Citrus Sinensis ID: 027294

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-----
Protein Sequence
MEDGNGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQSPSLQPPWLNNHPHNYP
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHcccHHHHHHHHcccccccccEEEEEEcccccccEEEEEcccccccHHHHHHHHHHHHHccccEEEEEEEcccccHHHHHHHcccccEEEEEEEccEEEEccccccccccEEccHHHHHHHHHHccccccccccEEEEEEEcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEcccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccEccHHHHcccHHHHHHHHcccccccccEEEEEccccccccEEEEEcccccccHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHccccEEEEEEHHHEEEEEcccEEccccEEccHHHHHHHHHHcccccccccccEEEEEEccccccccccHHcccccccc
Coil and Loop (DISEMBL)
medgngydssmemeggngyngeptesclsgfvdngsrdsLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAiygqdpdvdrlrisishqsdpskrILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKhvlkpkhqvlTDQEKEKLLKKYSIEEKQQHNrhlcwtttkqspslqppwlnnhphnyp
Flexible Loop (DISEMBL)
medgngydssMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRIsishqsdpskriLVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVlkpkhqvltdqeKEKLLKKYSIEEKQQHNRHLCWTTTkqspslqppwlnnhphnyp
Low Complexity Region (SEG)
MEDGNGYDSSmemeggngyngePTESCLSGFVDNGsrdslryylsrrTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQSPSLQPPWLNNHPHNYP
Disordered region (IsUnstruct)
***************************LSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISH****SKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLT*********************HLCWT*********************
Disordered Region (DISOPRED)
************************************RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTT********************
Disordered Region (DISEMBL)
**************GGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQSPSLQPPWLNNHPHNYP
Disordered Region (DISPRO)
*********S**MEG*NGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQSPSLQPPWLNN******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEDGNGYDSSMEMEGGNGYNGEPTESCLSGFVDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQSPSLQPPWLNNHPHNYP
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	225	2.2.26 [Sep-21-2011]
Q757H7	215	DNA-directed RNA polymera	yes	no	0.711	0.744	0.364	4e-19
Q9N5K2	211	DNA-directed RNA polymera	yes	no	0.697	0.744	0.309	1e-18
A8XGH1	211	DNA-directed RNA polymera	N/A	no	0.697	0.744	0.303	3e-18
Q9P4B9	215	DNA-directed RNA polymera	N/A	no	0.68	0.711	0.367	3e-17
Q6CJ62	215	DNA-directed RNA polymera	yes	no	0.697	0.730	0.358	4e-17
Q6FQA6	215	DNA-directed RNA polymera	yes	no	0.68	0.711	0.355	6e-17
P20434	215	DNA-directed RNA polymera	yes	no	0.697	0.730	0.352	7e-17
Q09191	210	DNA-directed RNA polymera	yes	no	0.702	0.752	0.327	8e-17
Q5R587	210	DNA-directed RNA polymera	yes	no	0.715	0.766	0.278	6e-16
Q6BIJ0	214	DNA-directed RNA polymera	yes	no	0.72	0.757	0.325	7e-16

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

 Score = 94.7 bits (234), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 63/173 (36%), Positives = 97/173 (56%), Gaps = 13/173 (7%)

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

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

Query: 144 KAV-GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           K +  +    +E F  T L+VNIT H L PKH  L+D+EK++LLK+Y ++E Q
Sbjct: 122 KLLPSVAPATIETFNETALVVNITHHELVPKHIKLSDEEKKELLKRYRLKESQ 174

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.
Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

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

 Score = 93.2 bits (230), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 51/165 (30%), Positives = 98/165 (59%), Gaps = 8/165 (4%)

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

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

Query: 151 FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           + +E F   +L+VNIT+H L P+H V+T +EK +LL +Y +++ Q
Sbjct: 126 YMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQ 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.

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 = 92.0 bits (227), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 98/165 (59%), Gaps = 8/165 (4%)

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

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

Query: 151 FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           + +E F   +L+VNIT+H L P+H V+T +EK +LL +Y +++ Q
Sbjct: 126 YMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQ 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.

Caenorhabditis briggsae (taxid: 6238)

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

 Score = 88.6 bits (218), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 61/166 (36%), Positives = 90/166 (54%), Gaps = 13/166 (7%)

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

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

Query: 151 FKV-EMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             V E F    L+VNIT H L PKH  L+D EK++LLK+Y ++E Q
Sbjct: 129 PAVIETFPEASLVVNITHHELVPKHIRLSDAEKKELLKRYRLKESQ 174

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

Kluyveromyces marxianus (taxid: 4911)

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

 Score = 88.2 bits (217), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 61/170 (35%), Positives = 93/170 (54%), Gaps = 13/170 (7%)

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

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

Query: 147 GLFQFKV-EMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
                 V E F    L+VNIT H L PKH  L++ EK++LLK+Y ++E Q
Sbjct: 125 PTAAPAVIETFPEASLVVNITHHELVPKHIRLSEAEKKELLKRYRLKESQ 174

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

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

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

 Score = 87.4 bits (215), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 59/166 (35%), Positives = 90/166 (54%), Gaps = 13/166 (7%)

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

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

Query: 150 QFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
              +E F    L+VNIT H L PKH  L ++EK +LLK+Y ++E Q
Sbjct: 129 PATIETFHEAALVVNITHHDLVPKHIRLNEEEKAELLKRYRLKESQ 174

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)

>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 = 87.4 bits (215), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 60/170 (35%), Positives = 90/170 (52%), Gaps = 13/170 (7%)

Query: 37  RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPS 96
           R+  R + + RTV EM+KDRGY +   E+ L ++DF+A Y  D      R  +S Q++P+
Sbjct: 7   RNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYC-DSMGRPQRKMMSFQANPT 65

Query: 97  KR----------ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV 146
           +           + V FC    V V  +++ +  I  ++  TG I + QN IT  A K V
Sbjct: 66  EESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLV 124

Query: 147 -GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             +    +E F    L+VNIT H L PKH  L+  EK +LLK+Y ++E Q
Sbjct: 125 PSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQ 174

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

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

>sp|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 = 87.0 bits (214), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 54/165 (32%), Positives = 97/165 (58%), Gaps = 7/165 (4%)

