Citrus Sinensis ID: 029683

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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-------19
Protein Sequence
MGGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
Secondary Structure (PSIPRED)
ccccccccccEEEccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHccccEEEEEEEccccccccccEEccccEEccHHHHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHccccccccccHHHHHHHHHHHHHHHHHHHHcccEccHHHHcccHHHHHHHHcccccHHHcEEEccccccccccEEEEEcccccccHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHccccEEEEEHHHEEEEEcccEEccccEEccHHHHHHHHHHccccHHcccHHccc
Coil and Loop (DISEMBL)
mggsggggecitrsshvmegggsLESYRYFLSRRTVLQMLNdrgyavpnseltrsLTEFRFtfgdkcdleslrlclplrsnpskKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHilqpkhevlsagERDKLMKKYKIEGKQVTILVKQ
Flexible Loop (DISEMBL)
mggsggggecitrsshvmegGGSLESYRYFLSRRTVLQMLNDRGyavpnseltrsLTEFRFTFGDKCDLESLRlclplrsnpskKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHIlqpkhevlsagerdklmkkykiegkqvtilvkq
Low Complexity Region (SEG)
MGGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
Disordered region (IsUnstruct)
**********************SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSA*****LMKKYKIEGKQVTI****
Disordered Region (DISOPRED)
***************************RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLES***CL*****PSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILV**
Disordered Region (DISEMBL)
********ECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
Disordered Region (DISPRO)
***************HVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVT*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
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	189	2.2.26 [Sep-21-2011]
A8XGH1	211	DNA-directed RNA polymera	N/A	no	0.862	0.772	0.304	1e-18
Q9N5K2	211	DNA-directed RNA polymera	yes	no	0.862	0.772	0.292	6e-18
Q5R587	210	DNA-directed RNA polymera	yes	no	0.835	0.752	0.295	5e-16
B0BNE2	210	DNA-directed RNA polymera	yes	no	0.835	0.752	0.289	1e-15
Q80UW8	210	DNA-directed RNA polymera	yes	no	0.835	0.752	0.289	1e-15
P19388	210	DNA-directed RNA polymera	yes	no	0.835	0.752	0.283	1e-14
Q2T9T3	210	DNA-directed RNA polymera	yes	no	0.835	0.752	0.277	1e-13
Q6BIJ0	214	DNA-directed RNA polymera	yes	no	0.814	0.719	0.293	3e-11
Q6FQA6	215	DNA-directed RNA polymera	yes	no	0.814	0.716	0.275	3e-10
Q9P4B9	215	DNA-directed RNA polymera	N/A	no	0.814	0.716	0.281	5e-10

>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 = 92.4 bits (228), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 52/171 (30%), Positives = 97/171 (56%), Gaps = 8/171 (4%)

Query: 20  GGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD-----KCDLESLRL 74
               LE+YR +  R+TVLQM++DRGY V   EL + L  F+ TFGD     K     L +
Sbjct: 2   ADDELETYRLWRIRKTVLQMVHDRGYLVAQEELDQPLETFKETFGDRPSEKKPARSDLTI 61

Query: 75  CLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEV- 133
            +    +P+ +M V +    +I  + I+ +  Q + ++ +   I+++Q+ M   A++ + 
Sbjct: 62  LVAHNDDPADQMFVFFPEDTKIGIKTIKAICQQ-MQEQNISRAIIVVQTGMTPSAKQSIG 120

Query: 134 -LKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
            +   + +E F   +L+VN+T+H L P+H V++A E+ +L+ +YK++  Q+
Sbjct: 121 DMAPKYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQL 171

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.
Caenorhabditis briggsae (taxid: 6238)

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

 Score = 90.5 bits (223), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 96/171 (56%), Gaps = 8/171 (4%)

Query: 20  GGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD-----KCDLESLRL 74
               LE+YR +  R+TVLQM++DRGY V   EL + L  F+  +GD     K     L +
Sbjct: 2   ADDELETYRLWRIRKTVLQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLTI 61

Query: 75  CLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEV- 133
            +    +P+ +M V +    +I  + I+ +  Q + ++ +   I+++Q+ M   A++ + 
Sbjct: 62  LVAHNDDPADQMFVFFPEDAKIGIKTIKAICQQ-MQEQNISRAIIVVQTGMTPSAKQSIG 120

Query: 134 -LKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
            +   + +E F   +L+VN+T+H L P+H V++A E+ +L+ +YK++  Q+
Sbjct: 121 DMAPKYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQL 171

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, 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|Q5R587|RPAB1_PONAB DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Pongo abelii GN=POLR2E PE=2 SV=1

 Score = 84.0 bits (206), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/166 (29%), Positives = 93/166 (56%), Gaps = 8/166 (4%)

Query: 25  ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
           E+YR +  R+T++Q+ +DRGY V   EL ++L EFR  FGDK          L + +   
Sbjct: 6   ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLVAHN 65

Query: 80  SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
            +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct: 66  DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query: 140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct: 125 YILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 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, 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|B0BNE2|RPAB1_RAT DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus GN=Polr2e PE=2 SV=1

 Score = 82.8 bits (203), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 48/166 (28%), Positives = 93/166 (56%), Gaps = 8/166 (4%)

Query: 25  ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
           E+YR +  R+T++Q+ +DRGY V   EL ++L EF+  FGDK          L + +   
Sbjct: 6   ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHN 65

Query: 80  SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
            +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct: 66  DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query: 140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct: 125 YVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQL 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, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Rattus norvegicus (taxid: 10116)

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

 Score = 82.8 bits (203), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 48/166 (28%), Positives = 93/166 (56%), Gaps = 8/166 (4%)

Query: 25  ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
           E+YR +  R+T++Q+ +DRGY V   EL ++L EF+  FGDK          L + +   
Sbjct: 6   ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHN 65

Query: 80  SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
            +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct: 66  DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query: 140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct: 125 YVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQL 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, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Mus musculus (taxid: 10090)

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

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 47/166 (28%), Positives = 92/166 (55%), Gaps = 8/166 (4%)

Query: 25  ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
           E+YR +  R+T++Q+ +DRGY V   EL ++L EF+   GDK          L + +   
Sbjct: 6   ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQSGDKPSEGRPRRTDLTVLVAHN 65

Query: 80  SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
            +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct: 66  DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query: 140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct: 125 YILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 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, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Homo sapiens (taxid: 9606)

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

 Score = 76.3 bits (186), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/166 (27%), Positives = 91/166 (54%), Gaps = 8/166 (4%)

Query: 25  ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
           E+YR +  R+T++Q+ +DRGY V    L ++L EF+  FG K          L + +   
Sbjct: 6   ETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVAHN 65

Query: 80  SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
            +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct: 66  DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query: 140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct: 125 YILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 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, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Bos taurus (taxid: 9913)

>sp|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 = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 49/167 (29%), Positives = 83/167 (49%), Gaps = 13/167 (7%)

Query: 28  RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKML 87
           R + S +TV +M+ DRGY +   E+  SL EFR    D  ++   +L +  ++NP+ + L
Sbjct: 10  RLWRSFKTVKEMVRDRGYYITQEEIDMSLAEFRSRICDSMNVPQRKL-MCFQANPTAESL 68

Query: 88  ----------VVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKF- 136
                     V +     +  + +R     I  K    G I I QS++   A K +    
Sbjct: 69  EKFPDLGSLWVEFCDEASVGIKTMRNFCIHISEKNFSTG-IFIYQSSITPSANKLIPTVS 127

Query: 137 PFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
           P  +E F   DL+VN+T H L PKH  L+  E+ +L+++Y+++  Q+
Sbjct: 128 PASIETFQEGDLVVNITHHDLVPKHIKLARDEKKELLERYRLKESQL 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.

