Psyllid ID: psy12829

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-
Protein Sequence
MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG
Secondary Structure (PSIPRED)
ccccccccEEEEEccccEEEEEEEcccHHHHHHHHHHHHHcccEEEEEEEEEEEccccccHHHHHHHHcccEEEcHHHHHHHcccccccccccccccEEEEEEEEEEcccccEEEEEccccccccEEEEcccccccccccccccccccEEEEcccccEEEEEEEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEEccccEEEEEEEcccHHHHHHHHHHHHHHccEEEEEEEEEEccccHHHHHHHHHHccccEccccccHHHccccccccccccccccEEEEEEEEEEccccccEEEccHccccccEEEEccccccccccccccccccEEEEEEccccEEEEEEEEEccccccccccccccc
Coil and Loop (DISEMBL)
mpyanqpsvhitdltdenvkfqvEDTELSVANSLRRVFIAETPTMAIDWVQLeanstvlsdefiasriglipltsdevvdrilysrdctcvdfcsecsveftldvkcvddqtrhvttadlkstdarvvpvtsrnrdadmneygetDDILIVKLRKGQELRLRAYAKkgfgkehakwnptag
Flexible Loop (DISEMBL)
mpyanqpsvhitdltdenvKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASriglipltsdevVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRhvttadlkstdarvvpvtsrnrdadmneygetddiliVKLRKGQELRLRAyakkgfgkehakwnptag
Low Complexity Region (SEG)
MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG
Disordered region (IsUnstruct)
*************LTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLK*****VV*************YGETDDILIVKLRKGQELRLRAYAKKG*************
Disordered Region (DISOPRED)
****NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPV************GETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG
Disordered Region (DISEMBL)
MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG
Disordered Region (DISPRO)
*PYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEH********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG
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	181	2.2.26 [Sep-21-2011]
Q3T0Q3	275	DNA-directed RNA polymera	yes	N/A	1.0	0.658	0.773	1e-81
P19387	275	DNA-directed RNA polymera	yes	N/A	1.0	0.658	0.767	4e-81
P97760	275	DNA-directed RNA polymera	yes	N/A	1.0	0.658	0.745	2e-78
Q54DH7	302	DNA-directed RNA polymera	yes	N/A	0.933	0.559	0.508	9e-48
Q39211	319	DNA-directed RNA polymera	yes	N/A	0.972	0.551	0.519	4e-45
Q39212	319	DNA-directed RNA polymera	no	N/A	0.977	0.554	0.488	7e-41
P16370	318	DNA-directed RNA polymera	yes	N/A	0.933	0.531	0.482	9e-38
P37382	297	DNA-directed RNA polymera	yes	N/A	0.900	0.548	0.427	5e-32
P16925	310	Conjugation stage-specifi	N/A	N/A	0.911	0.532	0.402	6e-27
Q2NFZ6	270	DNA-directed RNA polymera	yes	N/A	0.861	0.577	0.364	7e-23

>sp|Q3T0Q3|RPB3_BOVIN DNA-directed RNA polymerase II subunit RPB3 OS=Bos taurus GN=POLR2C PE=2 SV=1

 Score =  302 bits (773), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 140/181 (77%), Positives = 162/181 (89%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct: 1   MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct: 61  DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
            S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.
Bos taurus (taxid: 9913)

>sp|P19387|RPB3_HUMAN DNA-directed RNA polymerase II subunit RPB3 OS=Homo sapiens GN=POLR2C PE=1 SV=2

 Score =  300 bits (768), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 139/181 (76%), Positives = 161/181 (88%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct: 1   MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEFIA R+GLIPL SD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct: 61  DEFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
            S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Homo sapiens (taxid: 9606)

>sp|P97760|RPB3_MOUSE DNA-directed RNA polymerase II subunit RPB3 OS=Mus musculus GN=Polr2c PE=2 SV=1

 Score =  291 bits (744), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 135/181 (74%), Positives = 158/181 (87%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQP+V IT+LT+ENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ NS+VL 
Sbjct: 1   MPYANQPTVRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDGNSSVLH 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct: 61  DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
            S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAY KK  GKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYVKKRSGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Mus musculus (taxid: 10090)

>sp|Q54DH7|RPB3_DICDI DNA-directed RNA polymerase II subunit rpb3 OS=Dictyostelium discoideum GN=polr2c PE=3 SV=1

 Score =  189 bits (480), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 89/175 (50%), Positives = 131/175 (74%), Gaps = 6/175 (3%)

Query: 6   QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
           QP + I ++ ++++ F + +T++SVAN+LRRV IAE PTM ID V+ E+N++VL DEFIA
Sbjct: 11  QPELEILEIKNDSIIFILSNTDISVANALRRVMIAEVPTMCIDLVEFESNNSVLCDEFIA 70

Query: 66  SRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
            R+GLIPL SD  +D+  Y+RDC+C D C +CSVE  L+VKC +++ R VT++DL S ++
Sbjct: 71  HRLGLIPLVSDN-IDKFCYTRDCSCSDRCDQCSVELRLNVKCTENRPRDVTSSDLLSQNS 129

Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
            V+PV+S+   ++  +     +I IVKLR+GQE++LRA AKKG GKEHAKW+P+ 
Sbjct: 130 AVIPVSSQVTSSNSEQ-----EIPIVKLRRGQEIKLRAIAKKGVGKEHAKWSPSC 179

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. Rpb3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Dictyostelium discoideum (taxid: 44689)

>sp|Q39211|RPB3A_ARATH DNA-directed RNA polymerase II subunit RPB3-A OS=Arabidopsis thaliana GN=RPB36A PE=2 SV=1

 Score =  180 bits (457), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 94/181 (51%), Positives = 126/181 (69%), Gaps = 5/181 (2%)

Query: 3   YANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDE 62
           Y   P + I +L D+  KF++ +T++S+AN+LRRV I+E PT+AID V++E NS+VL+DE
Sbjct: 6   YQRFPKIKIRELKDDYAKFELRETDVSMANALRRVMISEVPTVAIDLVEIEVNSSVLNDE 65

Query: 63  FIASRIGLIPLTSDEVVDRILYSRDCTCVDF---CSECSVEFTLDVKCVDDQTRHVTTAD 119
           FIA R+GLIPLTS+  +  + +SRDC   D    C  CSVEF L  KCV DQT  VT+ D
Sbjct: 66  FIAHRLGLIPLTSERAM-SMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDVTSRD 124

Query: 120 LKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
           L S D  V PV     D+ +++  E   I+IVKLR+GQEL+LRA A+KG GK+HAKW+P 
Sbjct: 125 LYSADPTVTPV-DFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKWSPA 183

Query: 180 A 180
           A
Sbjct: 184 A 184

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39212|RPB3B_ARATH DNA-directed RNA polymerase II subunit RPB3-B OS=Arabidopsis thaliana GN=RPB36B PE=1 SV=2

 Score =  166 bits (421), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 88/180 (48%), Positives = 119/180 (66%), Gaps = 3/180 (1%)

Query: 3   YANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDE 62
           Y   P+V I +L D+  KF++ +T++S+AN+LRRV I+E PTMAI  V++E NS+VL+DE
Sbjct: 6   YQRFPTVKIRELKDDYAKFELRETDVSMANALRRVMISEVPTMAIHLVKIEVNSSVLNDE 65

Query: 63  FIASRIGLIPLTSDEVVDRILYS--RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           FIA R+ LIPLTS+  +         DC   + C  CSVEF L  KCV DQT  VT+ DL
Sbjct: 66  FIAQRLSLIPLTSERAMSMRFCQDCEDCNGDEHCEFCSVEFPLSAKCVTDQTLDVTSRDL 125

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
            S D  V PV     ++  ++  E   I+I KLR+GQEL+L+A A+KG GK+HAKW+P A
Sbjct: 126 YSADPTVTPV-DFTSNSSTSDSSEHKGIIIAKLRRGQELKLKALARKGIGKDHAKWSPAA 184

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

Arabidopsis thaliana (taxid: 3702)

>sp|P16370|RPB3_YEAST DNA-directed RNA polymerase II subunit RPB3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB3 PE=1 SV=2

 Score =  155 bits (393), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)

Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
           P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA 
Sbjct: 6   PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65

Query: 67  RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           R+GLIPL S + ++++ YSRDC C D C +CSV  TL      + T +V + DL      
Sbjct: 66  RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 120

Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           V  +  RN    + +  E + +LI KLRKGQEL+L   AKKG  KEHAKW P A
Sbjct: 121 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 174

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination.

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

>sp|P37382|RPB3_SCHPO DNA-directed RNA polymerase II subunit RPB3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb3 PE=1 SV=2

 Score =  137 bits (344), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 77/180 (42%), Positives = 109/180 (60%), Gaps = 17/180 (9%)

Query: 10  HIT--DLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
           HIT  +++  +V F + +T L+VANSLRRV +AE PT+AID V++  N++V+ DEF+A R
Sbjct: 6   HITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHR 65

Query: 68  IGLIPLTSDEVVDR----ILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL--K 121
           +G+IPL S  + +     + Y+R+C C  +C +CSVE  L+ KC  + T  +   DL   
Sbjct: 66  LGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVS 125

Query: 122 STDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
           S  +   P+      AD    G     LI KLRK QE+ LR  AKKG  KEHAKW+PT+ 
Sbjct: 126 SNSSLGHPIL-----ADPKSRGP----LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA 176

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft.

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

>sp|P16925|CNJC_TETTH Conjugation stage-specific protein OS=Tetrahymena thermophila GN=CNJC PE=2 SV=1

 Score =  120 bits (300), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 72/179 (40%), Positives = 104/179 (58%), Gaps = 14/179 (7%)

Query: 11  ITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGL 70
           +T+L +   +F +E+ ++S+ANSLRR+ +AE  T+AI  V++  N++ L DE+IA R+GL
Sbjct: 8   LTNLEEFKCEFTLENCDISLANSLRRILLAEIETIAIHNVKVYENTSSLPDEYIAHRLGL 67

Query: 71  IPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKS----TD-- 124
           IPL S + VD   Y  +C C   C  C++ F L V    ++   VT+ DLK     TD  
Sbjct: 68  IPLNSAK-VDDYNYIWNCNCQGECDRCTIHFDLRVSNFTNEVLEVTSLDLKQRQDHTDED 126

Query: 125 -ARVVPVTSRNRDADMNEYGETDD--ILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
             R + V S  RD    EYG   +  I I+KL KGQ++     A+KG GK H+KWNP  
Sbjct: 127 AVRPIKVYSILRD----EYGNKREVGIPIIKLSKGQQIHFECEAQKGIGKMHSKWNPVC 181

May be a stage-specific RNA polymerase subunit.