Query: 37  RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIY-GQDPDVDRLRISI-SHQSD 94
           ++ +R + + +T  +++ DRGY V+ +E++L++  F+A++ G   ++DR  +S  +  S+
Sbjct: 6   KNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSN 65

Query: 95  PSKR--ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--Q 150
            S +  I + F     V +  +R+ +  + + +  TG ILI  N +T  A K +     Q
Sbjct: 66  DSNKGTIYIEFAKEPSVGIKEMRTFVHTLGDHNHKTG-ILIYANSMTPSAAKIIATVTGQ 124

Query: 151 FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           F +E FQ +DL+VNIT H L PKH +L+  EK++LL +Y + E Q
Sbjct: 125 FTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQ 169

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

 Score = 84.3 bits (207), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 95/169 (56%), Gaps = 8/169 (4%)

Query: 34  NGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDR-----LRIS 88
           +   ++ R +  R+T++++  DRGY V   E++ ++++FRA +G  P   R     L + 
Sbjct: 2   DDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVL 61

Query: 89  ISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGL 148
           ++H  DP+ ++ V F     V +  I+ +  Q +  + +T  ++++Q  +T  A +++  
Sbjct: 62  VAHNDDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVD 120

Query: 149 F--QFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
              ++ +E F   +LL+NIT+H L P+H V+T +E  +LL +Y + E Q
Sbjct: 121 MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQ 169

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

 Score = 84.3 bits (207), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 57/175 (32%), Positives = 93/175 (53%), Gaps = 13/175 (7%)

Query: 32  VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISH 91
           +++  R   R + S +TV EM++DRGY +   EI++S+ +FR+      +V + ++ +  
Sbjct: 1   MEDTDRTISRLWRSFKTVKEMVRDRGYYITQEEIDMSLAEFRSRICDSMNVPQRKL-MCF 59

Query: 92  QSDPSKRIL----------VVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQ 141
           Q++P+   L          V FC    V +  +R+    I  ++  TG I I Q+ IT  
Sbjct: 60  QANPTAESLEKFPDLGSLWVEFCDEASVGIKTMRNFCIHISEKNFSTG-IFIYQSSITPS 118

Query: 142 ATKAVGLFQ-FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           A K +       +E FQ  DL+VNIT H L PKH  L   EK++LL++Y ++E Q
Sbjct: 119 ANKLIPTVSPASIETFQEGDLVVNITHHDLVPKHIKLARDEKKELLERYRLKESQ 173

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

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

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	225
255576548	238	DNA-directed RNA polymerase II, putative	0.831	0.785	0.673	2e-69
224139746	216	predicted protein [Populus trichocarpa]	0.773	0.805	0.695	5e-66
297739911	330	unnamed protein product [Vitis vinifera]	0.822	0.560	0.652	6e-66
351723899	237	uncharacterized protein LOC100306033 [Gl	0.764	0.725	0.720	7e-66
359482221	229	PREDICTED: DNA-directed RNA polymerases	0.813	0.799	0.659	2e-65
357509489	248	DNA-directed RNA polymerases I, II, and	0.857	0.778	0.639	2e-64
449437743	227	PREDICTED: DNA-directed RNA polymerases	0.795	0.788	0.655	2e-64
388510192	248	unknown [Medicago truncatula]	0.857	0.778	0.634	9e-64
297817026	222	eukaryotic rpb5 RNA polymerase subunit f	0.751	0.761	0.644	2e-58
15230206	222	rpb5 RNA polymerase subunit family prote	0.777	0.788	0.621	1e-57

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

 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 130/193 (67%), Positives = 160/193 (82%), Gaps = 6/193 (3%)

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

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

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

Query: 183 EKLLKKYSIEEKQ 195
           +KLLK Y IEEKQ
Sbjct: 185 QKLLKDYCIEEKQ 197

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  256 bits (654), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 121/174 (69%), Positives = 150/174 (86%)

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

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

Query: 142 ATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           A KA+ LF+FK+E+FQITDLLVNITKH+LKPKHQVL++Q K++LLKKYSIEEKQ
Sbjct: 122 AMKALDLFKFKIEIFQITDLLVNITKHILKPKHQVLSEQAKQRLLKKYSIEEKQ 175

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  256 bits (653), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 124/190 (65%), Positives = 154/190 (81%), Gaps = 5/190 (2%)

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

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

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

Query: 186 LKKYSIEEKQ 195
           LKKYS+ EKQ
Sbjct: 280 LKKYSLNEKQ 289

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  255 bits (652), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 124/172 (72%), Positives = 146/172 (84%)

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

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

Query: 144 KAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           KAV LF FKVE+FQITDLLVNITKHVLKPKHQVLTD++K  LLKKY+IEEKQ
Sbjct: 145 KAVNLFSFKVEIFQITDLLVNITKHVLKPKHQVLTDKQKINLLKKYNIEEKQ 196

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 124/188 (65%), Positives = 153/188 (81%), Gaps = 5/188 (2%)

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

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

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

Query: 188 KYSIEEKQ 195
           KYS+ EKQ
Sbjct: 181 KYSLNEKQ 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  251 bits (640), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/205 (63%), Positives = 157/205 (76%), Gaps = 12/205 (5%)

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

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

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

Query: 171 KPKHQVLTDQEKEKLLKKYSIEEKQ 195
           KPKHQVLTD++K+ LLKKY I+EKQ
Sbjct: 183 KPKHQVLTDKQKKNLLKKYDIQEKQ 207

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  251 bits (640), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 120/183 (65%), Positives = 148/183 (80%), Gaps = 4/183 (2%)

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

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

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

Query: 193 EKQ 195
           EKQ
Sbjct: 184 EKQ 186

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  248 bits (634), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 130/205 (63%), Positives = 156/205 (76%), Gaps = 12/205 (5%)

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

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

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

Query: 171 KPKHQVLTDQEKEKLLKKYSIEEKQ 195
           KPKHQVLTD++K+ LLKKY I+EKQ
Sbjct: 183 KPKHQVLTDKQKKNLLKKYDIQEKQ 207

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  231 bits (589), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 109/169 (64%), Positives = 140/169 (82%)