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

>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 = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 46/167 (27%), Positives = 84/167 (50%), Gaps = 13/167 (7%)

Query: 28  RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKK-- 85
           R + + RTV +M+ DRGY +   EL  +L +F+  + D     + R  +  ++NP+++  
Sbjct: 11  RLWRTFRTVKEMVRDRGYFIAQEELDLTLEDFKVKYCDSMG-RAQRKMMSFQANPTEESM 69

Query: 86  --------MLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP 137
                   + V +     +  + ++     I  K+   G I I Q+N+   A K V   P
Sbjct: 70  TKFPDMGTLWVEFCDEPSVGVKTMKTFVIHIQEKQFQTG-IFIYQNNITPSAMKLVPSIP 128

Query: 138 -FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
              +E F+   L+VN+T H L PKH  L+  E+ +L+K+Y+++  Q+
Sbjct: 129 PATIETFHEAALVVNITHHDLVPKHIRLNEEEKAELLKRYRLKESQL 175

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

 Score = 63.9 bits (154), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 47/167 (28%), Positives = 81/167 (48%), Gaps = 13/167 (7%)

Query: 28  RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKK-- 85
           R + + RTV +M+ DRGY +   E+  SL +F+  + D    +  R  +  +SNP+++  
Sbjct: 11  RLWRAFRTVKEMVRDRGYFITQEEIDLSLEDFKVKYCDSMG-KPQRKMMSFQSNPTEESI 69

Query: 86  --------MLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEV-LKF 136
                   + V +     +  + ++     I  K    G I I QS +   A K +    
Sbjct: 70  EKFPEMGSLWVEFCDEASVGVKTMKNFVVHITEKNFQTG-IFIYQSGITPSANKILPTAA 128

Query: 137 PFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
           P  +E F    L+VN+T H L PKH  LS  E+ +L+K+Y+++  Q+
Sbjct: 129 PAVIETFPEASLVVNITHHELVPKHIRLSDAEKKELLKRYRLKESQL 175

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)

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	189
224053296	233	predicted protein [Populus trichocarpa]	0.857	0.695	0.660	6e-57
359487223	221	PREDICTED: DNA-directed RNA polymerases	0.962	0.823	0.598	3e-55
297742693	731	unnamed protein product [Vitis vinifera]	0.968	0.250	0.595	3e-55
255544029	239	DNA-directed RNA polymerase II, putative	0.904	0.715	0.571	4e-49
15232524	233	RNA polymerase II fifth largest subunit,	0.941	0.763	0.5	2e-46
297816744	223	eukaryotic rpb5 RNA polymerase subunit f	0.947	0.802	0.480	9e-45
449437743	227	PREDICTED: DNA-directed RNA polymerases	0.936	0.779	0.502	8e-43
224139746	216	predicted protein [Populus trichocarpa]	0.941	0.824	0.510	5e-42
255576548	238	DNA-directed RNA polymerase II, putative	0.952	0.756	0.489	1e-41
357509489	248	DNA-directed RNA polymerases I, II, and	0.862	0.657	0.509	4e-41

>gi|224053296|ref|XP_002297750.1| predicted protein [Populus trichocarpa] gi|222845008|gb|EEE82555.1| predicted protein [Populus trichocarpa]

 Score =  225 bits (574), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 107/162 (66%), Positives = 135/162 (83%)

Query: 22  GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSN 81
           GS ESYRY++SRRTVL+ML DRGY V +SEL RSLTEFR  FG+  DL+SLR  + LRS 
Sbjct: 32  GSAESYRYYISRRTVLEMLKDRGYDVLDSELNRSLTEFRSVFGNSPDLDSLRFSVSLRSI 91

Query: 82  PSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVE 141
           P KK LV++LGT+EI+T  IR +YGQILNKE+LHGLILILQS MN FA+KE+ KFPFKVE
Sbjct: 92  PHKKTLVMFLGTDEIKTANIRTVYGQILNKESLHGLILILQSKMNHFAKKELEKFPFKVE 151

Query: 142 IFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
           +F ITDLLVN+TKH+LQP+ ++L+A ++ ++M KYK+E KQ+
Sbjct: 152 VFQITDLLVNITKHVLQPQMDILTAEQKQQVMNKYKLEDKQL 193

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487223|ref|XP_002269723.2| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Vitis vinifera]

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 112/187 (59%), Positives = 141/187 (75%), Gaps = 5/187 (2%)

Query: 2   GGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRF 61
            GS G G CIT     ME G S+ESYRY+LSRRT+ QML+DRGY VP+SELTRSL++FR 
Sbjct: 5   AGSHGNGSCITAD---MEQG-SIESYRYYLSRRTLFQMLSDRGYNVPHSELTRSLSDFRA 60

Query: 62  TFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILIL 121
           +FG   D   LR+CLPL S+PSKK+LVV+ GT+EIR   IR ++ QI N+E LH LIL+L
Sbjct: 61  SFGHNPDPSRLRICLPLISSPSKKILVVFCGTDEIRKAVIRVIFQQI-NREGLHRLILVL 119

Query: 122 QSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGK 181
           QS MN+ ARK V ++P KVE F IT+LL+N+TKH+  PKHE+LSA E+ KL+ KYK+E K
Sbjct: 120 QSKMNSHARKVVDEYPIKVEFFQITELLINITKHVSVPKHEILSAQEKRKLVNKYKLEDK 179

Query: 182 QVTILVK 188
           Q  I+ K
Sbjct: 180 QFPIMQK 186

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742693|emb|CBI35146.3| unnamed protein product [Vitis vinifera]

 Score =  219 bits (559), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 112/188 (59%), Positives = 141/188 (75%), Gaps = 5/188 (2%)

Query: 2   GGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRF 61
            GS G G CIT     ME G S+ESYRY+LSRRT+ QML+DRGY VP+SELTRSL++FR 
Sbjct: 515 AGSHGNGSCITAD---MEQG-SIESYRYYLSRRTLFQMLSDRGYNVPHSELTRSLSDFRA 570