Tetrahymena thermophila (taxid: 5911)

>sp|Q2NFZ6|RPOD_METST DNA-directed RNA polymerase subunit D OS=Methanosphaera stadtmanae (strain DSM 3091) GN=rpoD PE=3 SV=1

 Score =  106 bits (265), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 63/173 (36%), Positives = 93/173 (53%), Gaps = 17/173 (9%)

Query: 8   SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
           ++ I +  DE   F VE  + +  N++RR+ + E PT+AI+ V +  N   + DE +A R
Sbjct: 2   NIEIREKDDERAVFVVEGVDDTFINTIRRICLVEIPTLAIEDVNIYKNDAKMFDEVLAHR 61

Query: 68  IGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVD-DQTRHVTTADLKSTDAR 126
           +GLIP+ +D  +D  +   +C C   C  C V F L  KC + + ++ V + DLKS D  
Sbjct: 62  LGLIPIVTD--LDSYVMPSECDCESGCQHCRVSFLLKEKCEEGNDSKIVYSKDLKSDDPA 119

Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
           V PV               D I IV+LR+G+E+ L A A+ G G EHAKW  T
Sbjct: 120 VKPV--------------YDTIPIVRLREGEEVELEAIAELGLGSEHAKWQAT 158

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Methanosphaera stadtmanae (strain DSM 3091) (taxid: 339860)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

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	181
242011218	275	DNA-directed RNA polymerase II 33 kDa po	1.0	0.658	0.872	3e-91
350400985	276	PREDICTED: DNA-directed RNA polymerase I	1.0	0.655	0.856	4e-90
383848177	276	PREDICTED: DNA-directed RNA polymerase I	1.0	0.655	0.850	5e-90
114051193	275	DNA-directed RNA polymerase II polypepti	1.0	0.658	0.867	5e-90
66517558	276	PREDICTED: DNA-directed RNA polymerase I	1.0	0.655	0.850	6e-90
307175611	276	DNA-directed RNA polymerase II subunit R	1.0	0.655	0.845	8e-90
322793846	325	hypothetical protein SINV_07940 [Solenop	1.0	0.556	0.845	2e-89
40645083	275	homologue of DNA-directed RNA polymerase	1.0	0.658	0.861	2e-89
307202125	276	DNA-directed RNA polymerase II subunit R	1.0	0.655	0.845	4e-89
156551093	276	PREDICTED: DNA-directed RNA polymerase I	1.0	0.655	0.839	1e-88

>gi|242011218|ref|XP_002426352.1| DNA-directed RNA polymerase II 33 kDa polypeptide, putative [Pediculus humanus corporis] gi|212510429|gb|EEB13614.1| DNA-directed RNA polymerase II 33 kDa polypeptide, putative [Pediculus humanus corporis]

 Score =  339 bits (869), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 158/181 (87%), Positives = 172/181 (95%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHITDLTDENVKFQ+EDTELSVANS+RRVFIAETPTMAIDWVQLEANSTVL+
Sbjct: 1   MPYANQPSVHITDLTDENVKFQIEDTELSVANSMRRVFIAETPTMAIDWVQLEANSTVLA 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEFI+ R+GLIPLTSDEVVDRI Y+RDCTC+DFC ECSVEFTLDVKC DD TRHVTTADL
Sbjct: 61  DEFISHRVGLIPLTSDEVVDRIQYTRDCTCLDFCPECSVEFTLDVKCTDDHTRHVTTADL 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RV+PVTSR+R+ D +EYGE D+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVLPVTSRHREDDTSEYGEADEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350400985|ref|XP_003486021.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Bombus impatiens]

 Score =  335 bits (860), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 155/181 (85%), Positives = 171/181 (94%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHI+DLT+ENVKFQVEDTELSVANS+RRVFIAETPTMAIDWVQLEANSTVLS
Sbjct: 1   MPYANQPSVHISDLTEENVKFQVEDTELSVANSMRRVFIAETPTMAIDWVQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIG+IPL SD+VVDRI Y+RDC C+DFC ECSVEFTLDVKC +DQTRHVTTAD 
Sbjct: 61  DEFLAHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTRHVTTADF 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RV+PVTSR+R+ D +EYGETD+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383848177|ref|XP_003699728.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Megachile rotundata]

 Score =  335 bits (859), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 154/181 (85%), Positives = 171/181 (94%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHI+DLT+ENVKFQVEDTELSVANS+RRVFIAETPTMAIDW+QLEANSTVLS
Sbjct: 1   MPYANQPSVHISDLTEENVKFQVEDTELSVANSMRRVFIAETPTMAIDWIQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIG+IPL SD+VVDRI Y+RDC C+DFC ECSVEFTLDVKC +DQTRHVTTAD 
Sbjct: 61  DEFLAHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTRHVTTADF 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RV+PVTSR+R+ D +EYGETD+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114051193|ref|NP_001040388.1| DNA-directed RNA polymerase II polypeptide [Bombyx mori] gi|95102714|gb|ABF51298.1| DNA-directed RNA polymerase II polypeptide [Bombyx mori]

 Score =  335 bits (858), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 157/181 (86%), Positives = 170/181 (93%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHIT+L+DENVKF VEDTELSVANS+RRVFIAETPTMAIDWVQLEANSTVLS
Sbjct: 1   MPYANQPSVHITELSDENVKFVVEDTELSVANSMRRVFIAETPTMAIDWVQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIGLIPL SD+VVD+I YSRDC CVDFCSECSVEFTLDVKC D+QTRHVTTADL
Sbjct: 61  DEFLAHRIGLIPLISDDVVDKIRYSRDCMCVDFCSECSVEFTLDVKCTDEQTRHVTTADL 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RVVPVTSR+RD D  +YGE D+ILI+KLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVVPVTSRHRDEDQADYGEADEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66517558|ref|XP_624836.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Apis mellifera] gi|380029804|ref|XP_003698555.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Apis florea]

 Score =  335 bits (858), Expect = 6e-90,   Method: Compositional matrix adjust.
 Identities = 154/181 (85%), Positives = 171/181 (94%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHI+DLT+ENVKFQVEDTELSVANS+RRVFIAETPTMAIDW+QLEANSTVLS
Sbjct: 1   MPYANQPSVHISDLTEENVKFQVEDTELSVANSMRRVFIAETPTMAIDWIQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIG+IPL SD+VVDRI Y+RDC C+DFC ECSVEFTLDVKC +DQTRHVTTAD 
Sbjct: 61  DEFLAHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTRHVTTADF 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RV+PVTSR+R+ D +EYGETD+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307175611|gb|EFN65520.1| DNA-directed RNA polymerase II subunit RPB3 [Camponotus floridanus]

 Score =  334 bits (857), Expect = 8e-90,   Method: Compositional matrix adjust.
 Identities = 153/181 (84%), Positives = 172/181 (95%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHI+DLT+ENVKFQVEDTELSVANS+RRVFIAETPTMAIDW+QLEANSTVLS
Sbjct: 1   MPYANQPSVHISDLTEENVKFQVEDTELSVANSMRRVFIAETPTMAIDWIQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIG+IPL SD+VVDRI ++RDC C+DFC ECSVEFTLDVKC++DQTRHVTTAD 
Sbjct: 61  DEFLAHRIGMIPLISDDVVDRIQFTRDCQCMDFCPECSVEFTLDVKCIEDQTRHVTTADF 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RV+PVTSR+R+ D +EYGETD+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322793846|gb|EFZ17186.1| hypothetical protein SINV_07940 [Solenopsis invicta]

 Score =  333 bits (854), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 153/181 (84%), Positives = 171/181 (94%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHI+DLT+ENVKFQVEDTELSVANS+RRVFIAETPTMAIDW+QLEANSTVLS
Sbjct: 1   MPYANQPSVHISDLTEENVKFQVEDTELSVANSMRRVFIAETPTMAIDWIQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIG+IPL SD+VVDRI Y+RDC C+DFC ECSVEFTLDVKC +DQTRHVTTAD 
Sbjct: 61  DEFLAHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTRHVTTADF 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RV+PVTSR+R+ + +EYGETD+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVLPVTSRHREDEASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|40645083|dbj|BAD06460.1| homologue of DNA-directed RNA polymerase II subunit [Antheraea pernyi] gi|40645085|dbj|BAD06461.1| homologue of DNA-directed RNA polymerase II subunit [Antheraea pernyi]

 Score =  333 bits (853), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 156/181 (86%), Positives = 169/181 (93%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHIT+L D+NVKF VEDTELSVANS+RRVFIAETPTMAIDW+QLEANSTVLS
Sbjct: 1   MPYANQPSVHITELNDDNVKFVVEDTELSVANSMRRVFIAETPTMAIDWIQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIGLIPL SD+VVD+I YSRDC C DFCSECSVEFTLDVKC DDQTRHVTTADL
Sbjct: 61  DEFLAHRIGLIPLISDDVVDKIRYSRDCMCADFCSECSVEFTLDVKCTDDQTRHVTTADL 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RVVPVTSR+RD D  +YGETD+ILI+KLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVVPVTSRHRDEDQADYGETDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Antheraea pernyi

Species: Antheraea pernyi

Genus: Antheraea

Family: Saturniidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307202125|gb|EFN81625.1| DNA-directed RNA polymerase II subunit RPB3 [Harpegnathos saltator]

 Score =  332 bits (851), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 153/181 (84%), Positives = 170/181 (93%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQPSVHI+DLT+ENVKFQVE TELSVANS+RRVFIAETPTMAIDW+QLEANSTVLS
Sbjct: 1   MPYANQPSVHISDLTEENVKFQVEYTELSVANSMRRVFIAETPTMAIDWIQLEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIG+IPL SD+VVDRI Y+RDC C+DFC ECSVEFTLDVKC +DQTRHVTTAD 
Sbjct: 61  DEFLAHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTRHVTTADF 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS+D RV+PVTSR+R+ D +EYGETD+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSDPRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156551093|ref|XP_001603079.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Nasonia vitripennis]

 Score =  330 bits (846), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 152/181 (83%), Positives = 170/181 (93%)

Query: 1   MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
           MPYANQP+VHI++LT+EN+KFQVEDTELSVANS+RRVFIAETPTMAIDWVQ+EANSTVLS
Sbjct: 1   MPYANQPTVHISELTEENIKFQVEDTELSVANSMRRVFIAETPTMAIDWVQIEANSTVLS 60

Query: 61  DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           DEF+A RIG+IPL SDEVVDRI Y+RDC C+DFC EC VEFTLDVKC D+ TRHVTTADL
Sbjct: 61  DEFLAHRIGMIPLISDEVVDRIQYTRDCQCMDFCPECCVEFTLDVKCSDETTRHVTTADL 120

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           KS++ RVVPVTS++RD D NEYGETD+ILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct: 121 KSSEQRVVPVTSKHRDDDANEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query: 181 G 181
           G
Sbjct: 181 G 181