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

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

Query: 147 GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
            LF FKVE+FQITDLLVNITKH LKP+H+VL D+EK  LLKK+SIEEKQ
Sbjct: 133 ELFSFKVEIFQITDLLVNITKHALKPQHRVLNDKEKTTLLKKFSIEEKQ 181

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  228 bits (582), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 110/177 (62%), Positives = 143/177 (80%), Gaps = 2/177 (1%)

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

Query: 79  DPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQI 138
            PDVDRLRIS  H+SD +K++ +VF G  +VKVN IRS+++ I++++T+TGLIL+LQN +
Sbjct: 65  RPDVDRLRISALHRSDSTKKVKIVFFGTSMVKVNAIRSVVADILSQETITGLILVLQNHV 124

Query: 139 TSQATKAVGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           T+QA KA+ LF FKVE+FQITDLLVNITKH LKP+HQVL D+EK  LLKK+SIEEKQ
Sbjct: 125 TNQALKAIELFSFKVEIFQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQ 181

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	225
TAIR|locus:2080650	222	NRPE5 [Arabidopsis thaliana (t	0.751	0.761	0.585	2e-49
TAIR|locus:2040257	218	RPB5D ""RNA polymerase II fift	0.657	0.678	0.662	3.2e-49
TAIR|locus:2096971	233	RPB5E ""RNA polymerase II fift	0.755	0.729	0.429	5.8e-34
WB|WBGene00019246	211	rpb-5 [Caenorhabditis elegans	0.653	0.696	0.316	8.3e-19
POMBASE|SPAC23C4.15	210	rpb5 "DNA-directed RNA polymer	0.653	0.7	0.344	3.6e-18
TAIR|locus:2087842	205	NRPB5 [Arabidopsis thaliana (t	0.653	0.717	0.313	1.2e-17
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.653	0.7	0.296	5.3e-17
MGI|MGI:1913670	210	Polr2e "polymerase (RNA) II (D	0.653	0.7	0.290	8.6e-17
RGD|1589817	210	Polr2e "polymerase (RNA) II (D	0.653	0.7	0.290	8.6e-17
SGD|S000000358	215	RPB5 "RNA polymerase subunit A	0.648	0.679	0.345	8.6e-17

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

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 99/169 (58%), Positives = 129/169 (76%)

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

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

Query:   147 GLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
              LF FKVE+FQITDLLVNITKH LKP+HQVL D+EK  LLKK+SIEEKQ
Sbjct:   133 ELFSFKVEIFQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQ 181

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

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

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

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

 Score = 513 (185.6 bits), Expect = 3.2e-49, P = 3.2e-49
 Identities = 98/148 (66%), Positives = 124/148 (83%)

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

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

Query:   168 HVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             HVL+PKHQVL D+EKE LLKK+SIEEKQ
Sbjct:   150 HVLRPKHQVLNDKEKESLLKKFSIEEKQ 177

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

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

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

 Score = 369 (135.0 bits), Expect = 5.8e-34, P = 5.8e-34
 Identities = 73/170 (42%), Positives = 113/170 (66%)

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

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

Query:   146 VGLFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             +  F F VE F I DLLVNITKH+ +PK ++L  +EKE+LL+K+++E+KQ
Sbjct:   143 LTTFPFTVETFPIEDLLVNITKHIQQPKIEILNKEEKEQLLRKHALEDKQ 192

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

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

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

 Score = 226 (84.6 bits), Expect = 8.3e-19, P = 8.3e-19
 Identities = 49/155 (31%), Positives = 92/155 (59%)

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

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

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             L+VNIT+H L P+H V+T +EK +LL +Y +++ Q
Sbjct:   136 LMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQ 170

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0032502 "developmental process" evidence=IMP

POMBASE|SPAC23C4.15 rpb5 "DNA-directed RNA polymerase I, II and III subunit Rpb5" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 53/154 (34%), Positives = 89/154 (57%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIY-GQDPDVDRLRISI--SHQSDPSK-RILVVF 103
             T  +++ DRGY V+ +E++L++  F+A++ G   ++DR  +S      +D +K  I + F
Sbjct:    17 TAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEF 76

Query:   104 CGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--QFKVEMFQITDL 161
                  V +  +R+ +  + + +  TG ILI  N +T  A K +     QF +E FQ +DL
Sbjct:    77 AKEPSVGIKEMRTFVHTLGDHNHKTG-ILIYANSMTPSAAKIIATVTGQFTIETFQESDL 135

Query:   162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             +VNIT H L PKH +L+  EK++LL +Y + E Q
Sbjct:   136 IVNITHHELVPKHILLSPDEKKELLDRYKLRETQ 169

GO:0003677 "DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

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

GO:0005829 "cytosol" evidence=IDA

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

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

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

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

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

 Score = 215 (80.7 bits), Expect = 1.2e-17, P = 1.2e-17
 Identities = 47/150 (31%), Positives = 91/150 (60%)

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

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

Query:   166 TKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
              +HVL P+HQVLT +EK+ LL++Y+++E Q
Sbjct:   135 KEHVLVPEHQVLTTEEKKTLLERYTVKETQ 164

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

GO:0051604 "protein maturation" evidence=RCA

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

 Score = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 46/155 (29%), Positives = 89/155 (57%)

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

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

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             LL+NIT+H L P+H V+T +E  +LL +Y + E Q
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRENQ 169

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 = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 45/155 (29%), Positives = 89/155 (57%)

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

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

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             LL+NIT+H L P+H V+T +E  +LL +Y + E Q
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRESQ 169

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 = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 45/155 (29%), Positives = 89/155 (57%)

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

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

Query:   161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
             LL+NIT+H L P+H V+T +E  +LL +Y + E Q
Sbjct:   135 LLINITEHELVPEHVVMTKEEVTELLARYKLRESQ 169

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

SGD|S000000358 RPB5 "RNA polymerase subunit ABC27" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 55/159 (34%), Positives = 85/159 (53%)

Query:    48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRIL------- 100
             TV EM+KDRGY +   E+ L ++DF+A Y       + ++ +S Q++P++  +       
Sbjct:    18 TVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKM-MSFQANPTEESISKFPDMG 76

Query:   101 ---VVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-GLFQFKVEMF 156
                V FC    V V  +++ +  I  ++  TG I + QN IT  A K V  +    +E F
Sbjct:    77 SLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLVPSIPPATIETF 135

