Citrus Sinensis ID: 030295

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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-------18
Protein Sequence
MGGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
Secondary Structure (PSIPRED)
cccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHcccHHHHHHHHcccccccccEEEEccccccccccEEEEccccccHHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHccccEEEEEEEEEEcccEEccHHHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHccccccccccHHHHHHHHHHHHHHHHHHHHcccEccHHHHcccHHHHHHHHcccccHcccEEEEcccccccccEEEEEcccccccHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHcccEEEEEEEEEccccEEccHHHHHHHHHHccccHHccHHHccc
Coil and Loop (DISEMBL)
mggsggggecitrsshvmegggsLESYRYFLSRRTVLQMLNdrgyavpnseltrsLTEFRFtfgdkcdleslrlclplrsnpskKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHIlqpkhevlsagERDKLMKKYKIEGKQVTILVKQ
Flexible Loop (DISEMBL)
mggsggggecitrsshvmegGGSLESYRYFLSRRTVLQMLNDRGyavpnseltrsLTEFRFTFGDKCDLESLRlclplrsnpskKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILqpkhevlsagerDKLMkkykiegkqvtilvkq
Low Complexity Region (SEG)
MGGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
Disordered region (IsUnstruct)
**********************SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILQPKHEVLSAGE**KLMKKYKIEGKQVTI****
Disordered Region (DISOPRED)
***************************RYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLES***C******PSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVK*
Disordered Region (DISEMBL)
********ECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
Disordered Region (DISPRO)
******************EGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTI****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ
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	179	2.2.26 [Sep-21-2011]
A8XGH1	211	DNA-directed RNA polymera	N/A	no	0.854	0.725	0.286	1e-14
Q9N5K2	211	DNA-directed RNA polymera	yes	no	0.854	0.725	0.274	6e-14
Q5R587	210	DNA-directed RNA polymera	yes	no	0.826	0.704	0.265	1e-11
B0BNE2	210	DNA-directed RNA polymera	yes	no	0.826	0.704	0.259	3e-11
Q80UW8	210	DNA-directed RNA polymera	yes	no	0.826	0.704	0.259	3e-11
P19388	210	DNA-directed RNA polymera	yes	no	0.826	0.704	0.253	3e-10
Q2T9T3	210	DNA-directed RNA polymera	yes	no	0.826	0.704	0.246	3e-09
Q6BIJ0	214	DNA-directed RNA polymera	yes	no	0.804	0.672	0.263	2e-06
Q9P4B9	215	DNA-directed RNA polymera	N/A	no	0.804	0.669	0.263	2e-06
Q6FQA6	215	DNA-directed RNA polymera	yes	no	0.804	0.669	0.251	2e-06

>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 = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 88/171 (51%), Gaps = 18/171 (10%)

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 -----------LKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                      L+    V I  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 = 77.0 bits (188), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/171 (27%), Positives = 87/171 (50%), Gaps = 18/171 (10%)

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 -----------LKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                      L+    V I  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 = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 84/166 (50%), Gaps = 18/166 (10%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                       + I  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 = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 84/166 (50%), Gaps = 18/166 (10%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                       + I  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 = 68.2 bits (165), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 84/166 (50%), Gaps = 18/166 (10%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                       + I  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 = 64.7 bits (156), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 42/166 (25%), Positives = 83/166 (50%), Gaps = 18/166 (10%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                       + I  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 = 61.6 bits (148), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 41/166 (24%), Positives = 82/166 (49%), Gaps = 18/166 (10%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                       + I  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 = 52.4 bits (124), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 77/167 (46%), Gaps = 23/167 (13%)

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 PFKVEIF----------YHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
           P  +E F          +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|Q9P4B9|RPAB1_KLUMA DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Kluyveromyces marxianus GN=RPB5 PE=3 SV=1

 Score = 52.0 bits (123), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 76/167 (45%), Gaps = 23/167 (13%)

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

Query: 86  --------MLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARK------ 131
                   + V +     +  + ++     I  K    G I I QS +   A K      
Sbjct: 70  EKFPEMGSLWVEFCDEASVGVKTMKNFVVHITEKNFQTG-IFIYQSGITPSANKILPTAA 128

Query: 132 --EVLKFP---FKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
              +  FP     V I +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)

>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 = 52.0 bits (123), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 42/167 (25%), Positives = 77/167 (46%), Gaps = 23/167 (13%)

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 -----------FKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                        V I +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)

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	179
224053296	233	predicted protein [Populus trichocarpa]	0.849	0.652	0.604	4e-49
359487223	221	PREDICTED: DNA-directed RNA polymerases	0.960	0.778	0.561	4e-48
297742693	731	unnamed protein product [Vitis vinifera]	0.966	0.236	0.558	5e-48
255544029	239	DNA-directed RNA polymerase II, putative	0.899	0.673	0.525	1e-41
15232524	233	RNA polymerase II fifth largest subunit,	0.938	0.721	0.456	2e-39
297816744	223	eukaryotic rpb5 RNA polymerase subunit f	0.944	0.757	0.448	7e-39
449437743	227	PREDICTED: DNA-directed RNA polymerases	0.905	0.713	0.465	4e-35
224139746	216	predicted protein [Populus trichocarpa]	0.938	0.777	0.461	3e-34
87162511	224	RNA polymerase subunit, RPB5; RNA polyme	0.944	0.754	0.439	6e-34
255576548	238	DNA-directed RNA polymerase II, putative	0.949	0.714	0.440	7e-34

