++
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 56999999999999999999999999999999999999999999   688999999999999999999999999999


Q ss_pred             cchhHHHHHHHHHh
Q 032325           78 VGVKTMKTYTNRMK   91 (143)
Q Consensus        78 vgvk~ik~~~~~~~   91 (143)
                      ||+|+||+|+++|+
T Consensus        80 vgvk~Ir~~~~~m~   93 (93)
T PF03871_consen   80 VGVKTIRKYCERMK   93 (93)
T ss_dssp             ESCCCCHHHCHHH-
T ss_pred             cCHHHHHHHHHhcC
Confidence            99999999999985

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

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

Probab=97.40  E-value=0.00051  Score=47.51  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=42.5

Q ss_pred             eEEEeecCCCCCCcEEEEcCC-CCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceE
Q 032325           54 LVINKALRNDSSDQIYVFFPD-EQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVF  131 (143)
Q Consensus        54 L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~EL  131 (143)
                      .-+.+.+.+.....++|.+-. ..+++.+.|+.++..+...+..++|+|+.+++||.|++.+....   .|+++.-++|
T Consensus        36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~~~~~~~~~iivt~~~~t~~a~~~~~~~~---~I~l~d~~~L  111 (115)
T PF04471_consen   36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKAKKYGADKGIIVTSSGFTPEAKEFAEKFK---NIELIDGEDL  111 (115)
T ss_dssp             EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHHGGGT-SEEEEE-SSEE-HHHHHHHH----------------
T ss_pred             EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhhhccCCCEEEEEECCcCCHHHHHHHHhhc---cccccccccc
Confidence            334444433233467777633 35899999999999999999999999999999999999888754   4777766665

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.

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain

Probab=80.85  E-value=8.5  Score=28.37  Aligned_cols=86  Identities=10%  Similarity=0.074  Sum_probs=56.4

Q ss_pred             HHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhhcCC
Q 032325           16 RTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENV   95 (143)
Q Consensus        16 rTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~en~   95 (143)
                      +-+.-||++-||.|-+.-...|.++|.+..-+. +.+               +++. |.-..-.+..++..++.+++++.
T Consensus        20 ~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~e~-~ad---------------ii~i-Ssl~~~~~~~~~~~~~~L~~~g~   82 (132)
T TIGR00640        20 KVIATAYADLGFDVDVGPLFQTPEEIARQAVEA-DVH---------------VVGV-SSLAGGHLTLVPALRKELDKLGR   82 (132)
T ss_pred             HHHHHHHHhCCcEEEECCCCCCHHHHHHHHHHc-CCC---------------EEEE-cCchhhhHHHHHHHHHHHHhcCC
Confidence            445679999999999988889999998876432 111               1111 22112336678999999999887


Q ss_pred             CeEEEEEcCCCCHHHHHHHHhcc
Q 032325           96 FRAILVVQQNLTPFARTCIQEIS  118 (143)
Q Consensus        96 ~r~IlV~q~~ltp~Ar~~i~~~~  118 (143)
                      ....+++.+.+.+.-...+.++.
T Consensus        83 ~~i~vivGG~~~~~~~~~l~~~G  105 (132)
T TIGR00640        83 PDILVVVGGVIPPQDFDELKEMG  105 (132)
T ss_pred             CCCEEEEeCCCChHhHHHHHHCC
Confidence            65555566656655445555543

Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	143
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		8e-16
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		8e-14

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 70/131 (53%), Gaps = 4/131 (3%)
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 ISAKFHLEVFQ 127
           ++ +F +E FQ
Sbjct: 121 VTGQFTIETFQ 131

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 43/121 (35%), Positives = 63/121 (52%), Gaps = 9/121 (7%)
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 A 119
Sbjct: 129 P 129

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	143
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	5e-36
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	9e-34

>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 =  122 bits (307), Expect = 5e-36
 Identities = 43/133 (32%), Positives = 71/133 (53%), Gaps = 4/133 (3%)

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 ISAKFHLEVFQVN 129
           ++ +F +E FQ +
Sbjct: 121 VTGQFTIETFQES 133

>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 =  116 bits (292), Expect = 9e-34
 Identities = 45/141 (31%), Positives = 70/141 (49%), Gaps = 10/141 (7%)