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	181
FB|FBgn0026373	275	RpII33 "RNA polymerase II 33kD	1.0	0.658	0.813	3.8e-78
UNIPROTKB|Q3T0Q3	275	POLR2C "DNA-directed RNA polym	1.0	0.658	0.773	7.3e-75
UNIPROTKB|E2RQ42	275	POLR2C "Uncharacterized protei	1.0	0.658	0.773	7.3e-75
RGD|1306935	275	Polr2c "polymerase (RNA) II (D	1.0	0.658	0.767	1.9e-74
UNIPROTKB|D4A8A8	330	Polr2c "Protein Polr2c" [Rattu	1.0	0.548	0.767	1.9e-74
UNIPROTKB|I3LCH3	275	POLR2C "Uncharacterized protei	1.0	0.658	0.767	2.5e-74
UNIPROTKB|P19387	275	POLR2C "DNA-directed RNA polym	1.0	0.658	0.767	3.1e-74
UNIPROTKB|E1BV97	275	POLR2C "Uncharacterized protei	1.0	0.658	0.762	6.5e-74
ZFIN|ZDB-GENE-030131-6609	275	polr2c "polymerase (RNA) II (D	1.0	0.658	0.745	8.4e-74
MGI|MGI:109299	275	Polr2c "polymerase (RNA) II (D	1.0	0.658	0.745	6.7e-72

FB|FBgn0026373 RpII33 "RNA polymerase II 33kD subunit" [Drosophila melanogaster (taxid:7227)]

 Score = 786 (281.7 bits), Expect = 3.8e-78, P = 3.8e-78
 Identities = 148/182 (81%), Positives = 170/182 (93%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQPSV IT+LTD+NVKF +EDTELSVANSLRRVFIAETPT+AIDWVQLEANSTVLS
Sbjct:     1 MPYANQPSVQITELTDDNVKFVLEDTELSVANSLRRVFIAETPTLAIDWVQLEANSTVLS 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEF+A RIGLIPL SD+VV+R+ Y+RDC C+DFC ECSVEFTLDVKC ++QTRHVTTADL
Sbjct:    61 DEFLAHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGET-DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
             KS++A+V+PVTSRN+  + NEYGE+ D+ILI+KLRKGQEL+LRAYAKKGFGKEHAKWNPT
Sbjct:   121 KSSNAKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPT 180

Query:   180 AG 181
             AG
Sbjct:   181 AG 182

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

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0034605 "cellular response to heat" evidence=IEP

GO:0005634 "nucleus" evidence=IDA

GO:0005703 "polytene chromosome puff" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

UNIPROTKB|Q3T0Q3 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Bos taurus (taxid:9913)]

 Score = 755 (270.8 bits), Expect = 7.3e-75, P = 7.3e-75
 Identities = 140/181 (77%), Positives = 162/181 (89%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct:   121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

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

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RQ42 POLR2C "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 755 (270.8 bits), Expect = 7.3e-75, P = 7.3e-75
 Identities = 140/181 (77%), Positives = 162/181 (89%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct:   121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

GO:0015630 "microtubule cytoskeleton" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

RGD|1306935 Polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Rattus norvegicus (taxid:10116)]

 Score = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 139/181 (76%), Positives = 162/181 (89%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LT+ENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct:   121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

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=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA;ISO

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|D4A8A8 Polr2c "Protein Polr2c" [Rattus norvegicus (taxid:10116)]

 Score = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 139/181 (76%), Positives = 162/181 (89%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LT+ENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct:   121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|I3LCH3 POLR2C "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 750 (269.1 bits), Expect = 2.5e-74, P = 2.5e-74
 Identities = 139/181 (76%), Positives = 162/181 (89%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S   RV+PVTSRNRD D ++Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct:   121 ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

GO:0015630 "microtubule cytoskeleton" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P19387 POLR2C "DNA-directed RNA polymerase II subunit RPB3" [Homo sapiens (taxid:9606)]

 Score = 749 (268.7 bits), Expect = 3.1e-74, P = 3.1e-74
 Identities = 139/181 (76%), Positives = 161/181 (88%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPL SD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct:   121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

GO:0003677 "DNA binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0015630 "microtubule cytoskeleton" evidence=IDA

UNIPROTKB|E1BV97 POLR2C "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 746 (267.7 bits), Expect = 6.5e-74, P = 6.5e-74
 Identities = 138/181 (76%), Positives = 163/181 (90%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LTDENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLTSDDIVDKMQYSRDCTCDEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S + RV+PVTSR+RD D N+Y E DDILIVKLRKGQEL+LRAYAKKGFGKEHAKWNPTA
Sbjct:   121 ISNNPRVIPVTSRSRDNDPNDYVEQDDILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

GO:0003677 "DNA binding" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0015630 "microtubule cytoskeleton" evidence=IEA

ZFIN|ZDB-GENE-030131-6609 polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Danio rerio (taxid:7955)]

 Score = 745 (267.3 bits), Expect = 8.4e-74, P = 8.4e-74
 Identities = 135/181 (74%), Positives = 163/181 (90%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+L+DENVKF +E+T+L+VANS+RRVF++E PT+AIDWVQ++ANS+VL 
Sbjct:     1 MPYANQPTVKITELSDENVKFVIENTDLAVANSIRRVFMSEVPTIAIDWVQIDANSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEF+A R+GLIPLTSD++VD++ YSRDCTC DFC ECSVE TLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFVAHRVGLIPLTSDDIVDKMQYSRDCTCDDFCPECSVELTLDVRCTEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S + RV+PVTSR+RD D N+Y E DDIL+VKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct:   121 LSNNPRVIPVTSRSRDNDPNDYVEQDDILLVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

MGI|MGI:109299 Polr2c "polymerase (RNA) II (DNA directed) polypeptide C" [Mus musculus (taxid:10090)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 135/181 (74%), Positives = 158/181 (87%)

Query:     1 MPYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLS 60
             MPYANQP+V IT+LT+ENVKF +E+T+L+VANS+RRVFIAE P +AIDWVQ++ NS+VL 
Sbjct:     1 MPYANQPTVRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDGNSSVLH 60

Query:    61 DEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
             DEFIA R+GLIPLTSD++VD++ YSRDCTC +FC ECSVEFTLDV+C +DQTRHVT+ DL
Sbjct:    61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120

Query:   121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
              S   RV+PVTSRNRD D N+Y E DDILIVKLRKGQELRLRAY KK  GKEHAKWNPTA
Sbjct:   121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYVKKRSGKEHAKWNPTA 180

Query:   181 G 181
             G
Sbjct:   181 G 181

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

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

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0046983 "protein dimerization activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q54DH7	RPB3_DICDI	No assigned EC number	0.5085	0.9337	0.5596	yes	N/A
P97760	RPB3_MOUSE	No assigned EC number	0.7458	1.0	0.6581	yes	N/A
Q57648	RPOD_METJA	2, ., 7, ., 7, ., 6	0.3112	0.6408	0.6073	yes	N/A
Q39211	RPB3A_ARATH	No assigned EC number	0.5193	0.9723	0.5517	yes	N/A
P19387	RPB3_HUMAN	No assigned EC number	0.7679	1.0	0.6581	yes	N/A
Q3T0Q3	RPB3_BOVIN	No assigned EC number	0.7734	1.0	0.6581	yes	N/A

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	181
cd07031	265	cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic	1e-103
smart00662	224	smart00662, RPOLD, RNA polymerases D	1e-57
cd07030	259	cd07030, RNAP_D, D subunit of Archaeal RNA polymer	2e-50
PRK00783	263	PRK00783, PRK00783, DNA-directed RNA polymerase su	1e-47
cd07028	212	cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polym	4e-44
cd07032	291	cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryoti	4e-37
pfam01000	117	pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA	3e-28
COG0202	317	COG0202, RpoA, DNA-directed RNA polymerase, alpha	2e-27
PRK14979	195	PRK14979, PRK14979, DNA-directed RNA polymerase su	3e-19
pfam01193	88	pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 di	2e-05

>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase II

 Score =  296 bits (760), Expect = e-103
 Identities = 111/175 (63%), Positives = 133/175 (76%)

Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
           P V IT+LTD+ VKF +E+T+LSVANSLRRV IAE PT+AID V++E N++VL DEFIA 
Sbjct: 1   PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAH 60

Query: 67  RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           R+GLIPLTSD+V + + YSRDC C +FC +CSVE TLDVKC  DQTR VT+ DL S+  +
Sbjct: 61  RLGLIPLTSDDVDEFLYYSRDCDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSSGPK 120

Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
           V  V       D  + GE D ILIVKLRKGQEL+LR  AKKG GKEHAKW+PTA 
Sbjct: 121 VNDVVPVPIRNDSEDNGEEDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAA 175

The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. Length = 265

>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D

 Score =  180 bits (458), Expect = 1e-57
 Identities = 71/164 (43%), Positives = 92/164 (56%), Gaps = 21/164 (12%)

Query: 19  VKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV 78
            KF +E   L++AN+LRRV ++  P MA+  V +E N++ + DE +A R+GL PL SD  
Sbjct: 1   AKFVLEPYGLTLANALRRVLLSSVPGMAVTSVYIEGNTSGVQDEVLAHRLGLKPLASDPD 60

Query: 79  VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKS-TDARVVPVTSRNRDA 137
            D   Y RDC C + C +CSV  TLDVK   +    VT  DLKS +D  V  V       
Sbjct: 61  GD--EYQRDCECEEGCEKCSVTLTLDVKGPGE----VTAGDLKSDSDPDVEIV------- 107

Query: 138 DMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
                    DI I KLR+GQEL L A A+KG G  HAKW+P + 
Sbjct: 108 -------NPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVST 144

DNA-directed RNA polymerase subunit D and bacterial alpha chain. Length = 224

>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase

 Score =  162 bits (413), Expect = 2e-50
 Identities = 72/173 (41%), Positives = 98/173 (56%), Gaps = 21/173 (12%)

Query: 8   SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
            + + +L D+  +F +E    + AN++RR  I+E PT+AID V +  N++VL DE +A R
Sbjct: 2   EIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHR 61

Query: 68  IGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           +GLIPL +D   D   Y  +C+C    C  C+V  TL V+        V + DLKS+D  
Sbjct: 62  LGLIPLRTDL--DLYKYRSECSCGGAGCPLCTVTLTLSVEG----PGTVYSGDLKSSDPD 115

Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
           V PV               D+I IVKL KGQ+L L AYA+ G GKEHAKW PT
Sbjct: 116 VKPV--------------YDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPT 154

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer. Length = 259

>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D; Provisional

 Score =  155 bits (394), Expect = 1e-47
 Identities = 72/174 (41%), Positives = 103/174 (59%), Gaps = 21/174 (12%)

Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
             + I +L D + +F VE    + AN++RR  IA+ PTMAID V+   N++VL DE +A 
Sbjct: 1   MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAH 60

Query: 67  RIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
           R+GLIPLT+D  +D+     +CTC  + C +C+V  +L+V+      + V + DLKS+D 
Sbjct: 61  RLGLIPLTTD--LDKYKPPEECTCEGEGCPDCTVTLSLEVE----GPKTVYSGDLKSSDP 114

Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
            V PV                +I IVKL++GQ+L L AYA+ G GKEHAKW P 
Sbjct: 115 DVKPV--------------DPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPG 154