Query:   157 QITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
                 L+VNIT H L PKH  L+  EK +LLK+Y ++E Q
Sbjct:   136 NEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQ 174

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IGI;IMP

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

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

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

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

GO:0001054 "RNA polymerase I activity" evidence=IC

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

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

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

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

---

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

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	225
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	4e-85
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	2e-27
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	2e-25
pfam01191	74	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-	5e-13
COG2012	80	COG2012, RPB5, DNA-directed RNA polymerase, subuni	1e-07
PRK09570	79	PRK09570, rpoH, DNA-directed RNA polymerase subuni	1e-06

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

 Score =  250 bits (642), Expect = 4e-85
 Identities = 84/166 (50%), Positives = 118/166 (71%), Gaps = 3/166 (1%)

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

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

Query: 151 -FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
            FK+E+FQ T+LLVNITKHVL PKHQVLTD+EK+ LLK+Y+++E Q
Sbjct: 120 KFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQ 165

Length = 206

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

 Score =  103 bits (259), Expect = 2e-27
 Identities = 59/160 (36%), Positives = 89/160 (55%), Gaps = 7/160 (4%)

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

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

Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           F  T+LLVNITKH L PKH  LTD EK  LL++Y ++E Q
Sbjct: 125 FLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQ 164

Length = 205

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

 Score = 94.6 bits (236), Expect = 2e-25
 Identities = 36/88 (40%), Positives = 52/88 (59%), Gaps = 2/88 (2%)

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

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

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

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

 Score = 61.7 bits (151), Expect = 5e-13
 Identities = 22/33 (66%), Positives = 30/33 (90%)

Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           VNITKH L PKH+VL+++EK+KLLK+Y I+E+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 = 47.3 bits (113), Expect = 1e-07
 Identities = 14/36 (38%), Positives = 25/36 (69%)

Query: 160 DLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
            L  N+  H L P+H+VL+++E +++LK+  IE +Q
Sbjct: 4   MLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQ 39

Length = 80

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

 Score = 44.4 bits (106), Expect = 1e-06
 Identities = 13/33 (39%), Positives = 25/33 (75%)

Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
            ++  H L P+H++L+++E +KLLK+Y I+ +Q
Sbjct: 4   FDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQ 36

Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	225
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	99.97
PRK09570	79	rpoH DNA-directed RNA polymerase subunit H; Review	99.69
PF01191	74	RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal do	99.66
COG2012	80	RPB5 DNA-directed RNA polymerase, subunit H, RpoH/	99.63
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	96.39

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

Probab=100.00  E-value=3.9e-64  Score=431.77  Aligned_cols=170  Identities=40%  Similarity=0.679  Sum_probs=167.2

Q ss_pred             hhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecCCCccchhhH
Q 027294           36 SRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVI  114 (225)
Q Consensus        36 ~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~-p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgvK~I  114 (225)
                      +.|++||||+|||++||||||||.|+++|+++++++|+++||+. |+|++|+|+|.|++||+++|+|||+++++||+|+|
T Consensus         6 e~E~~rl~~ar~T~~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~   85 (208)
T KOG3218|consen    6 EEEIYRLYLARKTAMQMLRDRGYTVTQEELDLTLEEFKARYGDKMPDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTM   85 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCccccHHHhhhhHHHHHHHhccCCcchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHH
Confidence            78999999999999999999999999999999999999999998 99999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--cceeeeecceeeeecccccccCCcccCChHHHHHHHHHcCCC
Q 027294          115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE  192 (225)
Q Consensus       115 r~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~--~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y~i~  192 (225)
                      |.++.+| .++|+++||||+|+++||+|++++..++  |.||+|+|+||+||||+|+|||||++||+|||++||++|+++
T Consensus        86 k~~~~~~-~~~ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~  164 (208)
T KOG3218|consen   86 KTYVIQM-QSENIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLK  164 (208)
T ss_pred             HHHHHHH-HhcCceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCC
Confidence            9999999 8899999999999999999999999998  999999999999999999999999999999999999999999


Q ss_pred             CCCccceecCCCcc
Q 027294          193 EKQQHNRHLCWTTT  206 (225)
Q Consensus       193 ~~QLP~I~~~d~~~  206 (225)
                      ++|||||+.+||-.
T Consensus       165 e~qLPRIq~~Dpva  178 (208)
T KOG3218|consen  165 ETQLPRIQKKDPVA  178 (208)
T ss_pred             cccCCeeeccChHH
Confidence            99999999999853

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

Probab=100.00  E-value=4.8e-63  Score=428.74  Aligned_cols=177  Identities=47%  Similarity=0.741  Sum_probs=172.0

Q ss_pred             CCCChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCCCCCCceEEEeecCCCCCCcEEEEecCCCccch
Q 027294           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKV  111 (225)
Q Consensus        32 md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~p~r~~L~i~~~~~~dp~~kI~VfF~~e~kVgv  111 (225)
                      |+.++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|+|.+.+||+++|+|||+++++||+
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            46678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--cceeeeecceeeeecccccccCCcccCChHHHHHHHHHc
Q 027294          112 NVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKY  189 (225)
Q Consensus       112 K~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~--~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y  189 (225)
                      |+||.|+++| +++|++|||||+|+++||+|++++.+++  ++||+|+|+||+||||+|+|||+|++||+|||++||++|
T Consensus        81 k~ir~~~~~~-~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y  159 (206)
T PLN03111         81 KTIKTYAERM-KDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRY  159 (206)
T ss_pred             HHHHHHHHHH-hhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHc
Confidence            9999999999 9999999999999999999999999996  999999999999999999999999999999999999999


Q ss_pred             CCCCCCccceecCCCccccC
Q 027294          190 SIEEKQQHNRHLCWTTTKQS  209 (225)
Q Consensus       190 ~i~~~QLP~I~~~d~~~~~~  209 (225)
                      +++++|||||+.+||..+-+
T Consensus       160 ~i~~~qLPrI~~~DPvary~  179 (206)
T PLN03111        160 TVKETQLPRIQVSDPIARYY  179 (206)
T ss_pred             CCCHHHCCcccccChhhHhc
Confidence            99999999999999987653