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 QEISAKFHLEVFQVNVFSLMI 135
             I     +E F      + I
Sbjct: 125 PSIP-PATIETFNEAALVVNI 144

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	143
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

>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=2e-56  Score=353.83  Aligned_cols=142  Identities=30%  Similarity=0.488  Sum_probs=136.5

Q ss_pred             CCCcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCC---CCCcceEEEeecCCCC-CCcEEEEcCCCC
Q 032325            1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN---MKREDLVINKALRNDS-SDQIYVFFPDEQ   76 (143)
Q Consensus         1 m~~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~---~~r~~L~~~~~~~~dp-~~~i~VfF~~~~   76 (143)
                      |+++++|++||||+|||++|||+||||.|+++|+++|+++|+++||++   ++|++|+|++.+.+|| +++||||||+++
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            788899999999999999999999999999999999999999999986   6699999999999999 999999999999


Q ss_pred             ccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325           77 KVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN  142 (143)
Q Consensus        77 ~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~  142 (143)
                      +||+|+||.|+++|+++|+++||||+|+++||+|++++.+++++|+||+|+|+|||||||+|+|||
T Consensus        81 ~vgvk~Ir~~~~~~~~en~~~~IiV~q~~~t~~A~~~l~~~~~~~~iE~F~e~eLlvnit~H~lVP  146 (210)
T 3h0g_E           81 SVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVP  146 (210)
T ss_dssp             SCCTTTTGGGTHHHHHTTCSEEEECCSSCCCSHHHHTTTTTCTTCEECCCCSSSSCSCTTSBTTBC
T ss_pred             ccChHHHHHHHHHHHHcCCceEEEEECCCCCHHHHHHHHHhCcCcEEEEEeehHeeEecccccccC
Confidence            999999999999999999999999999999999999999999989999999999999999999999

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

Probab=100.00  E-value=1.2e-54  Score=344.52  Aligned_cols=139  Identities=32%  Similarity=0.505  Sum_probs=134.6

Q ss_pred             CcHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcC---CCCCcceEEEeecCCCCCCcE------EEEcC
Q 032325            3 LSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGE---NMKREDLVINKALRNDSSDQI------YVFFP   73 (143)
Q Consensus         3 ~~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~---~~~r~~L~~~~~~~~dp~~~i------~VfF~   73 (143)
                      +++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+   .++|++|+|++++++||++++      |||||
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            567999999999999999999999999999999999999999998   677999999999999999998      99999


Q ss_pred             CCCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEeeccccceec
Q 032325           74 DEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLMIYTCKLFN  142 (143)
Q Consensus        74 ~~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVNIT~H~LV~  142 (143)
                      ++++||+|+||+|+++|+++|++|||||+|++|||+|+++++++++ |+||+|+|+||+||||+|+|||
T Consensus        84 ~~~~vgvk~ir~~~~~~~~e~~~~~IlV~q~~itp~Ak~~l~~~~~-~~iE~F~e~eL~vni~~H~lVP  151 (215)
T 1dzf_A           84 DEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPP-ATIETFNEAALVVNITHHELVP  151 (215)
T ss_dssp             SSSEECHHHHHHHHHHHHHTTCSEEEEEESSEECHHHHTTTTSSTT-CEEEEEEHHHHSSCGGGSTTSC
T ss_pred             CCCccchHHHHHHHHHHHhcCCceEEEEECCCCChHHHHHHHHhcC-ceEEEeehHHheeccccceecc
Confidence            9999999999999999999999999999999999999999999998 8999999999999999999999

---

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	143
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	1e-45

>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 =  143 bits (362), Expect = 1e-45
 Identities = 44/135 (32%), Positives = 68/135 (50%), Gaps = 10/135 (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 QEISAKFHLEVFQVN 129
             I     +E F   
Sbjct: 121 PSIP-PATIETFNEA 134

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	143
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	100.0
d1y88a2	125	Hypothetical protein AF1548, N-terminal domain {Ar	91.61
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	85.62

>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=8.9e-53  Score=313.20  Aligned_cols=130  Identities=32%  Similarity=0.533  Sum_probs=123.2