Query: 62  TFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILIL 121
           +FG   D   LR+CLPL S+PSKK+LVV+ GT+EIR   IR ++ QI N+E LH LIL+L
Sbjct: 571 SFGHNPDPSRLRICLPLISSPSKKILVVFCGTDEIRKAVIRVIFQQI-NREGLHRLILVL 629

Query: 122 QSNMNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGK 181
           QS MN+ ARK V ++P KVE F IT+LL+N+TKH+  PKHE+LSA E+ KL+ KYK+E K
Sbjct: 630 QSKMNSHARKVVDEYPIKVEFFQITELLINITKHVSVPKHEILSAQEKRKLVNKYKLEDK 689

Query: 182 QVTILVKQ 189
           Q  I+ K 
Sbjct: 690 QFPIMQKD 697

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544029|ref|XP_002513077.1| DNA-directed RNA polymerase II, putative [Ricinus communis] gi|223548088|gb|EEF49580.1| DNA-directed RNA polymerase II, putative [Ricinus communis]

 Score =  199 bits (507), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 100/175 (57%), Positives = 132/175 (75%), Gaps = 4/175 (2%)

Query: 9   ECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD 68
           EC+T+         SLES RY+LSR+TV++ML DRGY V +SELT S TEF   FGD  D
Sbjct: 29  ECLTK----FVEQASLESQRYYLSRKTVMEMLRDRGYDVADSELTGSFTEFLSEFGDNPD 84

Query: 69  LESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTF 128
           +  LR+   L S+P KKM+VV++GTEEI+   IRGL  QI NKE+L+GLILILQS MN +
Sbjct: 85  ILKLRISASLHSHPDKKMVVVFMGTEEIKLANIRGLLCQIKNKESLNGLILILQSKMNHY 144

Query: 129 ARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
           ARKE+ +FP KVEIF+I+DLLVN+TKH+L+P+HEVL+A ++ +L+ K+  E KQ+
Sbjct: 145 ARKELGQFPSKVEIFHISDLLVNITKHVLKPRHEVLTAEQKQQLLNKFSSEDKQL 199

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232524|ref|NP_191013.1| RNA polymerase II fifth largest subunit, E [Arabidopsis thaliana] gi|7258352|emb|CAB77569.1| RNA polymerase 24kDa subunit-like protein [Arabidopsis thaliana] gi|332645717|gb|AEE79238.1| RNA polymerase II fifth largest subunit, E [Arabidopsis thaliana]

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/182 (50%), Positives = 130/182 (71%), Gaps = 4/182 (2%)

Query: 5   GGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFG 64
             G  CI+++    E  G +ES R++L+R T  +ML DRGY V  +EL+ +L+EFR  FG
Sbjct: 19  DDGTNCISKT----EDTGGIESKRFYLARTTAFEMLRDRGYEVNEAELSLTLSEFRSVFG 74

Query: 65  DKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSN 124
           +K +LE LR+C+PLRS+P KK+LVV++GTE I  +++R L+ QI N   LH +IL+LQS 
Sbjct: 75  EKPELERLRICVPLRSDPKKKILVVFMGTEPITVKSVRALHIQISNNVGLHAMILVLQSK 134

Query: 125 MNTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVT 184
           MN FA+K +  FPF VE F I DLLVN+TKHI QPK E+L+  E+++L++K+ +E KQ+ 
Sbjct: 135 MNHFAQKALTTFPFTVETFPIEDLLVNITKHIQQPKIEILNKEEKEQLLRKHALEDKQLP 194

Query: 185 IL 186
            L
Sbjct: 195 YL 196

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297816744|ref|XP_002876255.1| eukaryotic rpb5 RNA polymerase subunit family protein [Arabidopsis lyrata subsp. lyrata] gi|297322093|gb|EFH52514.1| eukaryotic rpb5 RNA polymerase subunit family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  185 bits (469), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 88/183 (48%), Positives = 128/183 (69%), Gaps = 4/183 (2%)

Query: 6   GGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD 65
            G  CI+++    E  G ++S R++L+R T  +ML DRGY V  +EL+ +L+EFR  FG+
Sbjct: 16  NGSHCISKT----EDTGGIDSKRFYLARTTAFEMLRDRGYEVNEAELSLTLSEFRSVFGE 71

Query: 66  KCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNM 125
           K DLE LR+C+PLRS+P KK+LVV++GTE I  +++R ++ QI N   ++ +ILILQS M
Sbjct: 72  KPDLERLRICVPLRSDPKKKILVVFMGTEPITVKSVRAIHSQISNNVGVNAMILILQSKM 131

Query: 126 NTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTI 185
           N FA KE+  FPF VE   I DLLVN+ KHI QPK E+L+  E+++L++K+ +E KQ   
Sbjct: 132 NHFAHKELTTFPFTVETIPIGDLLVNIAKHIQQPKIEILNKEEKEQLLRKHALEDKQEDS 191

Query: 186 LVK 188
            V+
Sbjct: 192 FVR 194

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  178 bits (452), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 91/181 (50%), Positives = 128/181 (70%), Gaps = 4/181 (2%)

Query: 8   GECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKC 67
           G C+  SS++    G+ ES+RYFLSRRTV++ML DRGY + +  +  SL +FR TFG   
Sbjct: 16  GTCL--SSYI--DDGTTESHRYFLSRRTVVEMLKDRGYTINSPNIDFSLQQFRETFGQFP 71

Query: 68  DLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNT 127
           D++ L+L     S+PSK++LVV+ GT  ++  AIR + GQI NK++LHGLILI+Q+ +  
Sbjct: 72  DVDRLKLSAAHHSDPSKRVLVVFCGTGAVKVNAIRNIAGQIANKDSLHGLILIVQNQITN 131

Query: 128 FARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILV 187
            A K V  F FKVEIF ITDLLVN+TKH L+P H+VL+  E+ KL+K+Y IE KQ+  ++
Sbjct: 132 QAMKAVELFSFKVEIFQITDLLVNITKHALKPNHQVLTEEEKQKLLKQYSIEEKQLPRML 191

Query: 188 K 188
           +
Sbjct: 192 R 192

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  176 bits (445), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 93/182 (51%), Positives = 130/182 (71%), Gaps = 4/182 (2%)

Query: 8   GECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKC 67
           G C+  SS V EG  S ES+RY+LSRRTVL+ML DRGY+VP+SE+  SL +FR  +G   
Sbjct: 5   GRCL--SSFVDEG--STESHRYYLSRRTVLEMLKDRGYSVPSSEIDISLQDFRGVYGQNP 60

Query: 68  DLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNT 127
           D+E L+     +S+PSK+MLV++ G   ++   IR +  QI ++++L GLIL+LQ+N+  
Sbjct: 61  DIELLKFSATHKSDPSKRMLVIFCGLGVVKVGMIRLITVQITDRDSLTGLILVLQNNITN 120