Length = 263

>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase

 Score =  145 bits (366), Expect = 4e-44
 Identities = 77/182 (42%), Positives = 103/182 (56%), Gaps = 24/182 (13%)

Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
           P V I +   +NV F +   +L++AN+LRRV IAE PTMA+D V++E N++VL+DE +A 
Sbjct: 1   PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAH 60

Query: 67  RIGLIPLTSDEVVDRILY---SRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKST 123
           R+GLIPL S +++   LY     DC C D C +CSV  TL      + T +V + DL   
Sbjct: 61  RLGLIPLQSMDILQ--LYRSPEEDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIV 118

Query: 124 DAR-----VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
                     P+                DILI KLRKGQE++L   AKKG GKEHAK+ P
Sbjct: 119 SNLMGRNIGHPI--------------IQDILICKLRKGQEIKLTCVAKKGIGKEHAKFGP 164

Query: 179 TA 180
            A
Sbjct: 165 VA 166

The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Length = 212

>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

 Score =  129 bits (326), Expect = 4e-37
 Identities = 65/196 (33%), Positives = 96/196 (48%), Gaps = 41/196 (20%)

Query: 9   VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
           + I  L+DE ++F +   + S+AN+ RR+ +AE PTMAI+ V +  N++V+ DE +A R+
Sbjct: 3   IEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRL 62

Query: 69  GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKC----------VDDQTR----H 114
           GLIP+ +D       Y R+ +  +   E ++ F L VKC           D         
Sbjct: 63  GLIPIKAD--PRLFEY-REDSDDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHK 119

Query: 115 VTTADLK----------STDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 164
           V + DLK            D  + PV                DILI KLR GQE+ L  +
Sbjct: 120 VYSGDLKWVPIGSQEKRFADNPIRPV--------------HPDILIAKLRPGQEIDLELH 165

Query: 165 AKKGFGKEHAKWNPTA 180
             KG GK+HAK++P A
Sbjct: 166 CVKGIGKDHAKFSPVA 181

The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC40 to RPB3 suggests a similar function. The AC40 subunit is likely to associate with the RPB11 counterpart, AC19, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. Length = 291

>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain

 Score =  101 bits (254), Expect = 3e-28
 Identities = 51/115 (44%), Positives = 61/115 (53%), Gaps = 20/115 (17%)

Query: 64  IASRIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKS 122
           +A   GLIP  S++V++ IL  ++  C ++ C ECSV  TLDVK        VT  DL+S
Sbjct: 6   VAHEFGLIPGVSEDVLEIILNLKELVCKIEGCEECSVTLTLDVKG----PGEVTAGDLES 61

Query: 123 TDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
            D  V  V                DILI  LRKGQEL L AYAKKG G  HAK N
Sbjct: 62  -DPDVEIVN--------------PDILIATLRKGQELELEAYAKKGRGYVHAKEN 101

Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal. Length = 117

>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]

 Score =  104 bits (262), Expect = 2e-27
 Identities = 41/192 (21%), Positives = 77/192 (40%), Gaps = 22/192 (11%)

Query: 9   VHITDLTDENVKFQVEDTE----LSVANSLRRVFIAETPTMAIDWVQLE------ANSTV 58
           V I +L+D   KF +E  E    +++ N+LRRV ++  P  A+  V+++       +   
Sbjct: 7   VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEG 66

Query: 59  LSDEFIASRIGLIPLTSD---EVVDRILYSRDCTCVDFCSECSVEFTLDVKC-------V 108
           + ++ +A R+ L PL      +    +   ++       S+ +V   L+V         +
Sbjct: 67  VQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATL 126

Query: 109 DDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKG 168
            +  +      + S D  V    +R  D  +       D     +RK Q +   A   +G
Sbjct: 127 TEDAKLEMELRVYSGDGYVPAEGNREDDPPVGP--IAVDAPFSPVRKVQYIVEEARVGQG 184

Query: 169 FGKEHAKWNPTA 180
             K+H KW P  
Sbjct: 185 TDKDHLKWEPET 196

Length = 317

>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D; Provisional

 Score = 80.7 bits (199), Expect = 3e-19
 Identities = 54/171 (31%), Positives = 77/171 (45%), Gaps = 50/171 (29%)

Query: 15  TDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLT 74
             E  KF ++   +S +++LRR+ I+E PT AI+ V    NS+ + DE +A R+GLIP+ 
Sbjct: 12  IGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIK 70

Query: 75  -----SDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVP 129
                 DEV+     S++  C                        V ++DLKS       
Sbjct: 71  GKPVSGDEVI-TFTLSKEGPCT-----------------------VYSSDLKS------- 99

Query: 130 VTSRNRDADMNEYGET--DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
                      E GE    +I IVKL +GQ+L +   A  G GK HAKW P
Sbjct: 100 -----------ENGEVAFKNIPIVKLAEGQKLEIECEALVGTGKIHAKWQP 139

Length = 195

>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation domain

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 11/35 (31%), Positives = 24/35 (68%)

Query: 19 VKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLE 53
          ++F +E  + ++ N+LRRV +++ P +AI  V++ 
Sbjct: 1  IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIP 35

The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	181
KOG1522|consensus	285		100.0
cd07032	291	RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA poly	100.0
cd07031	265	RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polyme	100.0
cd07028	212	RNAP_RPB3_like RPB3 subunit of RNA polymerase. The	100.0
KOG1521|consensus	338		100.0
PRK00783	263	DNA-directed RNA polymerase subunit D; Provisional	100.0
cd07030	259	RNAP_D D subunit of Archaeal RNA polymerase. The D	100.0
PRK14979	195	DNA-directed RNA polymerase subunit D; Provisional	100.0
smart00662	224	RPOLD RNA polymerases D. DNA-directed RNA polymera	100.0
PRK05182	310	DNA-directed RNA polymerase subunit alpha; Provisi	100.0
cd06928	215	RNAP_alpha_NTD N-terminal domain of the Alpha subu	100.0
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	100.0
PF01000	112	RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert dom	100.0
TIGR02027	297	rpoA DNA-directed RNA polymerase, alpha subunit, b	99.97
CHL00013	327	rpoA RNA polymerase alpha subunit	99.95
PF01193	66	RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation	98.99
COG0202	317	RpoA DNA-directed RNA polymerase, alpha subunit/40	98.49
cd00460	86	RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA pol	97.75
PRK01146	85	DNA-directed RNA polymerase subunit L; Provisional	97.04
cd06927	83	RNAP_L L subunit of Archaeal RNA polymerase. The a	96.6
cd07027	83	RNAP_RPB11_like RPB11 subunit of RNA polymerase. T	96.41
COG1761	99	RPB11 DNA-directed RNA polymerase, subunit L [Tran	95.95
cd06926	93	RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA poly	95.4
cd07029	85	RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA pol	93.68
PF13656	77	RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisatio	93.11
KOG3438|consensus	105		86.45

>KOG1522|consensus

Probab=100.00  E-value=1.5e-62  Score=404.24  Aligned_cols=178  Identities=67%  Similarity=1.084  Sum_probs=166.1

Q ss_pred             CCCCCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccce
Q psy12829          2 PYANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDR   81 (181)
Q Consensus         2 ~~~~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~   81 (181)
                      ||+++|.|+|.+++++.++|+|++.+.++||||||||||||||+||++|+|+-|||||+||||||||||||+.+++.+ .
T Consensus         1 ~y~~~p~v~I~Elt~d~vkF~L~nTdlsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~-~   79 (285)
T KOG1522|consen    1 PYANQPTVKIRELTDDNVKFVLSNTDLSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIV-E   79 (285)
T ss_pred             CCCCCCceEEEecCCCceEEEEecChHHHHHHHHHHHHhcCceeEEEEEEEecccccccHHHHHhhhcceeccchhhh-h
Confidence            799999999999999999999999999999999999999999999999999999999999999999999999999865 4


Q ss_pred             EEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEE
Q psy12829         82 ILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRL  161 (181)
Q Consensus        82 ~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~  161 (181)
                      ++|..+|.|+++|++|+|.|+|+++|+.++...||+.||++.++.+.|+.+ .+......+.-..+|+|+||++||+|++
T Consensus        80 l~ytrdC~C~~~C~eCSVef~L~~kc~~d~T~~VtsrDL~s~~~~v~pv~~-~~~~~~~~~~e~~gilI~KLRkgQELkL  158 (285)
T KOG1522|consen   80 LQYTRDCECDEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLDPTVTPVDS-NRGSEIDDDSESKGILIVKLRKGQELKL  158 (285)
T ss_pred             hhhcccCchhccCCcceEEEEEeeeecccceeeeehHhhhccCCccccccc-CCCCccccccccCCcEEEEeecCCceee
Confidence            999999999999999999999999999999999999999998999999987 2333333334468999999999999999


Q ss_pred             EEEEEeccccccceeccCCC
Q psy12829        162 RAYAKKGFGKEHAKWNPTAG  181 (181)
Q Consensus       162 e~~~~kG~G~~HAKw~pv~~  181 (181)
                      +|+|+||+||+||||+|+++
T Consensus       159 ra~akKGigKeHAKWsPta~  178 (285)
T KOG1522|consen  159 RAIAKKGIGKEHAKWSPTAA  178 (285)
T ss_pred             eeeecccccccccccCCcce
Confidence            99999999999999999985

>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=100.00  E-value=4.4e-59  Score=398.53  Aligned_cols=167  Identities=39%  Similarity=0.611  Sum_probs=151.9

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR   86 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~   86 (181)
                      .+|++.++++++++|+|+|+++|+||||||+|||||||||||.|+|++|||+|+||+|||||||||+.++.  +.+.|+.
T Consensus         1 ~~i~i~~~~~~~~~f~l~~~d~s~ANAlRRimiaEVPt~AId~V~i~~NTSvl~DE~lAHRLGLIPL~~d~--~~~~~~~   78 (291)
T cd07032           1 FKIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKADP--RLFEYRE   78 (291)
T ss_pred             CeEEEEECCCCEEEEEEecCCHHHHHHHHHHHHhcCcceeEEEEEEEECCccchhHHHHHhhcCceeecCH--HHccccc
Confidence            36899999999999999999999999999999999999999999999999999999999999999999973  6789999


Q ss_pred             cCCCcCCCCCceEEEEEEEEecCCCc--------------eeEEeccceeCCCeeeeccccCcCC-CCCCccCCCCeEEE
Q psy12829         87 DCTCVDFCSECSVEFTLDVKCVDDQT--------------RHVTTADLKSTDARVVPVTSRNRDA-DMNEYGETDDILIV  151 (181)
Q Consensus        87 ~~~~~~~~~~~~v~~~L~v~~~~~~~--------------~~V~s~di~~~~~~~~p~~~~~~~~-~~~~~~~~~di~I~  151 (181)
                      +| |+++|+.|++.|+|+++|+.++.              ..|||+||+     |.|.+.|.+.+ +.+..++++||+|+
T Consensus        79 ~~-~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~-----~~p~g~q~~~~~~~~v~~v~~dI~I~  152 (291)
T cd07032          79 DS-DDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLK-----WVPIGSQEKRFADNPIRPVHPDILIA  152 (291)
T ss_pred             cc-ccCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCE-----ecCCCccccccCCCCcEEeCCCcEEE
Confidence            98 77899999999999999987642              578888887     78988876543 44566889999999