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

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 98/162 (60%), Positives = 125/162 (77%), Gaps = 10/162 (6%)

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 IFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQV 173
           +F           H+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 =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 105/187 (56%), Positives = 131/187 (70%), Gaps = 15/187 (8%)

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 QSNMNTFARKEVLKFPFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGK 171
           QS MN+ ARK V ++P KVE F           H+  PKHE+LSA E+ KL+ KYK+E K
Sbjct: 120 QSKMNSHARKVVDEYPIKVEFFQITELLINITKHVSVPKHEILSAQEKRKLVNKYKLEDK 179

Query: 172 QVTILVK 178
           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 =  196 bits (497), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 105/188 (55%), Positives = 131/188 (69%), Gaps = 15/188 (7%)

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 QSNMNTFARKEVLKFPFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGK 171
           QS MN+ ARK V ++P KVE F           H+  PKHE+LSA E+ KL+ KYK+E K
Sbjct: 630 QSKMNSHARKVVDEYPIKVEFFQITELLINITKHVSVPKHEILSAQEKRKLVNKYKLEDK 689

Query: 172 QVTILVKQ 179
           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 =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 92/175 (52%), Positives = 122/175 (69%), Gaps = 14/175 (8%)

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 ARKEVLKFPFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQV 173
           ARKE+ +FP KVEIF+          H+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 =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 83/182 (45%), Positives = 121/182 (66%), Gaps = 14/182 (7%)

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 MNTFARKEVLKFPFKVEIF----------YHILQPKHEVLSAGERDKLMKKYKIEGKQVT 174
           MN FA+K +  FPF VE F           HI QPK E+L+  E+++L++K+ +E KQ+ 
Sbjct: 135 MNHFAQKALTTFPFTVETFPIEDLLVNITKHIQQPKIEILNKEEKEQLLRKHALEDKQLP 194

Query: 175 IL 176
            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 =  165 bits (417), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 82/183 (44%), Positives = 121/183 (66%), Gaps = 14/183 (7%)

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 NTFARKEVLKFPFKVE----------IFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTI 175
           N FA KE+  FPF VE          I  HI QPK E+L+  E+++L++K+ +E KQ   
Sbjct: 132 NHFAHKELTTFPFTVETIPIGDLLVNIAKHIQQPKIEILNKEEKEQLLRKHALEDKQEDS 191

Query: 176 LVK 178
            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 =  152 bits (385), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 82/176 (46%), Positives = 115/176 (65%), Gaps = 14/176 (7%)

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 FARKEVLKFPFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQV 173
            A K V  F FKVEIF           H L+P H+VL+  E+ KL+K+Y IE KQ+
Sbjct: 132 QAMKAVELFSFKVEIFQITDLLVNITKHALKPNHQVLTEEEKQKLLKQYSIEEKQL 187

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 =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 84/182 (46%), Positives = 120/182 (65%), Gaps = 14/182 (7%)

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 FARKEVLKFPFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQVTILV 177
            A K +  F FK+EIF           HIL+PKH+VLS   + +L+KKY IE KQ+  L+
Sbjct: 121 QAMKALDLFKFKIEIFQITDLLVNITKHILKPKHQVLSEQAKQRLLKKYSIEEKQLPRLL 180

Query: 178 KQ 179
           K+
Sbjct: 181 KK 182

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87162511|gb|ABD28306.1| RNA polymerase subunit, RPB5; RNA polymerase Rpb5, N-terminal [Medicago truncatula]

 Score =  149 bits (375), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 80/182 (43%), Positives = 116/182 (63%), Gaps = 13/182 (7%)

Query: 2   GGSGGGGECITRSSHVMEGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRF 61
            G+    EC+ R   +     ++E+ RYF  R+T++ ML+DRGY V  S+LT SL+EFR 
Sbjct: 6   NGNETRSECLVR---ICNEESNIETIRYFECRKTLMDMLHDRGYNVSESDLTLSLSEFRS 62

Query: 62  TFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILIL 121
            FG+     +L + + LRSNPS K+ VV+ GT++IR   +  +  QI++KE L  LIL++
Sbjct: 63  RFGEFPKPHTLGVSVSLRSNPSIKVQVVFPGTDDIRKSNLIVIQSQIVDKERLSRLILVM 122

Query: 122 QSNMNTFARKEVLKFPFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGK 171
           QS M ++ARKE+   PFKVEI            H+LQPK+EVL+A E+ KL+ KYK+E K
Sbjct: 123 QSKMTSYARKELENCPFKVEIIQLNDLLVNVTKHVLQPKYEVLTANEKQKLLNKYKVEEK 182

Query: 172 QV 173
           Q+
Sbjct: 183 QL 184

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 81/184 (44%), Positives = 118/184 (64%), Gaps = 14/184 (7%)

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 NTFARKEVLKFPFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQVTI 175
              A K V  F FKVE+F           H+L+PKH+VL+  E+ KL+K Y IE KQ+  
Sbjct: 141 TNQAMKAVDLFKFKVEMFQITDLLVNITKHVLKPKHQVLTDREKQKLLKDYCIEEKQLPR 200