Query: 128 FARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILV 187
            A K +  F FK+EIF ITDLLVN+TKHIL+PKH+VLS   + +L+KKY IE KQ+  L+
Sbjct: 121 QAMKALDLFKFKIEIFQITDLLVNITKHILKPKHQVLSEQAKQRLLKKYSIEEKQLPRLL 180

Query: 188 KQ 189
           K+
Sbjct: 181 KK 182

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 90/184 (48%), Positives = 128/184 (69%), Gaps = 4/184 (2%)

Query: 6   GGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD 65
           G G+C +  +      G+ E++RY+LSRRTVL+ML DRGY+VP+SE+  SL EFR   G 
Sbjct: 25  GLGKCFSSYA----DDGTHETHRYYLSRRTVLEMLRDRGYSVPSSEIDLSLQEFRAIHGP 80

Query: 66  KCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNM 125
             D++ L+      S+PSK+MLV++ G   I+   IR + GQI+NK++L GLIL+LQ+ +
Sbjct: 81  NPDIDRLKFSATHTSDPSKRMLVLFGGPGIIKVSTIRAIAGQIVNKDSLTGLILVLQNQI 140

Query: 126 NTFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTI 185
              A K V  F FKVE+F ITDLLVN+TKH+L+PKH+VL+  E+ KL+K Y IE KQ+  
Sbjct: 141 TNQAMKAVDLFKFKVEMFQITDLLVNITKHVLKPKHQVLTDREKQKLLKDYCIEEKQLPR 200

Query: 186 LVKQ 189
           L+++
Sbjct: 201 LLRK 204

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 83/163 (50%), Positives = 118/163 (72%)

Query: 21  GGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRS 80
            GS+ES+RY+LSRRTVL+ML DRGY++P+ E+  SL +FR   G   D++ LRL     +
Sbjct: 46  NGSIESHRYYLSRRTVLEMLKDRGYSIPSDEIQLSLDDFRQIHGQSPDVDRLRLTATHAT 105

Query: 81  NPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKV 140
           NPSK++LVV+ G   ++   +R + GQI+N+E+L GLILI+Q+ + + A K V    FKV
Sbjct: 106 NPSKRILVVFSGPGIVKVNGVRDIAGQIVNRESLTGLILIVQNQITSQALKAVNLLSFKV 165

Query: 141 EIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
           EIF ITDLLVN TKH+L+PKH+VL+  ++  L+KKY I+ KQ+
Sbjct: 166 EIFQITDLLVNATKHVLKPKHQVLTDKQKKNLLKKYDIQEKQL 208

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	189
TAIR|locus:2096971	233	RPB5E ""RNA polymerase II fift	0.931	0.755	0.505	5e-44
TAIR|locus:2080650	222	NRPE5 [Arabidopsis thaliana (t	0.883	0.752	0.461	7.2e-36
TAIR|locus:2040257	218	RPB5D ""RNA polymerase II fift	0.851	0.738	0.459	6.5e-35
TAIR|locus:2087842	205	NRPB5 [Arabidopsis thaliana (t	0.830	0.765	0.296	7.5e-18
WB|WBGene00019246	211	rpb-5 [Caenorhabditis elegans	0.841	0.753	0.299	9.5e-18
ZFIN|ZDB-GENE-040801-83	210	polr2eb "polymerase (RNA) II (	0.835	0.752	0.301	3.2e-17
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.835	0.752	0.295	6.7e-17
FB|FBgn0033571	210	Rpb5 "Rpb5" [Drosophila melano	0.814	0.733	0.290	8.6e-17
UNIPROTKB|F1NHV9	215	POLR2E "Uncharacterized protei	0.835	0.734	0.289	1.1e-16
MGI|MGI:1913670	210	Polr2e "polymerase (RNA) II (D	0.835	0.752	0.289	1.1e-16

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

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 91/180 (50%), Positives = 130/180 (72%)

Query:     7 GGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK 66
             G  CI+++    E  G +ES R++L+R T  +ML DRGY V  +EL+ +L+EFR  FG+K
Sbjct:    21 GTNCISKT----EDTGGIESKRFYLARTTAFEMLRDRGYEVNEAELSLTLSEFRSVFGEK 76

Query:    67 CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMN 126
              +LE LR+C+PLRS+P KK+LVV++GTE I  +++R L+ QI N   LH +IL+LQS MN
Sbjct:    77 PELERLRICVPLRSDPKKKILVVFMGTEPITVKSVRALHIQISNNVGLHAMILVLQSKMN 136

Query:   127 TFARKEVLKFPFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTIL 186
              FA+K +  FPF VE F I DLLVN+TKHI QPK E+L+  E+++L++K+ +E KQ+  L
Sbjct:   137 HFAQKALTTFPFTVETFPIEDLLVNITKHIQQPKIEILNKEEKEQLLRKHALEDKQLPYL 196

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:2080650 NRPE5 [Arabidopsis thaliana (taxid:3702)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 77/167 (46%), Positives = 117/167 (70%)

Query:    23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNP 82
             S ES+RY+L+RR  LQML DRGY V + ++  SL +FR  +G++ D++ LR+    RS+ 
Sbjct:    22 SEESHRYYLARRNGLQMLRDRGYEVSDEDINLSLHDFRTVYGERPDVDRLRISALHRSDS 81

Query:    83 SKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEI 142
             +KK+ +V+ GT  ++  AIR +   IL++E + GLIL+LQ+++   A K +  F FKVEI
Sbjct:    82 TKKVKIVFFGTSMVKVNAIRSVVADILSQETITGLILVLQNHVTNQALKAIELFSFKVEI 141

Query:   143 FYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 189
             F ITDLLVN+TKH L+P+H+VL+  E+  L+KK+ IE KQ+  + K+
Sbjct:   142 FQITDLLVNITKHSLKPQHQVLNDEEKTTLLKKFSIEEKQLPRISKK 188

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 = 378 (138.1 bits), Expect = 6.5e-35, P = 6.5e-35
 Identities = 74/161 (45%), Positives = 115/161 (71%)

Query:    23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNP 82
             S+E ++Y+L+RRT ++ML DRGY V + ++  SL +FR  +G+  D++ LR+    R + 
Sbjct:    18 SVECHKYYLARRTTMEMLRDRGYDVSDEDINLSLQQFRALYGEHPDVDLLRISAKHRFDS 77

Query:    83 SKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEI 142
             SKK+ VV+ GT  ++  A+R +   +L++E + GLIL+LQS++   A K V  F FKVE+
Sbjct:    78 SKKISVVFCGTGIVKVNAMRVIAADVLSRENITGLILVLQSHITNQALKAVELFSFKVEL 137

Query:   143 FYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             F ITDLLVNV+KH+L+PKH+VL+  E++ L+KK+ IE KQ+
Sbjct:   138 FEITDLLVNVSKHVLRPKHQVLNDKEKESLLKKFSIEEKQL 178

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:2087842 NRPB5 [Arabidopsis thaliana (taxid:3702)]