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=2.2e-61  Score=417.96  Aligned_cols=172  Identities=33%  Similarity=0.472  Sum_probs=165.8

Q ss_pred             hhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC-CCCCceEEEeecCCCCCCcEEEEecC-CCccchhhH
Q 027294           37 RDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD-PDVDRLRISISHQSDPSKRILVVFCG-PGIVKVNVI  114 (225)
Q Consensus        37 ~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~-p~r~~L~i~~~~~~dp~~kI~VfF~~-e~kVgvK~I  114 (225)
                      +++.||||+|||++|||+||||.|+++|+++|+++|+++||+. +.|++|+|+|++.+||+++|+|||++ +++||+|+|
T Consensus         3 ~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~i   82 (205)
T PTZ00061          3 DSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKPI   82 (205)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHHH
Confidence            6789999999999999999999999999999999999999987 47899999999999999999999998 579999999


Q ss_pred             HHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--cceeeeecceeeeecccccccCCcccCChHHHHHHHHHcCCC
Q 027294          115 RSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIE  192 (225)
Q Consensus       115 r~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~--~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y~i~  192 (225)
                      |.|+++| +++|++|||||+|+++||+|++++.+++  ++||+|+|+||+||||+|+|||+|++||+|||++||++|+++
T Consensus        83 r~~~~~~-~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~  161 (205)
T PTZ00061         83 RELTEKM-EEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVK  161 (205)
T ss_pred             HHHHHHH-hhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCC
Confidence            9999999 9999999999999999999999999996  899999999999999999999999999999999999999999


Q ss_pred             CCCccceecCCCccccC
Q 027294          193 EKQQHNRHLCWTTTKQS  209 (225)
Q Consensus       193 ~~QLP~I~~~d~~~~~~  209 (225)
                      ++|||||+.+||..+-+
T Consensus       162 ~~qLPrI~~~DPvary~  178 (205)
T PTZ00061        162 ESQLPRIQSADPVARYF  178 (205)
T ss_pred             HHHCCcccccChhhHhc
Confidence            99999999999987643

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

Probab=99.97  E-value=2.4e-32  Score=210.45  Aligned_cols=89  Identities=42%  Similarity=0.722  Sum_probs=74.7

Q ss_pred             CCCChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCC---CCCCCceEEEeecCCCCCCcEEEEecCCCc
Q 027294           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKRILVVFCGPGI  108 (225)
Q Consensus        32 md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~---~p~r~~L~i~~~~~~dp~~kI~VfF~~e~k  108 (225)
                      || ++.|++|||||||||+|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++.+.+||+++|+|||+++++
T Consensus         1 m~-~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~k   79 (93)
T PF03871_consen    1 MD-DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPK   79 (93)
T ss_dssp             ---TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSC
T ss_pred             Cc-cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCC
Confidence            45 44899999999999999999999999999999999999999998   799999999999999999999999999999


Q ss_pred             cchhhHHHHHHHH
Q 027294          109 VKVNVIRSIISQI  121 (225)
Q Consensus       109 VgvK~Ir~~~e~m  121 (225)
                      ||+|+||.|+++|
T Consensus        80 vgvk~Ir~~~~~m   92 (93)
T PF03871_consen   80 VGVKTIRKYCERM   92 (93)
T ss_dssp             ESCCCCHHHCHHH
T ss_pred             cCHHHHHHHHHhc
Confidence            9999999999998

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=99.69  E-value=7.2e-18  Score=127.59  Aligned_cols=48  Identities=29%  Similarity=0.463  Sum_probs=45.8

Q ss_pred             eeecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCccccC
Q 027294          162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQS  209 (225)
Q Consensus       162 l~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~~  209 (225)
                      .||||+|+|||+|++||+||+++||++|+++++|||||+.+||..+..
T Consensus         3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~   50 (79)
T PRK09570          3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAI   50 (79)
T ss_pred             ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhc
Confidence            589999999999999999999999999999999999999999987754

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

Probab=99.66  E-value=2.6e-17  Score=123.20  Aligned_cols=47  Identities=40%  Similarity=0.558  Sum_probs=39.7

Q ss_pred             eecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCccccC
Q 027294          163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQS  209 (225)
Q Consensus       163 ~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~~  209 (225)
                      ||||+|+|||+|++||+||+++||++|+++++|||||+.+||..+.+
T Consensus         1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~   47 (74)
T PF01191_consen    1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSSDPVARYL   47 (74)
T ss_dssp             S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHHHHHT
T ss_pred             CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCcccccChhhhhc
Confidence            79999999999999999999999999999999999999999987644

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=99.63  E-value=8.8e-17  Score=121.26  Aligned_cols=52  Identities=29%  Similarity=0.379  Sum_probs=48.5

Q ss_pred             cceeeeecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCccccC
Q 027294          158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQS  209 (225)
Q Consensus       158 E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~~  209 (225)
                      ++.+.||+++|+|||+|++||+||++++|++|+|+++|||||+.+||..+.+
T Consensus         2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPva~~l   53 (80)
T COG2012           2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPVAKAL   53 (80)
T ss_pred             ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcccccChhHHHc
Confidence            5778999999999999999999999999999999999999999999966543

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

Probab=96.39  E-value=0.01  Score=44.30  Aligned_cols=76  Identities=21%  Similarity=0.270  Sum_probs=41.6

Q ss_pred             eEEEeecCCCCCCcEEEEecC-CCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhccceeeeecceee
Q 027294           85 LRISISHQSDPSKRILVVFCG-PGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQFKVEMFQITDLL  162 (225)
Q Consensus        85 L~i~~~~~~dp~~kI~VfF~~-e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~~~IEvF~E~ELl  162 (225)
                      .-+.+.+......+++|-+-. ..+++.+.|+.++..+ ...+..++|||+.+++|+.|++.+.... .|+++.-++|.
T Consensus        36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~-~~~~~~~~iivt~~~~t~~a~~~~~~~~-~I~l~d~~~L~  112 (115)
T PF04471_consen   36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKA-KKYGADKGIIVTSSGFTPEAKEFAEKFK-NIELIDGEDLQ  112 (115)
T ss_dssp             EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHH-GGGT-SEEEEE-SSEE-HHHHHHHH---------------
T ss_pred             EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhh-hccCCCEEEEEECCcCCHHHHHHHHhhc-ccccccccccc
Confidence            344444433232456666633 3589999999999999 8889999999999999999999887743 57766666553