Q ss_pred             EeCCCCEEEEEEEEEeccccccceeccCCC
Q psy12829        152 KLRKGQELRLRAYAKKGFGKEHAKWNPTAG  181 (181)
Q Consensus       152 kL~~gq~i~~e~~~~kG~G~~HAKw~pv~~  181 (181)
                      ||++||+|+|+|+|+||+||+||||||||+
T Consensus       153 kL~~gQ~l~le~~a~kG~Gk~HAKwsPv~t  182 (291)
T cd07032         153 KLRPGQEIDLELHCVKGIGKDHAKFSPVAT  182 (291)
T ss_pred             EECCCCEEEEEEEEEcCcccccceecCcee
Confidence            999999999999999999999999999974

The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun

>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II

Probab=100.00  E-value=9.7e-57  Score=380.75  Aligned_cols=169  Identities=66%  Similarity=1.051  Sum_probs=146.2

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEe-
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYS-   85 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~-   85 (181)
                      |+|++.+.++++++|.++|+++|+||||||+|||||||+||+.|+|++|||+|+||||||||||||++++++ ..+.+. 
T Consensus         1 p~i~i~~~~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~~V~I~~NtSvl~DE~iaHRlglIPl~~e~~-~~~~~~~   79 (265)
T cd07031           1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDV-DEFLYYS   79 (265)
T ss_pred             CcEEEEEcCCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEEEEEEecCCcccccceeeeecccCCCccCcH-HHHhhhh
Confidence            579999999999999999999999999999999999999999999999999999999999999999999985 334444 


Q ss_pred             ecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCC-----CeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEE
Q psy12829         86 RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTD-----ARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELR  160 (181)
Q Consensus        86 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~-----~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~  160 (181)
                      ++|.|.+.|+.|++.|+|+++|++++++.|||+||++..     ....|+...     ......++||+|+||++||+|+
T Consensus        80 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~~~~~~pi~~~-----~~~~~~~~~i~I~kL~~gq~i~  154 (265)
T cd07031          80 RDCDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRND-----SEDNGEEDGILIVKLRKGQELK  154 (265)
T ss_pred             hhccccCCCCCCeEEEEEEEEeccCCCceEEHHHcccccccccccCCcccccc-----cccccCCCCeEEEEECCCCEEE
Confidence            578888889999999999999999999999999998742     111222210     0011346999999999999999


Q ss_pred             EEEEEEeccccccceeccCCC
Q psy12829        161 LRAYAKKGFGKEHAKWNPTAG  181 (181)
Q Consensus       161 ~e~~~~kG~G~~HAKw~pv~~  181 (181)
                      |+|+|+||+||+|||||||++
T Consensus       155 le~~a~kG~Gk~HAKwsPv~~  175 (265)
T cd07031         155 LRCIAKKGIGKEHAKWSPTAA  175 (265)
T ss_pred             EEEEEECCEeccCCEeccceE
Confidence            999999999999999999974

The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.

>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase

Probab=100.00  E-value=2.3e-54  Score=355.68  Aligned_cols=165  Identities=45%  Similarity=0.698  Sum_probs=141.3

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceE-EEe
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRI-LYS   85 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~-~~~   85 (181)
                      |.|++.+.++++++|.|+|+++|+||||||+|||||||+||+.|+|++|||+|+||++|||||||||++++++..+ +.+
T Consensus         1 ~~i~i~~~~~~~~~f~l~g~~~t~aNaLRRiLLsevP~~AI~~V~I~~NtS~~~DE~iaHrlglIP~~~e~~~~~~~n~k   80 (212)
T cd07028           1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLYRSPE   80 (212)
T ss_pred             CcEEEEEcCCCEEEEEEEccChhHHHHHHHHHHHcCcceEEEEEEEEcCCCcccceeeeeeeeecccccCcHHHhhhccc
Confidence            5689999999999999999999999999999999999999999999999999999999999999999999865432 234


Q ss_pred             ecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829         86 RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA  165 (181)
Q Consensus        86 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~  165 (181)
                      ..|.|...|..|++.++|+++++.+.+..|||+||++.+     .+..    .+...+++|||+|+||++||+|+|+|+|
T Consensus        81 ~~~~~~~~~~~~~v~~~l~~~g~~~~~~~V~s~DL~~~~-----~~~~----~~~v~pv~~di~I~kL~~gq~i~le~~~  151 (212)
T cd07028          81 EDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIVS-----NLMG----RNIGHPIIQDILICKLRKGQEIKLTCVA  151 (212)
T ss_pred             ccccccccccceeEEEEEEccCCCCCcceEEHHHcccCC-----cccc----CCCeEEeCCCcEEEEECCCCEEEEEEEE
Confidence            445577788889999999998555445689999998743     1100    0112367899999999999999999999


Q ss_pred             EeccccccceeccCC
Q psy12829        166 KKGFGKEHAKWNPTA  180 (181)
Q Consensus       166 ~kG~G~~HAKw~pv~  180 (181)
                      ++|+||+|||||||+
T Consensus       152 ~~G~G~~hAk~sPV~  166 (212)
T cd07028         152 KKGIGKEHAKFGPVA  166 (212)
T ss_pred             ECCCcCCCCEeCCce
Confidence            999999999999996

The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and

>KOG1521|consensus

Probab=100.00  E-value=8.3e-55  Score=366.51  Aligned_cols=176  Identities=37%  Similarity=0.553  Sum_probs=153.9

Q ss_pred             CCCCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceE
Q psy12829          3 YANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRI   82 (181)
Q Consensus         3 ~~~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~   82 (181)
                      |.++++|.+.+++++.++|++.|++.+||||+||+||||||||||+.|+|++||||++||+|||||||||+..++  +.|
T Consensus        42 f~~~~~V~iv~~~~~~leFDligIda~IANAfRRILiaEVPtmAiEkVyi~nNTSViqDEvLaHRlGLvPl~aDP--rlF  119 (338)
T KOG1521|consen   42 FKDNFKVDIVSLDEETLEFDLIGIDASIANAFRRILIAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLVPLRADP--RLF  119 (338)
T ss_pred             hhhceEEEEEeccCcceeEEEeeccHHHHHHHHHHHHhhcchhheeeeEEecCccccHHHHHHHhhcCcccccCc--chh
Confidence            677899999999999999999999999999999999999999999999999999999999999999999999998  567


Q ss_pred             EEeecCCCcCCCCCceEEEEEEEEecCCCceeEEecc---------ceeCCCeeeeccccCcCCCC-CCccCCCCeEEEE
Q psy12829         83 LYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTAD---------LKSTDARVVPVTSRNRDADM-NEYGETDDILIVK  152 (181)
Q Consensus        83 ~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~d---------i~~~~~~~~p~~~~~~~~~~-~~~~~~~di~I~k  152 (181)
                      .|..+..|++. ..++++|+|+|+|+.+....+.+.|         +++.+..|.|.+.|...+.+ ++.++++||+|+|
T Consensus       120 e~~~e~d~~~e-~~ntlvF~L~VkC~~n~~a~~~~sdpk~Ly~ns~vyS~~~~w~P~g~Q~~~f~e~~i~~~~~DILiAk  198 (338)
T KOG1521|consen  120 EYRSENDEDDE-KENTLVFKLNVKCTKNPNAKKDSSDPKELYNNSEVYSRDLTWKPKGYQAEIFAENPIRPVHDDILIAK  198 (338)
T ss_pred             hccccCCCccC-ccceEEEEEEeeccCCCCcccCCCChhHhccCcEEecCcceeccccchhhhcccCCccccCcceEEEe
Confidence            78776544432 2289999999999998444444444         55566669999999877655 4556799999999


Q ss_pred             eCCCCEEEEEEEEEeccccccceeccCCC
Q psy12829        153 LRKGQELRLRAYAKKGFGKEHAKWNPTAG  181 (181)
Q Consensus       153 L~~gq~i~~e~~~~kG~G~~HAKw~pv~~  181 (181)
                      |+|||+|+++++|+||+|++|||||||+.
T Consensus       199 LrPGQEI~le~havkGIGkdHAKfSPVaT  227 (338)
T KOG1521|consen  199 LRPGQEIELEAHAVKGIGKDHAKFSPVAT  227 (338)
T ss_pred             cCCCCEeeeeeeeecccCcccccccCccc
Confidence            99999999999999999999999999974

>PRK00783 DNA-directed RNA polymerase subunit D; Provisional

Probab=100.00  E-value=8.1e-53  Score=355.83  Aligned_cols=155  Identities=45%  Similarity=0.761  Sum_probs=142.7

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR   86 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~   86 (181)
                      ++|++.+.++++++|.+.|+++|+||||||+|||||||+||+.|+|++|||+++||+|+|||||||++++  +++++|+.
T Consensus         1 ~~~~~~~~~~~~~~f~~~g~~~t~~NalRRvlls~vp~~Ai~~v~i~~n~s~~~de~i~hrl~lip~~~~--~~~~~~~~   78 (263)
T PRK00783          1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAHRLGLIPLTTD--LDKYKPPE   78 (263)
T ss_pred             CceEEEEcCCcEEEEEEeCCCHHHHHHHHHHHHHcCCeeeEEEEEEEECCcchhHHHHHHhhcCcccccC--HHHCCCcc
Confidence            4689999999999999999999999999999999999999999999999999999999999999999996  58899998


Q ss_pred             cCCCc-CCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829         87 DCTCV-DFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA  165 (181)
Q Consensus        87 ~~~~~-~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~  165 (181)
                      +|.|+ +.|++|++.|+|+++    ||+.|||+||+..+..++              ++|||++|+||++||+|+|++++
T Consensus        79 ~~~~~~~~~~~~~~~~~l~~~----~~~~V~a~dl~~~~~~v~--------------~v~~~~~I~~L~~~~~l~~e~~~  140 (263)
T PRK00783         79 ECTCEGEGCPDCTVTLSLEVE----GPKTVYSGDLKSSDPDVK--------------PVDPNIPIVKLKEGQKLVLEAYA  140 (263)
T ss_pred             cccccCCCCCCcEEEEEEEec----CCCcEEccccccCCCCce--------------ecCCCcEEEEeCCCCEEEEEEEE
Confidence            88764 679999999999998    899999999986333333              67899999999999999999999


Q ss_pred             EeccccccceeccCCC
Q psy12829        166 KKGFGKEHAKWNPTAG  181 (181)
Q Consensus       166 ~kG~G~~HAKw~pv~~  181 (181)
                      .+|+||+||||+|+++
T Consensus       141 ~~G~G~~HAKw~p~~~  156 (263)
T PRK00783        141 RLGRGKEHAKWQPGSA  156 (263)
T ss_pred             EcCcccccCccCcceE
Confidence            9999999999999863