 Score = 217 (81.4 bits), Expect = 7.5e-18, P = 7.5e-18
 Identities = 48/162 (29%), Positives = 92/162 (56%)

Query:    25 ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSK 84
             E  R +  ++T++QML DRGY + +SELT +  +F    GD    E L + L  + N + 
Sbjct:     6 ELKRLYRIQKTLMQMLRDRGYFIADSELTMTKQQFIRKHGDNMKREDL-VTLKAKRNDNS 64

Query:    85 KMLVVYLGTE-EIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEV--LKFPFKVE 141
               L ++   E ++  + ++ +Y   +  E +   IL++Q N+  FAR  +  +   F +E
Sbjct:    65 DQLYIFFPDEAKVGVKTMK-MYTNRMKSENVFRAILVVQQNLTPFARTCISEISSKFHLE 123

Query:   142 IFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             +F   ++LVN+ +H+L P+H+VL+  E+  L+++Y ++  Q+
Sbjct:   124 VFQEAEMLVNIKEHVLVPEHQVLTTEEKKTLLERYTVKETQL 165

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

GO:0051604 "protein maturation" evidence=RCA

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

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 50/167 (29%), Positives = 96/167 (57%)

Query:    24 LESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD-----KCDLESLRLCLPL 78
             LE+YR +  R+TVLQM++DRGY V   EL + L  F+  +GD     K     L + +  
Sbjct:     6 LETYRLWRIRKTVLQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLTILVAH 65

Query:    79 RSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEV--LKF 136
               +P+ +M V +    +I  + I+ +  Q + ++ +   I+++Q+ M   A++ +  +  
Sbjct:    66 NDDPADQMFVFFPEDAKIGIKTIKAICQQ-MQEQNISRAIIVVQTGMTPSAKQSIGDMAP 124

Query:   137 PFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
              + +E F   +L+VN+T+H L P+H V++A E+ +L+ +YK++  Q+
Sbjct:   125 KYMLEHFLEAELMVNITEHELVPEHVVMTAEEKAELLARYKLKDSQL 171

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

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

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 50/166 (30%), Positives = 94/166 (56%)

Query:    25 ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
             E+YR +  R+T++Q+ +DRGY V   EL ++L EFR  FGDK          L + +   
Sbjct:     6 ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLDEFRSQFGDKPSEGRPRRNDLTVLVAHN 65

Query:    80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
              +P+ +M V +    ++  + I+ +Y Q + +E +   I+++Q  M   A++ ++    K
Sbjct:    66 DDPTDQMFVFFPEEPKVGIKTIK-MYCQRMQEENITRAIIVVQMGMTPSAKQSLVDMAPK 124

Query:   140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
               +E F   +LL+N+T+H L P+H V++  E  +L+ +YK++  Q+
Sbjct:   125 YILEQFLQQELLINITEHELVPEHIVMTKEEVTELLARYKLKESQL 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

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

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 49/166 (29%), Positives = 93/166 (56%)

Query:    25 ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
             E+YR +  R+T++Q+ +DRGY V   EL ++L EFR  FGDK          L + +   
Sbjct:     6 ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLVAHN 65

Query:    80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
              +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct:    66 DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query:   140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
               +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct:   125 YILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 170

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

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

 Score = 207 (77.9 bits), Expect = 8.6e-17, P = 8.6e-17
 Identities = 47/162 (29%), Positives = 94/162 (58%)

Query:    25 ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLE-----SLRLCLPLR 79
             E+Y+ +  R+T++Q+ +DRGY V   EL ++L +F+  FGDK   +      L + +   
Sbjct:     6 ETYKLWRIRKTIMQLSHDRGYLVTQDELDQTLEQFKEMFGDKPSEKRPARSDLIVLVAHN 65

Query:    80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
              +P+ +M V +    +I  + I+  Y   + +E +H  I+++Q  M   A++ ++    K
Sbjct:    66 DDPTDQMFVFFPEEPKIGIKTIK-TYCTRMQEENIHRAIVVVQGGMTPSAKQSLVDMAPK 124

Query:   140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIE 179
               +E F  ++LL+N+T+H L P+H V++  E+ +L+ +YK++
Sbjct:   125 YILEQFLESELLINITEHELVPEHVVMTVEEKQELLSRYKLK 166

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

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

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

GO:0003677 "DNA binding" evidence=IEA

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

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

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 48/166 (28%), Positives = 93/166 (56%)

Query:    25 ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
             E+YR +  R+T++Q+ +DRGY V   EL ++L EF+  FGDK          L + +   
Sbjct:    11 ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHN 70

Query:    80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK 139
              +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct:    71 DDPTDQMFVFFPEEPKVGIKTIK-MYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 129

Query:   140 --VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
               +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct:   130 YILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQL 175

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

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

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

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

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 48/166 (28%), Positives = 94/166 (56%)

Query:    25 ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCD-----LESLRLCLPLR 79
             E+YR +  R+T++Q+ +DRGY V   EL ++L EF+  FGDK          L + +   
Sbjct:     6 ETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHN 65

Query:    80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKF-P- 137
              +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++   P 
Sbjct:    66 DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query:   138 FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             + +E F   +LL+N+T+H L P+H V++  E  +L+ +YK+   Q+
Sbjct:   125 YVLEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRESQL 170

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

---

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	189
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	4e-70
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	1e-22
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	2e-15
pfam01191	74	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-	7e-10
COG2012	80	COG2012, RPB5, DNA-directed RNA polymerase, subuni	5e-07
PRK09570	79	PRK09570, rpoH, DNA-directed RNA polymerase subuni	3e-05

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

 Score =  211 bits (539), Expect = 4e-70
 Identities = 74/166 (44%), Positives = 108/166 (65%), Gaps = 3/166 (1%)

Query: 19  EGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPL 78
              GS ES R +L RRTVL+ML DRGY V +SEL  +L+EFR  FG+K   E LR+  P 
Sbjct: 1   MDTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPK 60

Query: 79  RSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKF-- 136
           RS+PSKK+LV +   E++  + I+      +  E +   IL+LQS +  FA++ + +F  
Sbjct: 61  RSDPSKKILVFFPEEEKVGVKTIKTYAE-RMKDENVSRAILVLQSKLTPFAKQALSEFNS 119

Query: 137 PFKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
            FK+E+F  T+LLVN+TKH+L PKH+VL+  E+  L+K+Y ++  Q
Sbjct: 120 KFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQ 165

Length = 206

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

 Score = 89.5 bits (222), Expect = 1e-22
 Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 5/160 (3%)

Query: 28  RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKML 87
           R+F  RRT  +ML DRGY + + E   +   F+  F +   L S  L +          +
Sbjct: 7   RFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRI 66

Query: 88  VVYLGTEEIRT--QAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK--VEIF 143
           +VY   E  +T  + IR L  + + +  +   IL+ Q+ +  FA+  +L+   +  +E F
Sbjct: 67  IVYFADETKKTGVKPIRELT-EKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENF 125