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	225
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		4e-17
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		1e-16

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

Iteration: 1
 Score = 84.3 bits (207), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 53/154 (34%), Positives = 90/154 (58%), Gaps = 7/154 (4%)
Query: 48  TVLEMLKDRGYAVALSEINLSVQDFRAIY-GQDPDVDRLRISI-SHQSDPSKR--ILVVF 103
           T  +++ DRGY V+ +E++L++  F+A++ G   ++DR  +S  +  S+ S +  I + F
Sbjct: 17  TAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEF 76
Query: 104 CGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--QFKVEMFQITDL 161
                V +  +R+ +  + + +  TG ILI  N +T  A K +     QF +E FQ +DL
Sbjct: 77  AKEPSVGIKEMRTFVHTLGDHNHKTG-ILIYANSMTPSAAKIIATVTGQFTIETFQESDL 135
Query: 162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           +VNIT H L PKH +L+  EK++LL +Y + E Q
Sbjct: 136 IVNITHHELVPKHILLSPDEKKELLDRYKLRETQ 169

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

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 57/159 (35%), Positives = 84/159 (52%), Gaps = 13/159 (8%)
Query: 48  TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKR--------- 98
           TV EM+KDRGY +   E+ L ++DF+A Y  D      R  +S Q++P++          
Sbjct: 18  TVKEMVKDRGYFITQEEVELPLEDFKAKYC-DSMGRPQRKMMSFQANPTEESISKFPDMG 76
Query: 99  -ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-GLFQFKVEMF 156
            + V FC    V V  +++ +  I  ++  TG I + QN IT  A K V  +    +E F
Sbjct: 77  SLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLVPSIPPATIETF 135
Query: 157 QITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
               L+VNIT H L PKH  L+  EK +LLK+Y ++E Q
Sbjct: 136 NEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQ 174

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	225
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	4e-42
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	6e-38
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	2e-10
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	1e-09
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	3e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>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 =  140 bits (355), Expect = 4e-42
 Identities = 51/169 (30%), Positives = 90/169 (53%), Gaps = 7/169 (4%)

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

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

Query: 149 F--QFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
              QF +E FQ +DL+VNIT H L PKH +L+  EK++LL +Y + E Q
Sbjct: 121 VTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQ 169

>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 =  130 bits (328), Expect = 6e-38
 Identities = 55/173 (31%), Positives = 83/173 (47%), Gaps = 11/173 (6%)

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

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

Query: 144 KAVG-LFQFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           K V  +    +E F    L+VNIT H L PKH  L+  EK +LLK+Y ++E Q
Sbjct: 122 KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQ 174

>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 = 54.3 bits (131), Expect = 2e-10
 Identities = 14/41 (34%), Positives = 23/41 (56%)

Query: 155 MFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           M   ++  ++   H L PKH+VL+  E  K+LK+  I  +Q
Sbjct: 1   MRGSSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQ 41

>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 = 52.4 bits (126), Expect = 1e-09
 Identities = 11/35 (31%), Positives = 20/35 (57%)

Query: 161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           +   I KH L P+H +L + E +++LK+     +Q
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQ 35

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

 Score = 51.3 bits (123), Expect = 3e-09
 Identities = 13/33 (39%), Positives = 26/33 (78%)

Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           + +T H+L PKH+++  +E E++LK+Y+I+ +Q
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQ 33

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

 Score = 41.4 bits (96), Expect = 1e-04
 Identities = 37/199 (18%), Positives = 60/199 (30%), Gaps = 68/199 (34%)

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

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

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

Query: 171 KPKHQVLTDQEKEKLLKKY 189
                 LT  E + LL KY
Sbjct: 292 DHHSMTLTPDEVKSLLLKY 310

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	225
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	99.75
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	99.71
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	99.69

>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=2.9e-61  Score=417.86  Aligned_cols=176  Identities=28%  Similarity=0.461  Sum_probs=168.6

Q ss_pred             CCCChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC---CCCCceEEEeecCCCC-CCcEEEEecCCC
Q 027294           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD---PDVDRLRISISHQSDP-SKRILVVFCGPG  107 (225)
Q Consensus        32 md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~---p~r~~L~i~~~~~~dp-~~kI~VfF~~e~  107 (225)
                      |++++.|++||||+||||+|||+||||.|+++|+++|+++|+++||+.   |+|++|+|++.+.+|| +++|+|||++++
T Consensus         1 m~~~~~e~~rl~rirrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~~~~~r~~l~~~~~~~~dp~~~~i~VfF~~~~   80 (210)
T 3h0g_E            1 MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEFAKEP   80 (210)
T ss_dssp             ---CTHHHHHHHGGGSSSSSTTTTTTEECCTTTTSCCHHHHHHHSCCSSSSCCCSSCCCEEEESSCSSCCCEEEECCCSS
T ss_pred             CCcchHHHHHHHHHHHHHHHHhcCCCCccCHHHHhCCHHHHHHHhcccCCCCCchheEEEEEcCCCCccCeEEEEECCCC
Confidence            567789999999999999999999999999999999999999999875   8899999999999999 999999999999


Q ss_pred             ccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc--cceeeeecceeeeecccccccCCcccCChHHHHHH
Q 027294          108 IVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ--FKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL  185 (225)
Q Consensus       108 kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~--~~IEvF~E~ELl~nit~H~lVPkH~vl~~eEk~~l  185 (225)
                      +||+|+||.|+++| .++|++++|||+|+++||+|++++.+++  ++||+|+|+||+||||+|+|||+|++||+|||++|
T Consensus        81 ~vgvk~Ir~~~~~~-~~en~~~~IiV~q~~~t~~A~~~l~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eE~~~l  159 (210)
T 3h0g_E           81 SVGIKEMRTFVHTL-GDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKEL  159 (210)
T ss_dssp             SCCTTTTGGGTHHH-HHTTCSEEEECCSSCCCSHHHHTTTTTCTTCEECCCCSSSSCSCTTSBTTBCCEECCCHHHHHHH
T ss_pred             ccChHHHHHHHHHH-HHcCCceEEEEECCCCCHHHHHHHHHhCcCcEEEEEeehHeeEecccccccCcEEEcCHHHHHHH
Confidence            99999999999999 9999999999999999999999999997  79999999999999999999999999999999999