Query: 176 LVKQ 179
           L+++
Sbjct: 201 LLRK 204

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	179
TAIR|locus:2096971	233	RPB5E ""RNA polymerase II fift	0.927	0.712	0.461	4.9e-37
TAIR|locus:2080650	222	NRPE5 [Arabidopsis thaliana (t	0.877	0.707	0.407	3.9e-28
TAIR|locus:2040257	218	RPB5D ""RNA polymerase II fift	0.843	0.692	0.403	1.7e-27
TAIR|locus:2087842	205	NRPB5 [Arabidopsis thaliana (t	0.821	0.717	0.277	4.4e-13
WB|WBGene00019246	211	rpb-5 [Caenorhabditis elegans	0.832	0.706	0.281	5.6e-13
ZFIN|ZDB-GENE-040801-83	210	polr2eb "polymerase (RNA) II (	0.826	0.704	0.271	5e-12
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.826	0.704	0.265	1e-11
UNIPROTKB|F1NHV9	215	POLR2E "Uncharacterized protei	0.826	0.688	0.259	1.7e-11
MGI|MGI:1913670	210	Polr2e "polymerase (RNA) II (D	0.826	0.704	0.259	1.7e-11
RGD|1589817	210	Polr2e "polymerase (RNA) II (D	0.826	0.704	0.259	1.7e-11

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

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 83/180 (46%), Positives = 121/180 (67%)

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 TFARKEVLKFPFKVEIF----------YHILQPKHEVLSAGERDKLMKKYKIEGKQVTIL 176
              FA+K +  FPF VE F           HI 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 = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 68/167 (40%), Positives = 107/167 (64%)

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 FY----------HILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ 179
             F           H 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 = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 65/161 (40%), Positives = 105/161 (65%)

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 FY----------HILQPKHEVLSAGERDKLMKKYKIEGKQV 173
             F           H+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 = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 45/162 (27%), Positives = 85/162 (52%)

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 IFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQV 173
             +F           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 = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 47/167 (28%), Positives = 87/167 (52%)

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

Query:    79 RSNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEV----- 133
               +P+ +M V +    +I  + I+ +  Q + ++ +   I+++Q+ M   A++ +     
Sbjct:    66 NDDPADQMFVFFPEDAKIGIKTIKAICQQ-MQEQNISRAIIVVQTGMTPSAKQSIGDMAP 124

Query:   134 -------LKFPFKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                    L+    V I  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 = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 45/166 (27%), Positives = 85/166 (51%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                         + I  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 = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 44/166 (26%), Positives = 84/166 (50%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                         + I  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

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

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 43/166 (25%), Positives = 84/166 (50%)

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 ------------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                         + I  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 = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 43/166 (25%), Positives = 86/166 (51%)

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

Query:    80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVL----K 135
              +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct:    66 DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query:   136 FPFK--------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
             +  +        + I  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

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

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 43/166 (25%), Positives = 86/166 (51%)

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

Query:    80 SNPSKKMLVVYLGTEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVL----K 135
              +P+ +M V +    ++  + I+ +Y Q + +E +   ++++Q  M   A++ ++    K
Sbjct:    66 DDPTDQMFVFFPEEPKVGIKTIK-VYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPK 124

Query:   136 FPFK--------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
             +  +        + I  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: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

---

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	179
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	8e-60
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	2e-15
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	2e-15
pfam01191	74	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-	1e-06
COG2012	80	COG2012, RPB5, DNA-directed RNA polymerase, subuni	7e-06
PRK09570	79	PRK09570, rpoH, DNA-directed RNA polymerase subuni	7e-05

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

 Score =  184 bits (470), Expect = 8e-60
 Identities = 67/166 (40%), Positives = 99/166 (59%), Gaps = 13/166 (7%)

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 PFKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQ 172
            FK+E+F           H+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 = 70.6 bits (173), Expect = 2e-15
 Identities = 43/160 (26%), Positives = 74/160 (46%), Gaps = 15/160 (9%)

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

Query: 88  VVYLGTEEIRT--QAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFPFK------ 139
           +VY   E  +T  + IR L  + + +  +   IL+ Q+ +  FA+  +L+   +      
Sbjct: 67  IVYFADETKKTGVKPIRELT-EKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENF 125

Query: 140 ------VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                 V I  H 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 = 67.3 bits (165), 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 = 43.6 bits (104), Expect = 1e-06
 Identities = 19/33 (57%), Positives = 24/33 (72%)

Query: 140 VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
           V I  H 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 = 42.0 bits (99), Expect = 7e-06
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 139 KVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
           K  +  H L P+HEVLS  E  +++K+  IE +Q
Sbjct: 6   KFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQ 39

Length = 80

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

 Score = 39.4 bits (93), Expect = 7e-05
 Identities = 15/34 (44%), Positives = 23/34 (67%)

Query: 139 KVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
           K ++  H L P+HE+LS  E  KL+K+Y I+ +Q
Sbjct: 3   KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQ 36

Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	179
KOG3218	208	consensus RNA polymerase, 25-kDa subunit (common t	100.0
PLN03111	206	DNA-directed RNA polymerase II subunit family prot	100.0
PTZ00061	205	DNA-directed RNA polymerase; Provisional	100.0
PF03871	93	RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal do	100.0
PRK09570	79	rpoH DNA-directed RNA polymerase subunit H; Review	99.51
PF01191	74	RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal do	99.45
COG2012	80	RPB5 DNA-directed RNA polymerase, subunit H, RpoH/	99.44
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	95.76

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

Probab=100.00  E-value=3e-59  Score=386.14  Aligned_cols=156  Identities=35%  Similarity=0.638  Sum_probs=153.1