Query: 144 YITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
             T+LLVN+TKH L PKH  L+  E+  L+++YK++  Q+
Sbjct: 126 LETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQL 165

Length = 205

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

 Score = 67.7 bits (166), Expect = 2e-15
 Identities = 28/84 (33%), Positives = 41/84 (48%), Gaps = 2/84 (2%)

Query: 23  SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEF--RFTFGDKCDLESLRLCLPLRS 80
             E YR +  RRTV++ML DRGY V   EL  SL EF  ++      D   L      + 
Sbjct: 4   ERELYRLWRVRRTVMEMLRDRGYLVTEEELNLSLEEFKEKYGDNGNPDRSKLTFSARPKD 63

Query: 81  NPSKKMLVVYLGTEEIRTQAIRGL 104
           +PS ++ V +   E++  + IR  
Sbjct: 64  DPSGRIYVFFCEEEKVGVKTIRTF 87

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 = 52.5 bits (127), Expect = 7e-10
 Identities = 21/33 (63%), Positives = 27/33 (81%)

Query: 150 VNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
           VN+TKH L PKHEVLS  E+ KL+K+YKI+ +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 = 45.4 bits (108), Expect = 5e-07
 Identities = 16/36 (44%), Positives = 22/36 (61%)

Query: 147 DLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
            L  NV  H L P+HEVLS  E  +++K+  IE +Q
Sbjct: 4   MLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQ 39

Length = 80

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

 Score = 40.2 bits (95), Expect = 3e-05
 Identities = 15/33 (45%), Positives = 22/33 (66%)

Query: 150 VNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
            +V  H L P+HE+LS  E  KL+K+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	189
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	99.65
PF01191	74	RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal do	99.63
COG2012	80	RPB5 DNA-directed RNA polymerase, subunit H, RpoH/	99.59
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	96.61

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

Probab=100.00  E-value=8.6e-65  Score=422.63  Aligned_cols=166  Identities=36%  Similarity=0.645  Sum_probs=163.4

Q ss_pred             chHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCC-CCCCccEEEecCCCCCCCcEEEEecCCCccchhHH
Q 029683           23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK-CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAI  101 (189)
Q Consensus        23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~I  101 (189)
                      +.|++||||+|||++|||+||||.|+++|+++++++|+++||+. |+|++|+|+|.|++||+++||||||++++||+|+|
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            68999999999999999999999999999999999999999998 99999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC--ceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcCCC
Q 029683          102 RGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIE  179 (189)
Q Consensus       102 r~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~--~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~~  179 (189)
                      |.|+.+| .++|++++|+|+|+++||+|++++..++  |+||+|+|+||+||||+|+|||||++||+|||++||++|+++
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             CCCCcccccC
Q 029683          180 GKQVTILVKQ  189 (189)
Q Consensus       180 ~~qLP~i~~~  189 (189)
                      ++||||||.+
T Consensus       165 e~qLPRIq~~  174 (208)
T KOG3218|consen  165 ETQLPRIQKK  174 (208)
T ss_pred             cccCCeeecc
Confidence            9999999863

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

Probab=100.00  E-value=2.3e-63  Score=418.10  Aligned_cols=167  Identities=44%  Similarity=0.732  Sum_probs=163.8

Q ss_pred             CchHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCCCCCCccEEEecCCCCCCCcEEEEecCCCccchhHH
Q 029683           22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAI  101 (189)
Q Consensus        22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~I  101 (189)
                      ++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+.|+|++|+|++++.+||+++|||||+++++||+|+|
T Consensus         4 ~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgvk~i   83 (206)
T PLN03111          4 GSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPKRSDPSKKILVFFPEEEKVGVKTI   83 (206)
T ss_pred             chHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHHcCCcCHHHcEeeeecCCCCCCcEEEEeCCCCccCHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC--ceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcCCC
Q 029683          102 RGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIE  179 (189)
Q Consensus       102 r~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~--~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~~  179 (189)
                      |.|+++| +++|++++|||+|+++||+|++++++++  ++||+|+|+||+||||+|+|||+|++||+|||++||++|+++
T Consensus        84 r~~~~~~-~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~i~  162 (206)
T PLN03111         84 KTYAERM-KDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVK  162 (206)
T ss_pred             HHHHHHH-hhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcCCC
Confidence            9999999 9999999999999999999999999995  899999999999999999999999999999999999999999


Q ss_pred             CCCCcccccC
Q 029683          180 GKQVTILVKQ  189 (189)
Q Consensus       180 ~~qLP~i~~~  189 (189)
                      ++|||||+.+
T Consensus       163 ~~qLPrI~~~  172 (206)
T PLN03111        163 ETQLPRIQVS  172 (206)
T ss_pred             HHHCCccccc
Confidence            9999999874

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=1e-62  Score=413.80  Aligned_cols=166  Identities=28%  Similarity=0.498  Sum_probs=160.7

Q ss_pred             chHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCCC-CCCCccEEEecCCCCCCCcEEEEecC-CCccchhH
Q 029683           23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK-CDLESLRLCLPLRSNPSKKMLVVYLG-TEEIRTQA  100 (189)
Q Consensus        23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~  100 (189)
                      ++++.||||+|||++|||+||||.|+++|+++|+++|+++||+. +.|++|+|+|++.+||+++|||||++ +++||+|+
T Consensus         2 ~~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~   81 (205)
T PTZ00061          2 DDSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKP   81 (205)
T ss_pred             cHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHH
Confidence            57899999999999999999999999999999999999999988 57899999999999999999999999 57999999


Q ss_pred             HHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccC--ceEEeeeeccceeccccceecCcccccCHHHHHHHHHHcCC
Q 029683          101 IRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKI  178 (189)
Q Consensus       101 Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~--~~iE~F~e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~  178 (189)
                      ||.|+++| +++|++|||||+|+++||+|++++.+++  ++||+|+|+||+||||+|+|||+|++||+|||++||++|++
T Consensus        82 ir~~~~~~-~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i  160 (205)
T PTZ00061         82 IRELTEKM-EEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKV  160 (205)
T ss_pred             HHHHHHHH-hhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCC
Confidence            99999999 9999999999999999999999999886  89999999999999999999999999999999999999999


Q ss_pred             CCCCCcccccC
Q 029683          179 EGKQVTILVKQ  189 (189)
Q Consensus       179 ~~~qLP~i~~~  189 (189)
                      +++|||||+.+
T Consensus       161 ~~~qLPrI~~~  171 (205)
T PTZ00061        161 KESQLPRIQSA  171 (205)
T ss_pred             CHHHCCccccc
Confidence            99999999874

>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=1.7e-33  Score=210.81  Aligned_cols=87  Identities=36%  Similarity=0.583  Sum_probs=75.0