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase

Probab=100.00  E-value=6.3e-50  Score=337.52  Aligned_cols=154  Identities=44%  Similarity=0.709  Sum_probs=138.1

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR   86 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~   86 (181)
                      ++|++.+.++++++|.++|++.|+||||||+|||||||+||+.|+|++|||+|+||+++|||||||++++++...+  ..
T Consensus         1 ~~~~~~~~~~~~~~f~~~g~~~s~~NalRRills~vp~~Ai~~V~i~~n~s~~~de~i~hrl~~ip~~~e~~~~~~--~~   78 (259)
T cd07030           1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYKY--RS   78 (259)
T ss_pred             CceEEEecCCCEEEEEEeCCCHHHHHHHHHHHHhcCCeeeEEEEEEEeCCchhhHHHHHHhhcCcccccCHHHhcc--cc
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999864332  22


Q ss_pred             cCCC-cCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829         87 DCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA  165 (181)
Q Consensus        87 ~~~~-~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~  165 (181)
                      +|.| ...|+.|++.|+|+++    +++.|||+||++.+..++              ++||+++|+||++||+|+|++++
T Consensus        79 ~~~~~~~~~~~~~~~~~l~~~----~~~~v~s~dl~~~~~~v~--------------~~~~~~~I~~l~~~~~l~~~~~~  140 (259)
T cd07030          79 ECSCGGAGCPLCTVTLTLSVE----GPGTVYSGDLKSSDPDVK--------------PVYDNIPIVKLGKGQKLVLEAYA  140 (259)
T ss_pred             cccccCCCCCCcEEEEEEEcc----CCceEEccccccCCCCcc--------------ccCCCcEEEEeCCCCEEEEEEEE
Confidence            5654 3568889999999998    889999999986443343              67899999999999999999999


Q ss_pred             EeccccccceeccCC
Q psy12829        166 KKGFGKEHAKWNPTA  180 (181)
Q Consensus       166 ~kG~G~~HAKw~pv~  180 (181)
                      .||+|++||||+|++
T Consensus       141 ~kg~g~~hakw~p~~  155 (259)
T cd07030         141 RLGRGKEHAKWQPTT  155 (259)
T ss_pred             ecCccCCCCCCCCcc
Confidence            999999999999985

The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w

>PRK14979 DNA-directed RNA polymerase subunit D; Provisional

Probab=100.00  E-value=3.1e-45  Score=297.48  Aligned_cols=139  Identities=36%  Similarity=0.527  Sum_probs=123.4

Q ss_pred             CCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEe
Q psy12829          6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYS   85 (181)
Q Consensus         6 ~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~   85 (181)
                      .+++++....+++++|.++ +++|+||||||+|||++||+||+.|+|++|||+++||+++||||+||++...      ++
T Consensus         3 ~~~~~~~~~~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~DEivaHe~~lIpLK~~~------~~   75 (195)
T PRK14979          3 TIKEKEKTRIGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKP------VS   75 (195)
T ss_pred             ccceeeeccCCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccchheeeeeeeeeeeeee------cc
Confidence            3567777778899999999 9999999999999999999999999999999999999999999999977653      11


Q ss_pred             ecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829         86 RDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA  165 (181)
Q Consensus        86 ~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~  165 (181)
                      .         ++++.++|+++    ||+.|||+||++.+.  +              ++|||++||||++||+|+|+|+|
T Consensus        76 ~---------~~~~~l~L~~~----gp~~Vta~Di~~~~~--~--------------ivnpdi~I~tL~~g~~l~~e~~~  126 (195)
T PRK14979         76 G---------DEVITFTLSKE----GPCTVYSSDLKSENG--E--------------VAFKNIPIVKLAEGQKLEIECEA  126 (195)
T ss_pred             C---------CCcEEEEEEEe----CCceEEHHHcCCCCC--c--------------ccCCCcEEEEECCCCEEEEEEEE
Confidence            1         24678999987    999999999986332  1              67899999999999999999999


Q ss_pred             EeccccccceeccCC
Q psy12829        166 KKGFGKEHAKWNPTA  180 (181)
Q Consensus       166 ~kG~G~~HAKw~pv~  180 (181)
                      .+|+||+||||+|+.
T Consensus       127 ~~G~Gy~hAk~~pvd  141 (195)
T PRK14979        127 LVGTGKIHAKWQPCN  141 (195)
T ss_pred             ECCCcccccccccee
Confidence            999999999999974

>smart00662 RPOLD RNA polymerases D

Probab=100.00  E-value=1.4e-45  Score=305.69  Aligned_cols=143  Identities=49%  Similarity=0.751  Sum_probs=131.7

Q ss_pred             eEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEeecCCCcCCCCCc
Q psy12829         18 NVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSEC   97 (181)
Q Consensus        18 ~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~~~~~~~~~~~~   97 (181)
                      +++|.++++++|+||||||+||||+||+||+.|+|++|+|.+.||+++|||||+|+....  +.+.++.+|.|+..|+.|
T Consensus         1 ~~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I~~n~~~v~eev~~~rLnL~pl~~~~--~~~~~~~~~~~~~~~~~~   78 (224)
T smart00662        1 RAKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEIEGNTSGVQDEVLAHRLGLKPLASDP--DGDEYQRDCECEEGCEKC   78 (224)
T ss_pred             CeEEEEEcCCchHHHHHHHHHHHcCccceEEEEEEecCCcchhHHHHHHHhCCeeEEEec--hhccccccccccccCCCc
Confidence            479999999999999999999999999999999999999999999999999999999864  456677889999999999


Q ss_pred             eEEEEEEEEecCCCceeEEeccceeC-CCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEecccccccee
Q psy12829         98 SVEFTLDVKCVDDQTRHVTTADLKST-DARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKW  176 (181)
Q Consensus        98 ~v~~~L~v~~~~~~~~~V~s~di~~~-~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAKw  176 (181)
                      ++.++|+++    ||+.|||+||++. +..++              ++|||++|+||++||+|+|+++|.+|+||+||||
T Consensus        79 ~~~~~L~~~----gp~~V~a~Dl~~~~~~~v~--------------~vnp~~~I~~L~~gq~l~~e~~~~~G~G~~hak~  140 (224)
T smart00662       79 SVTLTLDVK----GPGEVTAGDLKSDSDPDVE--------------IVNPDIPIAKLREGQELELEARAEKGRGYVHAKW  140 (224)
T ss_pred             eEEEEEEEE----cCCcEEHHHcccCCCCCcE--------------EeCCCcEEEEECCCCEEEEEEEEECCcccccCcc
Confidence            999999998    8889999999875 33344              6689999999999999999999999999999999


Q ss_pred             ccCC
Q psy12829        177 NPTA  180 (181)
Q Consensus       177 ~pv~  180 (181)
                      +|++
T Consensus       141 ~p~~  144 (224)
T smart00662      141 SPVS  144 (224)
T ss_pred             cccc
Confidence            9986

DNA-directed RNA polymerase subunit D and bacterial alpha chain

>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional

Probab=100.00  E-value=1.7e-33  Score=243.38  Aligned_cols=140  Identities=22%  Similarity=0.366  Sum_probs=121.8

Q ss_pred             CCCCCCCcEEEEEec--CCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccc
Q psy12829          1 MPYANQPSVHITDLT--DENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLT   74 (181)
Q Consensus         1 ~~~~~~~~i~i~~~~--~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~   74 (181)
                      +.|.....+++.+.+  +++++|.++    |++.|+||||||+|||++||+||+.|+|++         ++|||++||++
T Consensus         1 ~~~~~~~~i~~~e~~~~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~g---------v~hEf~~Ipgv   71 (310)
T PRK05182          1 TEFLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDG---------VLHEFSTIPGV   71 (310)
T ss_pred             CCcccCcEEEEEeccCCCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEcc---------eeeeccccCCc
Confidence            457777788888876  789999998    999999999999999999999999999966         89999999999


Q ss_pred             cccc------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCe
Q psy12829         75 SDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDI  148 (181)
Q Consensus        75 ~~~~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di  148 (181)
                      .||+      ++++.++.+|      . |++.++|+++    ||+.|||+||.+.. .++              ++|||+
T Consensus        72 ~Edv~eIllNlk~i~~~~~~------~-~~~~~~l~~~----gp~~VtA~Di~~~~-~v~--------------ivn~d~  125 (310)
T PRK05182         72 REDVTEIILNLKGLRLKLHG------D-EPVTLTLSKK----GPGEVTAGDIETDG-DVE--------------IVNPDL  125 (310)
T ss_pred             ccchhHhhhhhccceeecCC------C-ceEEEEEEec----CCeEEEHHHcCCCC-CcE--------------EeCCCe
Confidence            9986      4666666554      2 7789999987    99999999998622 233              678999


Q ss_pred             EEEEeCCCCEEEEEEEEEeccccccce
Q psy12829        149 LIVKLRKGQELRLRAYAKKGFGKEHAK  175 (181)
Q Consensus       149 ~I~kL~~gq~i~~e~~~~kG~G~~HAK  175 (181)
                      +||||++||+|+|+++|.+|+||++|+
T Consensus       126 ~IatL~~~~~l~ie~~~~kG~Gy~~~~  152 (310)
T PRK05182        126 VIATLNEGAKLEMELTVERGRGYVPAE  152 (310)
T ss_pred             EEEEECCCCEEEEEEEEECcCCCcccc
Confidence            999999999999999999999998776

>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase

Probab=100.00  E-value=1.8e-33  Score=232.22  Aligned_cols=132  Identities=25%  Similarity=0.350  Sum_probs=117.5

Q ss_pred             EEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc------cc
Q psy12829         11 ITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VD   80 (181)
Q Consensus        11 i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~------~~   80 (181)
                      +.+.++.+++|.++    |++.|+||||||+||||+||+||+.|+|++|         +|||++||++.|++      +|
T Consensus         3 ~~~~~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~~~---------~He~~~Ipgv~Edv~~IllNlk   73 (215)
T cd06928           3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGV---------LHEFSTIPGVREDVLEILLNLK   73 (215)
T ss_pred             eccCCCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEccc---------ccccccCCCccccHHHHhhccc
Confidence            45567889999995    8999999999999999999999999999995         79999999999996      47


Q ss_pred             eEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEE
Q psy12829         81 RILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELR  160 (181)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~  160 (181)
                      ++.++.+|.      .|++.++|+++    ||+.|||+||.+.+. ++              ++||+++||||.+||+|+
T Consensus        74 ~~~~~~~~~------~~~~~~~l~~~----gp~~V~a~Di~~~~~-i~--------------ivnp~~~IatL~~~~~l~  128 (215)
T cd06928          74 EIVFKSDSE------DEPQVLRLKVK----GPGVVTAADIELPSG-VE--------------IVNPDQYIATLTEDASLE  128 (215)
T ss_pred             cEEEEecCC------CceEEEEEEEe----cCeEEEhHhcCcCCC-cE--------------EeCCCcEEEEECCCCEEE
Confidence            888876652      57889999998    999999999987432 33              678999999999999999