Q ss_pred             chhHHHHHHHHHHHHHHhcCCCCccCcccccCCHHHHHHHhCCC-CCCCceEEEecCCCCCCCeEEEEecCCCccchhHH
Q 030295           23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK-CDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQAI  101 (179)
Q Consensus        23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~~F~~~f~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk~I  101 (179)
                      +.|++||||+|||++|||+||||.|+++|++++|++|+++||++ |+|+.|+|+|.|.+||+++||||||++++||+|+|
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             HHHHHHHhhccCCceEEEEEcCCCCHHHHHHhhccC--Cceeeee----------eeecCCccccCHHHHHHHHHHcCCC
Q 030295          102 RGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIE  169 (179)
Q Consensus       102 r~~~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~~--~~ie~f~----------H~lVPkH~~l~~eEk~~lL~~y~i~  169 (179)
                      |.|+.+| .++|++++|||+|++|||+|++++..++  |+||+|+          |+|||||++||+|||++||++|+++
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  9999998          9999999999999999999999999


Q ss_pred             CCCCcccccC
Q 030295          170 GKQVTILVKQ  179 (179)
Q Consensus       170 ~~qLP~i~~~  179 (179)
                      ++||||||.+
T Consensus       165 e~qLPRIq~~  174 (208)
T KOG3218|consen  165 ETQLPRIQKK  174 (208)
T ss_pred             cccCCeeecc
Confidence            9999999963

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

Probab=100.00  E-value=2.6e-58  Score=384.22  Aligned_cols=159  Identities=42%  Similarity=0.711  Sum_probs=154.4

Q ss_pred             CCCchhHHHHHHHHHHHHHHhcCCCCccCcccccCCHHHHHHHhCCCCCCCceEEEecCCCCCCCeEEEEecCCCccchh
Q 030295           20 GGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDKCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQ   99 (179)
Q Consensus        20 ~~~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~~F~~~f~~~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk   99 (179)
                      +.++.|+.||||+|||++|||+||||.|+++|+++|+++|+++||++|+|++|+|+|.+.+||+++|||||+++++||+|
T Consensus         2 ~~~~~e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgvk   81 (206)
T PLN03111          2 DTGSEESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSEFREKFGEKPKREDLRISAPKRSDPSKKILVFFPEEEKVGVK   81 (206)
T ss_pred             CcchHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHHcCCcCHHHcEeeeecCCCCCCcEEEEeCCCCccCHH
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhccCCceEEEEEcCCCCHHHHHHhhccC--Cceeeee----------eeecCCccccCHHHHHHHHHHcC
Q 030295          100 AIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFY----------HILQPKHEVLSAGERDKLMKKYK  167 (179)
Q Consensus       100 ~Ir~~~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~~--~~ie~f~----------H~lVPkH~~l~~eEk~~lL~~y~  167 (179)
                      +||.|+++| +++|++++|||+|++|||+|++++++++  ++||+|+          |+|||||++||+|||++||++|+
T Consensus        82 ~ir~~~~~~-~~e~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~  160 (206)
T PLN03111         82 TIKTYAERM-KDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYT  160 (206)
T ss_pred             HHHHHHHHH-hhcCcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcC
Confidence            999999999 9999999999999999999999999995  8999998          99999999999999999999999


Q ss_pred             CCCCCCcccccC
Q 030295          168 IEGKQVTILVKQ  179 (179)
Q Consensus       168 i~~~qLP~i~~~  179 (179)
                      ++++|||||+.+
T Consensus       161 i~~~qLPrI~~~  172 (206)
T PLN03111        161 VKETQLPRIQVS  172 (206)
T ss_pred             CCHHHCCccccc
Confidence            999999999874

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=3.8e-57  Score=376.78  Aligned_cols=157  Identities=25%  Similarity=0.463  Sum_probs=150.8

Q ss_pred             CchhHHHHHHHHHHHHHHhcCCCCccCcccccCCHHHHHHHhCCC-CCCCceEEEecCCCCCCCeEEEEecC-CCccchh
Q 030295           22 GSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK-CDLESLRLCLPLRSNPSKKMLVVYLG-TEEIRTQ   99 (179)
Q Consensus        22 ~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~~F~~~f~~~-~~r~~L~~~~~~~~dp~~~i~VfF~~-~~~vgvk   99 (179)
                      |++++.||||+|||++|||+||||.|+++|+++|+++|+++||++ +.|++|+|+|++.+||+++|||||++ +++||+|
T Consensus         1 ~~~~~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk   80 (205)
T PTZ00061          1 MDDSETRFFRCRRTCCEMLEDRGYIITSQEKLETFATFKERFEENERLRSRMLMVASHKTDPTNRIIVYFADETKKTGVK   80 (205)
T ss_pred             CcHHHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHHHHHhccCcccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHH
Confidence            457899999999999999999999999999999999999999988 47899999999999999999999999 5699999


Q ss_pred             HHHHHHHHHhhccCCceEEEEEcCCCCHHHHHHhhccC--Cceeeee----------eeecCCccccCHHHHHHHHHHcC
Q 030295          100 AIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFY----------HILQPKHEVLSAGERDKLMKKYK  167 (179)
Q Consensus       100 ~Ir~~~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~~--~~ie~f~----------H~lVPkH~~l~~eEk~~lL~~y~  167 (179)
                      +||.|+++| +++|+++||||+|++|||+|++++++++  ++||+|+          |+|||+|++||+|||++||++|+
T Consensus        81 ~ir~~~~~~-~~~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~  159 (205)
T PTZ00061         81 PIRELTEKM-EEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYK  159 (205)
T ss_pred             HHHHHHHHH-hhcCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhC
Confidence            999999999 9999999999999999999999999886  8999998          99999999999999999999999