Q ss_pred             CchHHHHHHHHHHHHHHHhcCCCCcCCcccccCCHHHHHHHhCC---CCCCCccEEEecCCCCCCCcEEEEecCCCccch
Q 029683           22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD---KCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRT   98 (189)
Q Consensus        22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~s~~eF~~~f~~---~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgv   98 (189)
                      ++.|++||||||||++|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++.+.+||+++|+|||+++++||+
T Consensus         3 ~~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~kvgv   82 (93)
T PF03871_consen    3 DDEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPKVGV   82 (93)
T ss_dssp             TTHHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSCESC
T ss_pred             cHHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCCcCH
Confidence            46899999999999999999999999999999999999999998   799999999999999999999999999999999


Q ss_pred             hHHHHHHHHH
Q 029683           99 QAIRGLYGQI  108 (189)
Q Consensus        99 k~Ir~~~~~~  108 (189)
                      |+||.|+++|
T Consensus        83 k~Ir~~~~~m   92 (93)
T PF03871_consen   83 KTIRKYCERM   92 (93)
T ss_dssp             CCCHHHCHHH
T ss_pred             HHHHHHHHhc
Confidence            9999999998

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=99.65  E-value=4.6e-17  Score=119.37  Aligned_cols=41  Identities=37%  Similarity=0.556  Sum_probs=39.4

Q ss_pred             eeccccceecCcccccCHHHHHHHHHHcCCCCCCCcccccC
Q 029683          149 LVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  189 (189)
Q Consensus       149 l~nit~H~lVPkH~~l~~eEk~~ll~~y~~~~~qLP~i~~~  189 (189)
                      .||||+|+|||+|++||+||+++||++|+++++|||||+.+
T Consensus         3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~   43 (79)
T PRK09570          3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKAS   43 (79)
T ss_pred             ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceecc
Confidence            58999999999999999999999999999999999999874

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

Probab=99.63  E-value=1.1e-16  Score=116.01  Aligned_cols=40  Identities=45%  Similarity=0.745  Sum_probs=33.7

Q ss_pred             eccccceecCcccccCHHHHHHHHHHcCCCCCCCcccccC
Q 029683          150 VNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  189 (189)
Q Consensus       150 ~nit~H~lVPkH~~l~~eEk~~ll~~y~~~~~qLP~i~~~  189 (189)
                      ||||+|+|||+|++||+||+++||++|+++++|||||+.+
T Consensus         1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~   40 (74)
T PF01191_consen    1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSS   40 (74)
T ss_dssp             S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETT
T ss_pred             CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCccccc
Confidence            7999999999999999999999999999999999999874

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=99.59  E-value=4.4e-16  Score=113.67  Aligned_cols=45  Identities=36%  Similarity=0.448  Sum_probs=42.7

Q ss_pred             eccceeccccceecCcccccCHHHHHHHHHHcCCCCCCCcccccC
Q 029683          145 ITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  189 (189)
Q Consensus       145 e~ELl~nit~H~lVPkH~~l~~eEk~~ll~~y~~~~~qLP~i~~~  189 (189)
                      ++.+.||+++|+|||+|++||+||++++|++|+|+++|||||+.+
T Consensus         2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~   46 (80)
T COG2012           2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKAS   46 (80)
T ss_pred             ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCccccc
Confidence            567899999999999999999999999999999999999999864

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

Probab=96.61  E-value=0.0048  Score=44.96  Aligned_cols=75  Identities=20%  Similarity=0.262  Sum_probs=41.8

Q ss_pred             cEEEecCCCCCCCcEEEEecC-CCccchhHHHHHHHHHhhccCcceEEEEEcCCCCHHHHHhhcccCceEEeeeeccc
Q 029683           72 LRLCLPLRSNPSKKMLVVYLG-TEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYITDL  148 (189)
Q Consensus        72 L~~~~~~~~dp~~~i~VfF~~-~~~vgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ar~~i~~~~~~iE~F~e~EL  148 (189)
                      ..+.+.+.+....+++|.+-. ..+++.+.|+.++..+ ...++..+|||+.+++|+.|++.+.... .|+++.-++|
T Consensus        36 iDi~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~-~~~~~~~~iivt~~~~t~~a~~~~~~~~-~I~l~d~~~L  111 (115)
T PF04471_consen   36 IDIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKA-KKYGADKGIIVTSSGFTPEAKEFAEKFK-NIELIDGEDL  111 (115)
T ss_dssp             EEEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHH-GGGT-SEEEEE-SSEE-HHHHHHHH--------------
T ss_pred             EEEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhh-hccCCCEEEEEECCcCCHHHHHHHHhhc-cccccccccc
Confidence            344444433233456666633 3579999999999999 8889999999999999999999988743 5766666655

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	189
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		5e-11
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		3e-10

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 81/167 (48%), Gaps = 17/167 (10%)
Query: 28  RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFT---FGDKCDLESLRLCLPLRSNPSK 84
           R F + +T  Q+++DRGY V  +EL  +L +F+      G   D  +L       ++ +K
Sbjct: 10  RVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNK 69
Query: 85  KMLVV------YLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP- 137
             + +       +G +E+RT      +   L        ILI  ++M   A K +     
Sbjct: 70  GTIYIEFAKEPSVGIKEMRT------FVHTLGDHNHKTGILIYANSMTPSAAKIIATVTG 123
Query: 138 -FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
            F +E F  +DL+VN+T H L PKH +LS  E+ +L+ +YK+   Q+
Sbjct: 124 QFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQL 170

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 45/167 (26%), Positives = 81/167 (48%), Gaps = 13/167 (7%)
Query: 28  RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKK-- 85
           R + + RTV +M+ DRGY +   E+   L +F+  + D       R  +  ++NP+++  
Sbjct: 11  RLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMG-RPQRKMMSFQANPTEESI 69
Query: 86  --------MLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP 137
                   + V +     +  + ++     I  K    G I + Q+N+   A K V   P
Sbjct: 70  SKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLVPSIP 128
Query: 138 -FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
              +E F    L+VN+T H L PKH  LS+ E+ +L+K+Y+++  Q+
Sbjct: 129 PATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQL 175

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	189
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	2e-38
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	7e-36
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	6e-09
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	2e-08
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	3e-08

>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 =  130 bits (327), Expect = 2e-38
 Identities = 44/164 (26%), Positives = 74/164 (45%), Gaps = 5/164 (3%)

Query: 25  ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK---CDLESLRLCLPLRSN 81
              R F + +T  Q+++DRGY V  +EL  +L +F+          D  +L       ++
Sbjct: 7   NIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSND 66

Query: 82  PSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FK 139
            +K  + +    E          +   L        ILI  ++M   A K +      F 
Sbjct: 67  SNKGTIYIEFAKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFT 126

Query: 140 VEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
           +E F  +DL+VN+T H L PKH +LS  E+ +L+ +YK+   Q+
Sbjct: 127 IETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQL 170

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

 Score =  124 bits (311), Expect = 7e-36
 Identities = 45/177 (25%), Positives = 82/177 (46%), Gaps = 13/177 (7%)