Q ss_pred             HHHcCCCCCCccceecCCCcccc
Q 027294          186 LKKYSIEEKQQHNRHLCWTTTKQ  208 (225)
Q Consensus       186 L~~y~i~~~QLP~I~~~d~~~~~  208 (225)
                      |++|+++++|||||+.+||..+-
T Consensus       160 L~~y~i~~~qLP~I~~~DPv~~~  182 (210)
T 3h0g_E          160 LDRYKLRETQLPRIQLADPVARY  182 (210)
T ss_dssp             HHHTCCCTTTSCCCCTTCHHHHH
T ss_pred             HHHcCCCHHHCCcccccCcchhh
Confidence            99999999999999999998764

>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=4.4e-60  Score=411.67  Aligned_cols=175  Identities=31%  Similarity=0.476  Sum_probs=167.4

Q ss_pred             CCCChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCC---CCCCCceEEEeecCCCCCCcE------EEE
Q 027294           32 VDNGSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQ---DPDVDRLRISISHQSDPSKRI------LVV  102 (225)
Q Consensus        32 md~~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~---~p~r~~L~i~~~~~~dp~~kI------~Vf  102 (225)
                      |+ ++.++.|||||||||+|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++++.+||++++      +||
T Consensus         3 m~-~~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~g~p~r~~L~~~~~~~~d~~~k~~~~~~~~Vf   81 (215)
T 1dzf_A            3 QE-NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVE   81 (215)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEE
T ss_pred             cc-hHHHHHHHHHHHHHHHHHHhcCCCccCHhHhcCCHHHHHHHHccccCCCchhheEEEecCCCChhhhhccCCceEEE
Confidence            44 46889999999999999999999999999999999999999987   689999999999999999998      999


Q ss_pred             ecCCCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc-cceeeeecceeeeecccccccCCcccCChHH
Q 027294          103 FCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ-FKVEMFQITDLLVNITKHVLKPKHQVLTDQE  181 (225)
Q Consensus       103 F~~e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~-~~IEvF~E~ELl~nit~H~lVPkH~vl~~eE  181 (225)
                      |+++++||+|+||+|+++| +++|++++|||+|+++||+|++++.+++ ++||+|+|+||+||||+|+|||+|++||+||
T Consensus        82 F~~~~~vgvk~ir~~~~~~-~~e~~~~~IlV~q~~itp~Ak~~l~~~~~~~iE~F~e~eL~vni~~H~lVP~H~~l~~eE  160 (215)
T 1dzf_A           82 FCDEPSVGVKTMKTFVIHI-QEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDE  160 (215)
T ss_dssp             ECSSSEECHHHHHHHHHHH-HHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEEHHHHSSCGGGSTTSCEEEECCHHH
T ss_pred             ecCCCccchHHHHHHHHHH-HhcCCceEEEEECCCCChHHHHHHHHhcCceEEEeehHHheeccccceeccceEEccHHH
Confidence            9999999999999999999 9999999999999999999999999998 8999999999999999999999999999999


Q ss_pred             HHHHHHHcCCCCCCccceecCCCcccc
Q 027294          182 KEKLLKKYSIEEKQQHNRHLCWTTTKQ  208 (225)
Q Consensus       182 k~~lL~~y~i~~~QLP~I~~~d~~~~~  208 (225)
                      |++||++|+++++|||||+.+||..+-
T Consensus       161 ~~~lL~~y~i~~~qLP~I~~~DPvar~  187 (215)
T 1dzf_A          161 KRELLKRYRLKESQLPRIQRADPVALY  187 (215)
T ss_dssp             HHHHHHHTTCCGGGSCEECTTCHHHHH
T ss_pred             HHHHHHHcCCCHHHCCceeccChhhHH
Confidence            999999999999999999999997653

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

Probab=99.75  E-value=2.6e-19  Score=133.76  Aligned_cols=48  Identities=25%  Similarity=0.348  Sum_probs=46.0

Q ss_pred             eeeecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCcccc
Q 027294          161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQ  208 (225)
Q Consensus       161 Ll~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~  208 (225)
                      |+||||+|+|||+|++||+|||++||++|+++++|||||+.+||..+-
T Consensus         1 l~vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLP~I~~~DPvar~   48 (77)
T 1eik_A            1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKA   48 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTTSHHHHG
T ss_pred             CcccCccceecCCEEEcCHHHHHHHHHHcCCCHHHCCeeeCcCHhhHH
Confidence            789999999999999999999999999999999999999999998664

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

Probab=99.71  E-value=1.7e-18  Score=129.59  Aligned_cols=46  Identities=28%  Similarity=0.475  Sum_probs=44.3

Q ss_pred             eecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCcccc
Q 027294          163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQ  208 (225)
Q Consensus       163 ~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~  208 (225)
                      ||||+|+|||+|++||+|||++||++|+++++|||||+.+||..+-
T Consensus         1 vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLPrI~~~DPvar~   46 (78)
T 1hmj_A            1 MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQE   46 (78)
T ss_pred             CCccceeeCCCeEECCHHHHHHHHHHcCCCHHHCCeeeCcCHhhHH
Confidence            7999999999999999999999999999999999999999998764

>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=99.69  E-value=3.6e-18  Score=129.39  Aligned_cols=51  Identities=25%  Similarity=0.276  Sum_probs=45.1

Q ss_pred             cceeeeecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCcccc
Q 027294          158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQ  208 (225)
Q Consensus       158 E~ELl~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~  208 (225)
                      .++++||||+|+|||+|++||+||+++||++|+++++|||+|+.+||..+.
T Consensus         4 ~~~~~~Ni~~H~LVPkH~vLs~eE~~~ll~~y~i~~~qLP~I~~~DPva~~   54 (84)
T 4ayb_H            4 SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPVARS   54 (84)
T ss_dssp             ----CCCCSSSSSCCEEEECCHHHHHHHHHHHTCCGGGSCCEESSSHHHHH
T ss_pred             cccceecccccccCCCeEECCHHHHHHHHHHhcCCHhHCCeecccCHhHHh
Confidence            468999999999999999999999999999999999999999999997653