Q ss_pred             CCCCCCcccccC
Q 030295          168 IEGKQVTILVKQ  179 (179)
Q Consensus       168 i~~~qLP~i~~~  179 (179)
                      ++++|||||+.+
T Consensus       160 i~~~qLPrI~~~  171 (205)
T PTZ00061        160 VKESQLPRIQSA  171 (205)
T ss_pred             CCHHHCCccccc
Confidence            999999999874

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

Probab=100.00  E-value=1.8e-34  Score=214.23  Aligned_cols=86  Identities=36%  Similarity=0.589  Sum_probs=74.4

Q ss_pred             chhHHHHHHHHHHHHHHhcCCCCccCcccccCCHHHHHHHhCC---CCCCCceEEEecCCCCCCCeEEEEecCCCccchh
Q 030295           23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD---KCDLESLRLCLPLRSNPSKKMLVVYLGTEEIRTQ   99 (179)
Q Consensus        23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~~F~~~f~~---~~~r~~L~~~~~~~~dp~~~i~VfF~~~~~vgvk   99 (179)
                      +.|++||||||||++|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++.+.+||+++|+|||+++++||+|
T Consensus         4 ~~e~~rl~rirrTv~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~kvgvk   83 (93)
T PF03871_consen    4 DEEVSRLFRIRRTVMEMLRDRGYLVSEEELNMSLEEFKEKYGENPGNPDRERLTISASKRDDPSDKIFVFFPEEPKVGVK   83 (93)
T ss_dssp             THHHHHHHHHHCCCCCCCCCCTEE--CCCCS--HHHHHHHCB-SSSSB-GCCT-EEEEESCHT--EEEEEE-SSSCESCC
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCccChhhhcCCHHHHHHHHcccCCCCCHHHeeeeccCCCCCCCeEEEEeCCCCCcCHH
Confidence            5899999999999999999999999999999999999999998   7999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 030295          100 AIRGLYGQI  108 (179)
Q Consensus       100 ~Ir~~~~~~  108 (179)
                      +||.|+++|
T Consensus        84 ~Ir~~~~~m   92 (93)
T PF03871_consen   84 TIRKYCERM   92 (93)
T ss_dssp             CCHHHCHHH
T ss_pred             HHHHHHHhc
Confidence            999999998

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=99.51  E-value=6.4e-15  Score=107.15  Aligned_cols=41  Identities=37%  Similarity=0.600  Sum_probs=38.4

Q ss_pred             ceeeeeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          139 KVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       139 ~ie~f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      .+++.+|+|||+|++||+||+++||++|+++++|||||+.+
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            46778899999999999999999999999999999999874

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

Probab=99.45  E-value=2e-14  Score=103.43  Aligned_cols=39  Identities=41%  Similarity=0.661  Sum_probs=32.2

Q ss_pred             eeeeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          141 EIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       141 e~f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      ++..|+|||+|++||+||+++||++|+++++|||||+.+
T Consensus         2 ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~   40 (74)
T PF01191_consen    2 NITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSS   40 (74)
T ss_dssp             -CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETT
T ss_pred             CcccceecCCeEEcCHHHHHHHHHHhCCChhhCCccccc
Confidence            567899999999999999999999999999999999874

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=99.44  E-value=4.6e-14  Score=102.22  Aligned_cols=41  Identities=34%  Similarity=0.511  Sum_probs=38.5

Q ss_pred             ceeeeeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          139 KVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       139 ~ie~f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      +++++.|+|||+|++||+||++++|++|+|+++|||||+.+
T Consensus         6 ~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~   46 (80)
T COG2012           6 KFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKAS   46 (80)
T ss_pred             ceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCccccc
Confidence            57788999999999999999999999999999999999864

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

Probab=95.76  E-value=0.03  Score=40.28  Aligned_cols=63  Identities=19%  Similarity=0.233  Sum_probs=41.2

Q ss_pred             EEEecCCCCCCCeEEEEecC-CCccchhHHHHHHHHHhhccCCceEEEEEcCCCCHHHHHHhhcc
Q 030295           73 RLCLPLRSNPSKKMLVVYLG-TEEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKF  136 (179)
Q Consensus        73 ~~~~~~~~dp~~~i~VfF~~-~~~vgvk~Ir~~~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~  136 (179)
                      .+.+.+.+.....++|.+-. ..+++.+.|+.++..+ ...+...+|||+.+.+|+.|++.+...
T Consensus        37 Di~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~-~~~~~~~~iivt~~~~t~~a~~~~~~~  100 (115)
T PF04471_consen   37 DIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKA-KKYGADKGIIVTSSGFTPEAKEFAEKF  100 (115)
T ss_dssp             EEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHH-GGGT-SEEEEE-SSEE-HHHHHHHH--
T ss_pred             EEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhh-hccCCCEEEEEECCcCCHHHHHHHHhh
Confidence            34444432222456666633 3579999999999999 889999999999999999999988764

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	179
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		1e-06
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		6e-06

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/167 (24%), Positives = 75/167 (44%), Gaps = 23/167 (13%)
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 -----------FKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
                        V I +H L PKH  LS+ E+ +L+K+Y+++  Q+
Sbjct: 129 PATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQL 175