Query: 18  MEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLP 77
           M+        R + + RTV +M+ DRGY +   E+   L +F+  + D       R  + 
Sbjct: 1   MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQ-RKMMS 59

Query: 78  LRSNPSKKML----------VVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNT 127
            ++NP+++ +          V +     +  + ++     I  K      I + Q+N+  
Sbjct: 60  FQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQT-GIFVYQNNITP 118

Query: 128 FARKEVLKFP-FKVEIFYITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQV 183
            A K V   P   +E F    L+VN+T H L PKH  LS+ E+ +L+K+Y+++  Q+
Sbjct: 119 SAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQL 175

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

 Score = 50.1 bits (120), Expect = 6e-09
 Identities = 14/38 (36%), Positives = 22/38 (57%)

Query: 145 ITDLLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
            ++  ++   H L PKHEVLS  E  K++K+  I  +Q
Sbjct: 4   SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQ 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 = 48.2 bits (115), Expect = 2e-08
 Identities = 9/35 (25%), Positives = 19/35 (54%)

Query: 148 LLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
           +   + KH L P+H +L+  E  +++K+     +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 = 48.2 bits (115), Expect = 3e-08
 Identities = 14/33 (42%), Positives = 24/33 (72%)

Query: 150 VNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
           + VT HIL PKHE++   E ++++K+Y I+ +Q
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQ 33

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

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	189
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	2e-32
d1eika_	77	d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA pol	3e-08
d1dzfa2	72	d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal do	5e-08

>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 =  111 bits (279), Expect = 2e-32
 Identities = 30/137 (21%), Positives = 52/137 (37%), Gaps = 11/137 (8%)

Query: 25  ESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKC---DLESLRLCLPLRSN 81
              R + + RTV +M+ DRGY +   E+   L +F+  + D       + +         
Sbjct: 4   NISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEE 63

Query: 82  PSKK------MLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEV-L 134
              K      + V +     +  + ++     I  K    G I + Q+N+   A K V  
Sbjct: 64  SISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLVPS 122

Query: 135 KFPFKVEIFYITDLLVN 151
             P  +E F    L+VN
Sbjct: 123 IPPATIETFNEAALVVN 139

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

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

 Score = 46.6 bits (111), Expect = 3e-08
 Identities = 9/35 (25%), Positives = 19/35 (54%)

Query: 148 LLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
           +   + KH L P+H +L+  E  +++K+     +Q
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQ 35

>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 = 45.8 bits (109), Expect = 5e-08
 Identities = 13/31 (41%), Positives = 22/31 (70%)

Query: 152 VTKHILQPKHEVLSAGERDKLMKKYKIEGKQ 182
           +T H L PKH  LS+ E+ +L+K+Y+++  Q
Sbjct: 1   ITHHELVPKHIRLSSDEKRELLKRYRLKESQ 31

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	189
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	100.0
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	99.28
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	99.01
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	98.08

>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=6.5e-42  Score=268.69  Aligned_cols=129  Identities=21%  Similarity=0.324  Sum_probs=121.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCC---CCCCCCEEEECCCCCC------CCCEEEEECC
Q ss_conf             966799999999989998449998679100037977899882999---9987507980288999------9818999449
Q 029683           22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK---CDLESLRLCLPLRSNP------SKKMLVVYLG   92 (189)
Q Consensus        22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~eF~~~f~~~---~~r~~L~~~~~~~~dp------~~~i~VfF~~   92 (189)
                      +++|++||||||||++|||+||||.|+++|+++|+++|+++||+.   |+|+.|++.+.+.++|      .++||||||+
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
T ss_conf             94888899999999999986489857788970899999999724667867898513578806655406788759999789


Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHCCCC-CEEEEEEECCCEEC
Q ss_conf             986436589999999842168666999975899998898601148-11784340310010
Q 029683           93 TEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP-FKVEIFYITDLLVN  151 (189)
Q Consensus        93 ~~kvgvk~Ir~~~~~~~~~eni~~~IiV~q~~lt~~Ak~~i~~~~-~~iE~F~e~ELl~n  151 (189)
                      +++||+|+||.|+++| .++|+++||||+|+++||+|++++.+++ ++||+|+|+|||||
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
T ss_conf             8853789999999998-7648746999988889989999987566865887155551349

>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=99.28  E-value=8e-13  Score=94.66  Aligned_cols=42  Identities=21%  Similarity=0.407  Sum_probs=40.2

Q ss_pred             CEECCCCCEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             001045420117511059789999998709998877652269
Q 029683          148 LLVNVTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  189 (189)
Q Consensus       148 Ll~nit~H~lVP~H~~l~~eE~~~lL~~y~~~~~qLP~i~~~  189 (189)
                      |.+||++|+|||+|++|++||++++|++|+++.+|||+|+.+
T Consensus         1 l~~NI~~H~lVPkH~il~~ee~~~~l~~~~i~~~qLP~I~~~   42 (77)
T d1eika_           1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTT   42 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTT
T ss_pred             CCCCCCCCCCCCCEEECCHHHHHHHHHHHCCCHHHCCEECCC
T ss_conf             985455655379819869999999999856998789940362

>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=99.01  E-value=4.8e-11  Score=84.00  Aligned_cols=38  Identities=34%  Similarity=0.625  Sum_probs=36.5

Q ss_pred             CCCCEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             45420117511059789999998709998877652269
Q 029683          152 VTKHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  189 (189)
Q Consensus       152 it~H~lVP~H~~l~~eE~~~lL~~y~~~~~qLP~i~~~  189 (189)
                      ||+|+|||+|++|++||++++|++|+++.+|||+|+.+
T Consensus         1 It~H~lVPkH~~l~~eE~~~il~~y~i~~~qLP~I~~~   38 (72)
T d1dzfa2           1 ITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRA   38 (72)
T ss_dssp             GGGSTTSCEEEECCHHHHHHHHHHTTCCGGGSCEECTT
T ss_pred             CCCCCCCCCEEECCHHHHHHHHHHHCCCHHHCCEECCC
T ss_conf             97674278808859999999999959897579954363

>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=98.08  E-value=5.2e-07  Score=59.86  Aligned_cols=31  Identities=29%  Similarity=0.630  Sum_probs=29.6

Q ss_pred             CCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             7511059789999998709998877652269
Q 029683          159 PKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  189 (189)
Q Consensus       159 P~H~~l~~eE~~~lL~~y~~~~~qLP~i~~~  189 (189)
                      |+|++|++||++++|++|+++.+|||+|+.+
T Consensus         1 PkH~il~~eE~~~ll~~y~i~~~qLP~I~~~   31 (68)
T d1hmja_           1 PKHEIVPKEEVEEILKRYNIKIQQLPKIYED   31 (68)
T ss_pred             CCCEECCHHHHHHHHHHHCCCHHHCCCCCCC
T ss_conf             9877879999999999929898899912251