Q ss_pred             cHHHHHHHHHHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCC---CCCcceEEEeecCCC------CCCcEEEEcCC
Q 032325            4 SDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGEN---MKREDLVINKALRND------SSDQIYVFFPD   74 (143)
Q Consensus         4 ~~~e~~rL~rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~---~~r~~L~~~~~~~~d------p~~~i~VfF~~   74 (143)
                      ||+|++||||+||||+|||+||||.|+++|+++|+++|+++||++   |+|+.|++.+.+.++      ++++||||||+
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            579999999999999999999999999999999999999999986   679999999988765      45679999999


Q ss_pred             CCccchhHHHHHHHHHhhcCCCeEEEEEcCCCCHHHHHHHHhccccceEeeeccceEEee
Q 032325           75 EQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFHLEVFQVNVFSLM  134 (143)
Q Consensus        75 ~~~vgvk~ik~~~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~ELlVN  134 (143)
                      +++||+|+||+|+++|+++|++|||||+|++|||+|++++.++++ ++||+|+|+|||||
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            999999999999999999999999999999999999999998876 79999999999999

>d1y88a2 c.52.1.30 (A:3-127) Hypothetical protein AF1548, N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: MRR-like
domain: Hypothetical protein AF1548, N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.61  E-value=0.12  Score=34.58  Aligned_cols=40  Identities=5%  Similarity=-0.030  Sum_probs=29.9

Q ss_pred             ccchhHHHHH-----HHHHhhcCCCeEEEEEcCCCCHHHHHHHHh
Q 032325           77 KVGVKTMKTY-----TNRMKSENVFRAILVVQQNLTPFARTCIQE  116 (143)
Q Consensus        77 ~vgvk~ik~~-----~~~~~~en~~r~IlV~q~~ltp~Ar~~i~~  116 (143)
                      ++++..++.+     ...+...+..++|+|+-++.|+.|++....
T Consensus        56 ~~~~~~v~~~~~~~~~~~~~~~~~~~~iiVTt~~Ft~~A~~~A~~  100 (125)
T d1y88a2          56 PVYTGLKEAMYTYARFLDVEKHGFTQPWIFTNTKFSEEAKKYAGC  100 (125)
T ss_dssp             SCEECHHHHHHHHHHHHHHGGGTCSEEEEECSSEECHHHHHHHHH
T ss_pred             CCCCChhhHHHHHHhhhhhhhcCCCeEEEEECCCCCHHHHHHHHH
Confidence            3455555443     345678899999999999999999876654

>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=85.62  E-value=0.61  Score=33.08  Aligned_cols=89  Identities=8%  Similarity=-0.004  Sum_probs=65.4

Q ss_pred             HHHHHHHHHhcCCCcccchhhhccCHHHHHHHhcCCCCCcceEEEeecCCCCCCcEEEEcCCCCccchhHHHHHHHHHhh
Q 032325           13 RIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKS   92 (143)
Q Consensus        13 rirrTv~eMl~DRGY~V~~~e~~~sl~~F~~~y~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~ik~~~~~~~~   92 (143)
                      +-.+.+.-++++.||.|..--...|.++|.+...+. +.+-+.++                .-..-.+..++.+++.+++
T Consensus        52 ~G~~~va~~l~~~G~eVi~lg~~~~~e~iv~aa~~~-~advI~iS----------------s~~~~~~~~~~~l~~~L~~  114 (168)
T d7reqa2          52 RGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEA-DVHVVGVS----------------SLAGGHLTLVPALRKELDK  114 (168)
T ss_dssp             HHHHHHHHHHHHTTCEEEECCTTBCHHHHHHHHHHH-TCSEEEEE----------------ECSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcceecCCCcCcHHHHHHHHHcc-CCCEEEEe----------------cCcccchHHHHHHHHHHHh
Confidence            456788889999999999877888999999887543 12222222                2223468899999999999


Q ss_pred             cCCCeEEEEEcCCCCHHHHHHHHhcc
Q 032325           93 ENVFRAILVVQQNLTPFARTCIQEIS  118 (143)
Q Consensus        93 en~~r~IlV~q~~ltp~Ar~~i~~~~  118 (143)
                      .+....++++.+.+.+.....+.+..
T Consensus       115 ~g~~~v~VivGG~ip~~d~~~l~~~G  140 (168)
T d7reqa2         115 LGRPDILITVGGVIPEQDFDELRKDG  140 (168)
T ss_dssp             TTCTTSEEEEEESCCGGGHHHHHHHT
T ss_pred             cCCCCeEEEEeCCCCHHHHHHHHhCC
Confidence            99888777887877777766666544