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 74/167 (44%), Gaps = 27/167 (16%)
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 -FKVEIF----------YHILQPKHEVLSAGERDKLMKKYKIEGKQV 173
            F +E F          +H L PKH +LS  E+ +L+ +YK+   Q+
Sbjct: 124 QFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQL 170

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	179
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	2e-30
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	8e-29
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	9e-06
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	2e-05
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	4e-05

>3h0g_E DNA-directed RNA polymerases I, II, and III subunit rpabc1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 210

 Score =  109 bits (273), Expect = 2e-30
 Identities = 39/164 (23%), Positives = 66/164 (40%), Gaps = 15/164 (9%)

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 VEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQV 173
           +E F           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 =  105 bits (262), Expect = 8e-29
 Identities = 41/177 (23%), Positives = 76/177 (42%), Gaps = 23/177 (12%)

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-FKVEIFY----------HILQPKHEVLSAGERDKLMKKYKIEGKQV 173
            A K V   P   +E F           H L PKH  LS+ E+ +L+K+Y+++  Q+
Sbjct: 119 SAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQL 175

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

 Score = 41.2 bits (97), Expect = 9e-06
 Identities = 12/33 (36%), Positives = 24/33 (72%)

Query: 140 VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
           +++  HIL PKHE++   E ++++K+Y I+ +Q
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQ 33

>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 = 40.1 bits (94), Expect = 2e-05
 Identities = 15/35 (42%), Positives = 21/35 (60%)

Query: 138 FKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
            K++   H L PKHEVLS  E  K++K+  I  +Q
Sbjct: 7   RKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQ 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 = 39.3 bits (92), Expect = 4e-05
 Identities = 11/34 (32%), Positives = 19/34 (55%)

Query: 139 KVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
           K EI  H L P+H +L+  E  +++K+     +Q
Sbjct: 2   KREILKHQLVPEHVILNESEAKRVLKELDAHPEQ 35

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	179
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
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	99.53
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	99.53
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	99.46

>3h0g_E DNA-directed RNA polymerases I, II, and III subunit rpabc1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.1e-56  Score=374.81  Aligned_cols=160  Identities=23%  Similarity=0.371  Sum_probs=152.7

Q ss_pred             cCCCchhHHHHHHHHHHHHHHhcCCCCccCcccccCCHHHHHHHhCCC---CCCCceEEEecCCCCC-CCeEEEEecCCC
Q 030295           19 EGGGSLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK---CDLESLRLCLPLRSNP-SKKMLVVYLGTE   94 (179)
Q Consensus        19 m~~~~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~~F~~~f~~~---~~r~~L~~~~~~~~dp-~~~i~VfF~~~~   94 (179)
                      |+.++.|++||||+|||++|||+||||.|+++|+++|+++|+++||+.   |+|++|+|++.+.+|| +++|+|||++++
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            456788999999999999999999999999999999999999999875   8899999999999999 999999999999


Q ss_pred             ccchhHHHHHHHHHhhccCCceEEEEEcCCCCHHHHHHhhccC--Cceeeee----------eeecCCccccCHHHHHHH
Q 030295           95 EIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP--FKVEIFY----------HILQPKHEVLSAGERDKL  162 (179)
Q Consensus        95 ~vgvk~Ir~~~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~~--~~ie~f~----------H~lVPkH~~l~~eEk~~l  162 (179)
                      +||+|+||.|+++| .++|++++|||+|+++||+|++++.+++  ++||+|+          |+|||+|++||+||+++|
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  7999997          999999999999999999


Q ss_pred             HHHcCCCCCCCcccccC
Q 030295          163 MKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       163 L~~y~i~~~qLP~i~~~  179 (179)
                      |++|+++++|||||+.+
T Consensus       160 L~~y~i~~~qLP~I~~~  176 (210)
T 3h0g_E          160 LDRYKLRETQLPRIQLA  176 (210)
T ss_dssp             HHHTCCCTTTSCCCCTT
T ss_pred             HHHcCCCHHHCCccccc
Confidence            99999999999999864

>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=3.7e-55  Score=366.56  Aligned_cols=156  Identities=24%  Similarity=0.395  Sum_probs=151.6

Q ss_pred             chhHHHHHHHHHHHHHHhcCCCCccCcccccCCHHHHHHHhCC---CCCCCceEEEecCCCCCCCeE------EEEecCC
Q 030295           23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGD---KCDLESLRLCLPLRSNPSKKM------LVVYLGT   93 (179)
Q Consensus        23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~~F~~~f~~---~~~r~~L~~~~~~~~dp~~~i------~VfF~~~   93 (179)
                      +.|+.||||+|||++|||+||||.|+++|+++|+++|+++||+   .|+|++|+|++.+.+||++++      |||||++
T Consensus         6 ~~e~~rl~r~rrTv~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~g~p~r~~L~~~~~~~~d~~~k~~~~~~~~VfF~~~   85 (215)
T 1dzf_A            6 ERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDE   85 (215)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECSS
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCccCHhHhcCCHHHHHHHHccccCCCchhheEEEecCCCChhhhhccCCceEEEecCC
Confidence            6889999999999999999999999999999999999999997   799999999999999999998      9999999