---

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	225
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	2e-38
d1dzfa2	72	d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal do	1e-09
d1eika_	77	d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA pol	1e-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 =  127 bits (321), Expect = 2e-38
 Identities = 40/138 (28%), Positives = 64/138 (46%), Gaps = 11/138 (7%)

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

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

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

>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 = 50.9 bits (122), Expect = 1e-09
 Identities = 16/31 (51%), Positives = 21/31 (67%)

Query: 165 ITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           IT H L PKH  L+  EK +LLK+Y ++E 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 = 50.9 bits (122), Expect = 1e-09
 Identities = 11/35 (31%), Positives = 20/35 (57%)

Query: 161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQ 195
           +   I KH L P+H +L + E +++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	225
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	100.0
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	99.6
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	99.47
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	98.89

>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=5.4e-44  Score=289.82  Aligned_cols=129  Identities=29%  Similarity=0.481  Sum_probs=121.9

Q ss_pred             ChhhHHHHHHHHHHHHHHhcCCCCccChhhhccCHHHHHHHhCCC---CCCCceEEEeecCCC------CCCcEEEEecC
Q 027294           35 GSRDSLRYYLSRRTVLEMLKDRGYAVALSEINLSVQDFRAIYGQD---PDVDRLRISISHQSD------PSKRILVVFCG  105 (225)
Q Consensus        35 ~~~e~~rL~rvrrTv~EMl~DRGY~V~~~El~~sldeF~~~yg~~---p~r~~L~i~~~~~~d------p~~kI~VfF~~  105 (225)
                      +++|++|||||||||+|||+||||.|+++|+++|+++|+++||+.   |+|+.|++.+.+.++      ..++|+|||++
T Consensus         1 ~d~e~~rlfr~rrTv~EMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~p~r~~l~~~~~~~~~~~~k~~~~~~I~V~F~~   80 (139)
T d1dzfa1           1 NERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCD   80 (139)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECS
T ss_pred             ChHHHHHHHHHHHHHHHHHhcCCCcCCHHHHcCCHHHHHHHHccccCCcCHHHhcccCCCchhhhhccCCCCeEEEEECC
Confidence            468999999999999999999999999999999999999999875   899999999987654      45679999999


Q ss_pred             CCccchhhHHHHHHHHhhcCCCcEEEEEEcCCCCHHHHHHHhhhc-cceeeeecceeeee
Q 027294          106 PGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLFQ-FKVEMFQITDLLVN  164 (225)
Q Consensus       106 e~kVgvK~Ir~~~e~m~~~env~r~IlVvq~~lT~~Ark~i~~~~-~~IEvF~E~ELl~n  164 (225)
                      +++||+|+||.|+++| +++|++|||||+|++|||+|++++.+++ ++||+|+|+|||||
T Consensus        81 ~~kvgvk~ir~~~~~m-~~~~~~r~IlV~q~~iTp~Ak~~i~~~~~~~iE~F~e~eLLVN  139 (139)
T d1dzfa1          81 EPSVGVKTMKTFVIHI-QEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVN  139 (139)
T ss_dssp             SSEECHHHHHHHHHHH-HHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEEHHHHSSC
T ss_pred             CCccCHHHHHHHHHHH-HhcCCceEEEEECCCCCHHHHHHHHhccCceEEEechhhcccC
Confidence            9999999999999999 9999999999999999999999999887 99999999999998

>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=99.60  E-value=6.9e-17  Score=118.59  Aligned_cols=48  Identities=25%  Similarity=0.348  Sum_probs=45.7

Q ss_pred             eeeecccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCcccc
Q 027294          161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQ  208 (225)
Q Consensus       161 Ll~nit~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~  208 (225)
                      |.+||++|+|||+|++||+||++++|++|+++.+|||+|+.+||..+.
T Consensus         1 l~~NI~~H~lVPkH~il~~ee~~~~l~~~~i~~~qLP~I~~~DPva~~   48 (77)
T d1eika_           1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKA   48 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTTSHHHHG
T ss_pred             CCccccccccCCCeEEcCHHHHHHHHHHhcCCHHHCCeecccCHhhhh
Confidence            679999999999999999999999999999999999999999997654

>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=99.47  E-value=4.7e-15  Score=107.45  Aligned_cols=44  Identities=36%  Similarity=0.456  Sum_probs=41.8

Q ss_pred             cccccccCCcccCChHHHHHHHHHcCCCCCCccceecCCCcccc
Q 027294          165 ITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQ  208 (225)
Q Consensus       165 it~H~lVPkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~  208 (225)
                      ||+|+|||+|++|++||++++|++|+++.+|||+|+.+||..+.
T Consensus         1 It~H~lVPkH~~l~~eE~~~il~~y~i~~~qLP~I~~~DPva~~   44 (72)
T d1dzfa2           1 ITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALY   44 (72)
T ss_dssp             GGGSTTSCEEEECCHHHHHHHHHHTTCCGGGSCEECTTCHHHHH
T ss_pred             CCcCccCCCeEEcCHHHHHHHHHHhCCCHhHCCeecccCHhhhh
Confidence            79999999999999999999999999999999999999997653

>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=98.89  E-value=1.5e-10  Score=82.47  Aligned_cols=38  Identities=26%  Similarity=0.385  Sum_probs=36.0

Q ss_pred             CCcccCChHHHHHHHHHcCCCCCCccceecCCCccccC
Q 027294          172 PKHQVLTDQEKEKLLKKYSIEEKQQHNRHLCWTTTKQS  209 (225)
Q Consensus       172 PkH~vl~~eEk~~lL~~y~i~~~QLP~I~~~d~~~~~~  209 (225)
                      |+|++|++||+++||++|+++.+|||+|+.+||..+.+
T Consensus         1 PkH~il~~eE~~~ll~~y~i~~~qLP~I~~~DPva~~~   38 (68)
T d1hmja_           1 PKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEI   38 (68)
T ss_pred             CCCEECCHHHHHHHHHHhCCCHHHCCcccccCHHHHHh
Confidence            99999999999999999999999999999999988743