Q ss_pred             EEEEEEecccccccee
Q psy12829        161 LRAYAKKGFGKEHAKW  176 (181)
Q Consensus       161 ~e~~~~kG~G~~HAKw  176 (181)
                      |+|++.+|+||.+|+|
T Consensus       129 ie~~i~~G~Gy~~~~~  144 (215)
T cd06928         129 MELRIEKGRGYVPAEE  144 (215)
T ss_pred             EEEEEECcCcceeccc
Confidence            9999999999999998

The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac

>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]

Probab=100.00  E-value=1.1e-33  Score=244.82  Aligned_cols=165  Identities=22%  Similarity=0.272  Sum_probs=134.8

Q ss_pred             EEEEEec----CCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEee--C---c-cccccceeeeeccCCccccccc
Q psy12829          9 VHITDLT----DENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEA--N---S-TVLSDEFIASRIGLIPLTSDEV   78 (181)
Q Consensus         9 i~i~~~~----~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~--N---t-Svl~DE~laHRlglIP~~~~~~   78 (181)
                      |++.+.+    ...++|...|+++|+||||||+|||||||+||+.|+|++  |   | +.++||+++|||||+|+....-
T Consensus         7 i~i~~~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~LnLk~L~~~~~   86 (317)
T COG0202           7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKPLAVKLD   86 (317)
T ss_pred             eEEEEcccccccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEEEeccccccccCcCcHHHHHHHHhcCceeeeecc
Confidence            8898888    456666667999999999999999999999999999999  3   3 3899999999999999998753


Q ss_pred             c---ceEEEeecCCCcCCCCCceEEEEEEEEecCCC------------ceeEEeccceeCCCeeeeccccCcCCCCCCcc
Q psy12829         79 V---DRILYSRDCTCVDFCSECSVEFTLDVKCVDDQ------------TRHVTTADLKSTDARVVPVTSRNRDADMNEYG  143 (181)
Q Consensus        79 ~---~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~------------~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~  143 (181)
                      .   +.+.+...|.|...|.+|++.+.|++.|+...            ...|+++|+++..     .+.+  ..+++..+
T Consensus        87 ~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~-----~~~~--~~~~~v~~  159 (317)
T COG0202          87 GDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPA-----EGNR--EDDPPVGP  159 (317)
T ss_pred             cccceEEEEeccCCccccHhhcccceeEEEECCCceeeeccCCcceEEEEEEEcCccEecc-----cccc--ccCCCcee
Confidence            2   24777777777788999999999999976544            3467888888621     1111  11122235


Q ss_pred             CCCCeEEEEeCCCCEEEEEEEEEeccccccceeccCC
Q psy12829        144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA  180 (181)
Q Consensus       144 ~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAKw~pv~  180 (181)
                      +.+|+++++|+++|.+..++++.+|+||+||||+|++
T Consensus       160 i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T  196 (317)
T COG0202         160 IAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPET  196 (317)
T ss_pred             eeCCCceeeeeeceEEEEeEEEeccCCceeEEEEEee
Confidence            6799999999999999999999999999999999976

>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2

Probab=100.00  E-value=4.2e-34  Score=213.41  Aligned_cols=110  Identities=39%  Similarity=0.634  Sum_probs=93.8

Q ss_pred             EEEeeCccccccceeeeeccCCccccccccceEEEeecC--CCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCee
Q psy12829         50 VQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDC--TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARV  127 (181)
Q Consensus        50 V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~~~--~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~  127 (181)
                      |+|++|||+++||+++||||+||++.|++++-+..-++|  .+...|+.|++.++|+++    |++.|||+||+..+..+
T Consensus         1 v~i~~n~s~~~dE~v~He~~~Ipgv~Edv~~iilnlk~i~~~~~~~~~~~~~~~~L~~~----g~~~V~a~di~~~~~~i   76 (112)
T PF01000_consen    1 VYIYENTSVLPDEGVAHEFGLIPGVSEDVLEIILNLKKIVIDCEEGCDDCSVTFSLKVK----GPGEVTAGDIKLEPSGI   76 (112)
T ss_dssp             EEEEEETSSS-HHHHHCHHHBSTCBSSCHHHHHHHHHTT-ESSSSSTTTSEEEEEEEEE----SSSCEEGGGSEESBTTE
T ss_pred             CEEEECCCeeccceeEeccccCCccccchhhhhhcchhhccccccCCCCceEEEEEEec----CCCccccceeEecCCce
Confidence            789999999999999999999999999975422233344  355788999999999999    88899999999754445


Q ss_pred             eeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEeccccccceec
Q psy12829        128 VPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN  177 (181)
Q Consensus       128 ~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAKw~  177 (181)
                      +              ++|||++||||++||+|+|++++.+|+||+|||||
T Consensus        77 ~--------------ivn~d~~I~tl~~~~~l~~e~~i~~G~Gy~~ak~~  112 (112)
T PF01000_consen   77 E--------------IVNPDIYIATLSEGQKLEMELYIEKGRGYVHAKWS  112 (112)
T ss_dssp             E--------------ESSTTSEEEEEESSTEEEEEEEEEEEESEECCTS-
T ss_pred             E--------------EecCCeEEEEECCCCEEEEEEEEECCCcccccccC
Confidence            5              67899999999999999999999999999999997

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....

>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type

Probab=99.97  E-value=6.1e-30  Score=220.12  Aligned_cols=124  Identities=23%  Similarity=0.345  Sum_probs=107.1

Q ss_pred             eEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc------cceEEEeec
Q psy12829         18 NVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRD   87 (181)
Q Consensus        18 ~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~------~~~~~~~~~   87 (181)
                      +++|.++    |++.|+||||||+|||++||+||+.|+|++         ++|||++||++.||+      +|++.++.+
T Consensus         1 y~~f~i~Ple~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g---------v~HEf~~I~GV~Edv~eIllNlK~i~~~~~   71 (297)
T TIGR02027         1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDG---------VLHEFSTIEGVKEDVTEIILNLKQLVVKSE   71 (297)
T ss_pred             CcEEEEecCCCCchhHHHHHHHHHHHhcCCceEEEEEEEcc---------eecccccCCCccccHHHHHhhhhceEEecc
Confidence            4689998    999999999999999999999999999998         999999999999997      478888765


Q ss_pred             CCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEe
Q psy12829         88 CTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKK  167 (181)
Q Consensus        88 ~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~k  167 (181)
                      |.      .+ ..++|+++    ||+.|||+||.+.+..++              ++|||++||||.+||+|+|++++.+
T Consensus        72 ~~------~~-~~~~l~~~----gp~~VtA~Di~~~p~~ie--------------ivnpd~~IatL~~~~~L~iel~i~~  126 (297)
T TIGR02027        72 GD------GE-RTMTLSKK----GPGVVTAGDIKAPPGDVE--------------IVNPDLVIATLTEPADLEIELRVER  126 (297)
T ss_pred             CC------Cc-EEEEEEEe----CCEEEEhhhcccCCCCcE--------------EeCCCeEEEEECCCCEEEEEEEEEc
Confidence            42      22 37888887    999999999984232233              7789999999999999999999999


Q ss_pred             ccccccce
Q psy12829        168 GFGKEHAK  175 (181)
Q Consensus       168 G~G~~HAK  175 (181)
                      |+||.+|+
T Consensus       127 G~Gy~~~~  134 (297)
T TIGR02027       127 GRGYVPAE  134 (297)
T ss_pred             ccccCccc
Confidence            99997664

This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.

>CHL00013 rpoA RNA polymerase alpha subunit

Probab=99.95  E-value=5.3e-27  Score=203.96  Aligned_cols=133  Identities=16%  Similarity=0.183  Sum_probs=115.1

Q ss_pred             CcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc----
Q psy12829          7 PSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV----   78 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~----   78 (181)
                      ...++.+.++.+++|.++    |++.|+||||||+|||++||+||+.|+|++         +.|+|..||++.||+    
T Consensus        10 ie~~~~~~~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g---------v~hEfs~i~GV~Edv~eIi   80 (327)
T CHL00013         10 VESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG---------VPHEYSTIPGIRESVLEIL   80 (327)
T ss_pred             eeEEEecCCCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC---------ccccccCCCCcccCHHHHH
Confidence            556667788899999999    788899999999999999999999999988         779999999999998    


Q ss_pred             --cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCC
Q psy12829         79 --VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKG  156 (181)
Q Consensus        79 --~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~g  156 (181)
                        +|++.++.++       .....+.|+++    ||+.|||+||... ..++              ++|||.+||+|..|
T Consensus        81 lNLK~I~~k~~~-------~~~~~~~l~~~----Gp~~vtA~Di~~p-~~ie--------------ivnpd~~Iatl~~~  134 (327)
T CHL00013         81 LNLKEIVLKSNL-------YGPQKASICVQ----GPKYVTAQDIILP-PSVE--------------IVDPTQHIATITEP  134 (327)
T ss_pred             HhhhcCeEEccC-------CCcEEEEEEEe----CCeEEEeeeeccC-CCeE--------------EeCCCeEEEEeCCC
Confidence              5788887543       13568888887    9999999999863 2233              78999999999999


Q ss_pred             CEEEEEEEEEeccccccc
Q psy12829        157 QELRLRAYAKKGFGKEHA  174 (181)
Q Consensus       157 q~i~~e~~~~kG~G~~HA  174 (181)
                      +.|+|++++.+|+||..|
T Consensus       135 ~~l~~el~ie~G~GY~~~  152 (327)
T CHL00013        135 IDLEIELKIEKGRGYRLK  152 (327)
T ss_pred             CEEEEEEEEECccCceec
Confidence            999999999999999544

>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2

Probab=98.99  E-value=3e-10  Score=77.25  Aligned_cols=31  Identities=32%  Similarity=0.682  Sum_probs=30.0

Q ss_pred             EEEEEEecCchhhHHHHHHHHhhCCcceEEE
Q psy12829         19 VKFQVEDTELSVANSLRRVFIAETPTMAIDW   49 (181)
Q Consensus        19 ~~F~l~g~~~siaNaLRRvLlsevPt~AI~~   49 (181)
                      ++|.++|.++|+||||||+||+++|++||+.
T Consensus         1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~   31 (66)
T PF01193_consen    1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG   31 (66)
T ss_dssp             EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE
T ss_pred             CEeEEcCCchHHHHHHHHHHHhcCCCceEEe
Confidence            5899999999999999999999999999998

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....