Q ss_pred             CccchhHHHHHHHHHhhccCCceEEEEEcCCCCHHHHHHhhccC-Cceeeee----------eeecCCccccCHHHHHHH
Q 030295           94 EEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP-FKVEIFY----------HILQPKHEVLSAGERDKL  162 (179)
Q Consensus        94 ~~vgvk~Ir~~~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~~-~~ie~f~----------H~lVPkH~~l~~eEk~~l  162 (179)
                      ++||+|+||+|+++| +++|++++|||+|+++||+|++++.+++ ++||+|+          |+|||+|++||+|||++|
T Consensus        86 ~~vgvk~ir~~~~~~-~~e~~~~~IlV~q~~itp~Ak~~l~~~~~~~iE~F~e~eL~vni~~H~lVP~H~~l~~eE~~~l  164 (215)
T 1dzf_A           86 PSVGVKTMKTFVIHI-QEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKREL  164 (215)
T ss_dssp             SEECHHHHHHHHHHH-HHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEEHHHHSSCGGGSTTSCEEEECCHHHHHHH
T ss_pred             CccchHHHHHHHHHH-HhcCCceEEEEECCCCChHHHHHHHHhcCceEEEeehHHheeccccceeccceEEccHHHHHHH
Confidence            999999999999999 9999999999999999999999999998 8999998          999999999999999999


Q ss_pred             HHHcCCCCCCCcccccC
Q 030295          163 MKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       163 L~~y~i~~~qLP~i~~~  179 (179)
                      |++|+++++|||||+.+
T Consensus       165 L~~y~i~~~qLP~I~~~  181 (215)
T 1dzf_A          165 LKRYRLKESQLPRIQRA  181 (215)
T ss_dssp             HHHTTCCGGGSCEECTT
T ss_pred             HHHcCCCHHHCCceecc
Confidence            99999999999999864

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

Probab=99.53  E-value=1.7e-15  Score=108.93  Aligned_cols=39  Identities=31%  Similarity=0.602  Sum_probs=36.6

Q ss_pred             eeeeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          141 EIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       141 e~f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      ++.+|+|||+|++||+|||++||++|+++++|||||+.+
T Consensus         2 nIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLPrI~~~   40 (78)
T 1hmj_A            2 KVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYED   40 (78)
T ss_pred             CccceeeCCCeEECCHHHHHHHHHHcCCCHHHCCeeeCc
Confidence            467899999999999999999999999999999999864

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

Probab=99.53  E-value=2.2e-15  Score=108.08  Aligned_cols=40  Identities=25%  Similarity=0.434  Sum_probs=37.5

Q ss_pred             eeeeeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          140 VEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       140 ie~f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      +++.+|+|||+|++||+||+++||++|+++++|||||+.+
T Consensus         3 vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLP~I~~~   42 (77)
T 1eik_A            3 REILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTT   42 (77)
T ss_dssp             CCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTT
T ss_pred             ccCccceecCCEEEcCHHHHHHHHHHcCCCHHHCCeeeCc
Confidence            5677899999999999999999999999999999999864

>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=99.46  E-value=1.5e-14  Score=105.17  Aligned_cols=42  Identities=36%  Similarity=0.446  Sum_probs=39.0

Q ss_pred             CceeeeeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          138 FKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       138 ~~ie~f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      +.+++.+|+|||+|++||+||+++||++|+++++|||+|+.+
T Consensus         7 ~~~Ni~~H~LVPkH~vLs~eE~~~ll~~y~i~~~qLP~I~~~   48 (84)
T 4ayb_H            7 RKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRAS   48 (84)
T ss_dssp             -CCCCSSSSSCCEEEECCHHHHHHHHHHHTCCGGGSCCEESS
T ss_pred             ceecccccccCCCeEECCHHHHHHHHHHhcCCHhHCCeeccc
Confidence            578889999999999999999999999999999999999864

---

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	179
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	2e-28
d1dzfa2	72	d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal do	9e-07
d1eika_	77	d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA pol	3e-06

>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 =  100 bits (251), Expect = 2e-28
 Identities = 27/129 (20%), Positives = 48/129 (37%), Gaps = 11/129 (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 KFPFKVEIF 143
             P  +E F
Sbjct: 123 IPPATIETF 131

>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 = 42.4 bits (100), Expect = 9e-07
 Identities = 13/31 (41%), Positives = 22/31 (70%)

Query: 142 IFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
           I +H L PKH  LS+ E+ +L+K+Y+++  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 = 41.2 bits (97), Expect = 3e-06
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 138 FKVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQ 172
            K EI  H L P+H +L+  E  +++K+     +Q
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQ 35

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	179
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	100.0
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	99.32
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	99.24
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	98.71
d1y88a2	125	Hypothetical protein AF1548, N-terminal domain {Ar	87.94

>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=3.1e-42  Score=269.40  Aligned_cols=121  Identities=20%  Similarity=0.315  Sum_probs=114.6

Q ss_pred             chhHHHHHHHHHHHHHHhcCCCCccCcccccCCHHHHHHHhCCC---CCCCceEEEecCCCCC------CCeEEEEecCC
Q 030295           23 SLESYRYFLSRRTVLQMLNDRGYAVPNSELTRSLTEFRFTFGDK---CDLESLRLCLPLRSNP------SKKMLVVYLGT   93 (179)
Q Consensus        23 ~~e~~rL~rvrrTv~eMl~DRGY~V~~~el~~sl~~F~~~f~~~---~~r~~L~~~~~~~~dp------~~~i~VfF~~~   93 (179)
                      ++|++||||+||||+|||+||||.|+++|+++|+++|+++||++   |+|+.|++.+.+.++|      .++||||||++
T Consensus         2 d~e~~rlfr~rrTv~EMl~DRGY~V~~~el~~s~~~F~~~~~~~~~~p~r~~l~~~~~~~~~~~~k~~~~~~I~V~F~~~   81 (139)
T d1dzfa1           2 ERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDE   81 (139)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTBCCCHHHHTCCHHHHHHHHBCTTSCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECSS
T ss_pred             hHHHHHHHHHHHHHHHHHhcCCCcCCHHHHcCCHHHHHHHHccccCCcCHHHhcccCCCchhhhhccCCCCeEEEEECCC
Confidence            68999999999999999999999999999999999999999975   8999999999887654      56799999999


Q ss_pred             CccchhHHHHHHHHHhhccCCceEEEEEcCCCCHHHHHHhhccC-Cceeeee
Q 030295           94 EEIRTQAIRGLYGQILNKEALHGLILILQSNMNTFARKEVLKFP-FKVEIFY  144 (179)
Q Consensus        94 ~~vgvk~Ir~~~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~~-~~ie~f~  144 (179)
                      ++||+|+||.|+++| +++|++|||||+|++|||+|++++++++ ++||+|+
T Consensus        82 ~kvgvk~ir~~~~~m-~~~~~~r~IlV~q~~iTp~Ak~~i~~~~~~~iE~F~  132 (139)
T d1dzfa1          82 PSVGVKTMKTFVIHI-QEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFN  132 (139)
T ss_dssp             SEECHHHHHHHHHHH-HHTTCSEEEEEESSEECHHHHTTTTSSTTCEEEEEE
T ss_pred             CccCHHHHHHHHHHH-HhcCCceEEEEECCCCCHHHHHHHHhccCceEEEec
Confidence            999999999999999 9999999999999999999999999887 8999997

>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=99.32  E-value=2.6e-13  Score=95.41  Aligned_cols=41  Identities=27%  Similarity=0.450  Sum_probs=38.1

Q ss_pred             ceeeeeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          139 KVEIFYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       139 ~ie~f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      .++++.|+|||+|++||+||++++|++|+++.+|||+|+.+
T Consensus         2 ~~NI~~H~lVPkH~il~~ee~~~~l~~~~i~~~qLP~I~~~   42 (77)
T d1eika_           2 KREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTT   42 (77)
T ss_dssp             CCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTT
T ss_pred             CccccccccCCCeEEcCHHHHHHHHHHhcCCHHHCCeeccc
Confidence            45678899999999999999999999999999999999864

>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=99.24  E-value=8.1e-13  Score=91.76  Aligned_cols=37  Identities=32%  Similarity=0.547  Sum_probs=34.9

Q ss_pred             eeeeecCCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          143 FYHILQPKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       143 f~H~lVPkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      .+|+|||+|++||+||++++|++|+++.+|||+|+.+
T Consensus         2 t~H~lVPkH~~l~~eE~~~il~~y~i~~~qLP~I~~~   38 (72)
T d1dzfa2           2 THHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRA   38 (72)
T ss_dssp             GGSTTSCEEEECCHHHHHHHHHHTTCCGGGSCEECTT
T ss_pred             CcCccCCCeEEcCHHHHHHHHHHhCCCHhHCCeeccc
Confidence            4699999999999999999999999999999999864

>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=98.71  E-value=1.8e-09  Score=73.72  Aligned_cols=31  Identities=29%  Similarity=0.630  Sum_probs=29.7

Q ss_pred             CCccccCHHHHHHHHHHcCCCCCCCcccccC
Q 030295          149 PKHEVLSAGERDKLMKKYKIEGKQVTILVKQ  179 (179)
Q Consensus       149 PkH~~l~~eEk~~lL~~y~i~~~qLP~i~~~  179 (179)
                      |+|++||+||+++||++|+++.+|||+|+.+
T Consensus         1 PkH~il~~eE~~~ll~~y~i~~~qLP~I~~~   31 (68)
T d1hmja_           1 PKHEIVPKEEVEEILKRYNIKIQQLPKIYED   31 (68)
T ss_pred             CCCEECCHHHHHHHHHHhCCCHHHCCccccc
Confidence            9999999999999999999999999999864

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

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

Probab=87.94  E-value=0.19  Score=35.34  Aligned_cols=41  Identities=10%  Similarity=0.088  Sum_probs=30.3

Q ss_pred             cchhHHHHH-----HHHHhhccCCceEEEEEcCCCCHHHHHHhhccC
Q 030295           96 IRTQAIRGL-----YGQILNKEALHGLILILQSNMNTFARKEVLKFP  137 (179)
Q Consensus        96 vgvk~Ir~~-----~~~~~~~eni~~~IlV~q~~lt~~Akk~l~~~~  137 (179)
                      +++..++.+     ...+ ...+.+++|+|+-+..|+.|++.....+
T Consensus        57 ~~~~~v~~~~~~~~~~~~-~~~~~~~~iiVTt~~Ft~~A~~~A~~~~  102 (125)
T d1y88a2          57 VYTGLKEAMYTYARFLDV-EKHGFTQPWIFTNTKFSEEAKKYAGCVG  102 (125)
T ss_dssp             CEECHHHHHHHHHHHHHH-GGGTCSEEEEECSSEECHHHHHHHHHHT
T ss_pred             CCCChhhHHHHHHhhhhh-hhcCCCeEEEEECCCCCHHHHHHHHHCC
Confidence            444454443     3456 6889999999999999999988766544