>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]

Probab=98.49  E-value=2.2e-07  Score=81.08  Aligned_cols=90  Identities=21%  Similarity=0.193  Sum_probs=70.1

Q ss_pred             ccccceeeeeccCCccccccc------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeecc
Q psy12829         58 VLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVT  131 (181)
Q Consensus        58 vl~DE~laHRlglIP~~~~~~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~  131 (181)
                      |--+++ .|+|..+|++.||+      ++.+.++.+-.      .. ++++++..    |++.+|++|+.... .++   
T Consensus        52 V~I~~v-~hef~s~~gv~Edvl~~~LnLk~L~~~~~~~------~~-~~~~~~~~----g~g~v~a~d~~~~~-~lE---  115 (317)
T COG0202          52 VEIDGV-LHEFDSIEGVQEDVLAHRLNLKPLAVKLDGD------EE-VTLELDKE----GPGEVTASDITVPL-DLE---  115 (317)
T ss_pred             EEEecc-ccccccCcCcHHHHHHHHhcCceeeeecccc------cc-eEEEEecc----CCccccHhhcccce-eEE---
Confidence            433444 59999999999997      35555554310      01 68888887    99999999998622 233   


Q ss_pred             ccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEeccccccc
Q psy12829        132 SRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHA  174 (181)
Q Consensus       132 ~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HA  174 (181)
                                 ++|||.+||+|+.+.+|+|++++..|+||..|
T Consensus       116 -----------v~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~  147 (317)
T COG0202         116 -----------VVNPDHVIATLTEDAKLEMELRVYSGDGYVPA  147 (317)
T ss_pred             -----------EECCCceeeeccCCcceEEEEEEEcCccEecc
Confidence                       78999999999999999999999999999964

>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase

Probab=97.75  E-value=6.2e-05  Score=53.70  Aligned_cols=32  Identities=31%  Similarity=0.580  Sum_probs=30.2

Q ss_pred             EEEEEecCCeEEEEEEecCchhhHHHHHHHHh
Q psy12829          9 VHITDLTDENVKFQVEDTELSVANSLRRVFIA   40 (181)
Q Consensus         9 i~i~~~~~~~~~F~l~g~~~siaNaLRRvLls   40 (181)
                      |++.+.+++.++|.++|-|+|+||+||+.|+.
T Consensus         1 ~ki~~~~~~~~~~~~~~edhTl~n~L~~~l~~   32 (86)
T cd00460           1 VKILEKEKNYVDFVLENEDHTLGNSLRRILLK   32 (86)
T ss_pred             CceecCCCCEEEEEEeCCCchHHHHHHHHHhC
Confidence            46788999999999999999999999999999

The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the

>PRK01146 DNA-directed RNA polymerase subunit L; Provisional

Probab=97.04  E-value=0.0011  Score=47.29  Aligned_cols=43  Identities=12%  Similarity=0.322  Sum_probs=36.1

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEE
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWV   50 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V   50 (181)
                      +++++.+.+++.++|.++|=|+|+||+||-.|+. -|...+-..
T Consensus         1 m~ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~-~~~V~fAgY   43 (85)
T PRK01146          1 MEIKVLEKEDNELELEIEGEDHTLMNLLKEELLE-DPGVEAASY   43 (85)
T ss_pred             CeEEEEecCCCEEEEEEeCCCchHHHHHHHHHhc-CCCeeEEEe
Confidence            4789999999999999999999999999999985 555544333

>cd06927 RNAP_L L subunit of Archaeal RNA polymerase

Probab=96.60  E-value=0.0033  Score=44.71  Aligned_cols=41  Identities=12%  Similarity=0.392  Sum_probs=34.3

Q ss_pred             EEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEE
Q psy12829          9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWV   50 (181)
Q Consensus         9 i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V   50 (181)
                      +++.+.+++.++|.+.|=|+|+||+||-.|+.. |..-+-..
T Consensus         1 ikvi~~~~n~~~~~i~~EDHTlgNlLr~~L~~~-~~V~fAgY   41 (83)
T cd06927           1 LKVIEKEDNELELEIEGEDHTLLNLLKEELLRD-PGVKVASY   41 (83)
T ss_pred             CeEEEcCCCEEEEEEeCCCchHHHHHHHHHhcC-CCeEEEEe
Confidence            478899999999999999999999999999876 55444333

The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.

>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase

Probab=96.41  E-value=0.0048  Score=43.89  Aligned_cols=36  Identities=17%  Similarity=0.376  Sum_probs=31.2

Q ss_pred             EEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcc
Q psy12829          9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTM   45 (181)
Q Consensus         9 i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~   45 (181)
                      +++.+.+++.++|.++|=|+|+||+||-.|+.. |..
T Consensus         1 ~kii~~~~n~~~~~i~~EdHTLgNlLr~~L~~~-~~V   36 (83)
T cd07027           1 LRIISKEKNSVTVEMENEDHTLGNLLREELLKD-DQV   36 (83)
T ss_pred             CeeEecCCCEEEEEEeCCCchHHHHHHHHHhcC-CCe
Confidence            467889999999999999999999999988765 443

The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/

>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]

Probab=95.95  E-value=0.014  Score=42.92  Aligned_cols=36  Identities=17%  Similarity=0.377  Sum_probs=33.3

Q ss_pred             CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHh
Q psy12829          5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIA   40 (181)
Q Consensus         5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLls   40 (181)
                      ..+++++.+.+++.++|.++|-|+|++|.||-.|+.
T Consensus         3 ~~~~l~ii~~~~n~~~i~i~gEdHTL~NlL~~~L~~   38 (99)
T COG1761           3 PEMELRIIKKDDNSLELEIEGEDHTLGNLLREELLK   38 (99)
T ss_pred             CceEEEEeccCCCEEEEEEecCCchHHHHHHHHHhC
Confidence            457888899999999999999999999999999987

>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II

Probab=95.40  E-value=0.026  Score=40.88  Aligned_cols=42  Identities=12%  Similarity=0.263  Sum_probs=32.6

Q ss_pred             CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceE
Q psy12829          5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAI   47 (181)
Q Consensus         5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI   47 (181)
                      .+..++..+..++.++|.+.|=|+|+||+||-.|+. -|..-+
T Consensus         5 ~kv~~~~d~k~~n~~~~~i~~EdHTLgNlLr~~L~~-~~~V~f   46 (93)
T cd06926           5 KKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLK-DPNVLF   46 (93)
T ss_pred             cceEEeecCCCCcEEEEEEeCCCchHHHHHHHHHhc-CCCeeE
Confidence            344455555678899999999999999999999987 555433

The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.

>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

Probab=93.68  E-value=0.084  Score=37.62  Aligned_cols=31  Identities=23%  Similarity=0.378  Sum_probs=26.5

Q ss_pred             EecCCeEEEEEEecCchhhHHHHHHHHhhCCc
Q psy12829         13 DLTDENVKFQVEDTELSVANSLRRVFIAETPT   44 (181)
Q Consensus        13 ~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt   44 (181)
                      ...++.++|.++|=|+|+||+||-.|+. -|.
T Consensus         5 ~~~~n~~~~~i~~EdHTLgNlLr~~L~~-~p~   35 (85)
T cd07029           5 GTDESCATFVFYGEDHTLGNSLRYVIMK-NPE   35 (85)
T ss_pred             cCCCCeEEEEEeCCCcchHHHHHHHHhh-CCC
Confidence            3567899999999999999999999887 344

The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass

>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K

Probab=93.11  E-value=0.1  Score=36.47  Aligned_cols=35  Identities=14%  Similarity=0.372  Sum_probs=26.1

Q ss_pred             CeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEE
Q psy12829         17 ENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL   52 (181)
Q Consensus        17 ~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I   52 (181)
                      +.+.|.+.|=|+|+||+||-.|+.. |...+-..++
T Consensus         1 n~~~f~i~~EDHTlgNlLr~~L~~~-p~V~fagY~v   35 (77)
T PF13656_consen    1 NEITFTIYGEDHTLGNLLRYELLKD-PDVEFAGYRV   35 (77)
T ss_dssp             TEEEEEEES--HHHHHHHHHCCTTS-TTEEEEEEEE
T ss_pred             CeEEEEEeCCCccHHHHHHHHHhhC-CCeEEEEecc
Confidence            4689999999999999999998875 6655554444

...

>KOG3438|consensus

Probab=86.45  E-value=0.8  Score=33.83  Aligned_cols=35  Identities=20%  Similarity=0.288  Sum_probs=27.4

Q ss_pred             cCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeC
Q psy12829         15 TDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEAN   55 (181)
Q Consensus        15 ~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~N   55 (181)
                      ......|.+..=|+|||||||=+|+-      =..|.+-+.
T Consensus        14 d~~~~Tf~~~eEDHTlgNalR~vI~k------~peVefcGY   48 (105)
T KOG3438|consen   14 DLSSATFQLREEDHTLGNALRYVIMK------NPEVEFCGY   48 (105)
T ss_pred             CCCceEEEEEecCcchhHHHHHHHhc------CCceEEEec
Confidence            44578999999999999999998876      235655554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	181
1i3q_C	318	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		8e-39
3i4m_C	324	8-oxoguanine Containing Rna Polymerase Ii Elongatio		8e-39
3j0k_C	268	Orientation Of Rna Polymerase Ii Within The Human V		1e-38
3how_C	347	Complete Rna Polymerase Ii Elongation Complex Iii W		1e-38
3h0g_C	297	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		4e-33
2waq_D	265	The Complete Structure Of The Archaeal 13-Subunit D		5e-19
2pa8_D	265	X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE		8e-19

>pdb|1I3Q|C Chain C, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 318

Iteration: 1
 Score =  155 bits (393), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)
Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
           P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA 
Sbjct: 6   PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 67  RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           R+GLIPL S + ++++ YSRDC C D C +CSV  TL      + T +V + DL      
Sbjct: 66  RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           V  +  RN    + +  E + +LI KLRKGQEL+L   AKKG  KEHAKW P A
Sbjct: 121 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 174

>pdb|3I4M|C Chain C, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex D Length = 324

Iteration: 1
 Score =  155 bits (393), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)
Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
           P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA 
Sbjct: 12  PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 71
Query: 67  RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           R+GLIPL S + ++++ YSRDC C D C +CSV  TL      + T +V + DL      
Sbjct: 72  RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 126
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           V  +  RN    + +  E + +LI KLRKGQEL+L   AKKG  KEHAKW P A
Sbjct: 127 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 180

>pdb|3J0K|C Chain C, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 268

Iteration: 1
 Score =  155 bits (393), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 84/175 (48%), Positives = 113/175 (64%), Gaps = 5/175 (2%)
Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
           P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA 
Sbjct: 6   PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 67  RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           R+GLIPL S + ++++ YSRDC C D C +CSV  TL      + T +V + DL      
Sbjct: 66  RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
           V  +  RN    + +  E + +LI KLRKGQEL+L   AKKG  KEHAKW P A 
Sbjct: 121 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAA 175

>pdb|3HOW|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U Mismatch And A Frayed Rna 3'-Uridine Length = 347

Iteration: 1
 Score =  155 bits (393), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)
Query: 7   PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
           P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA 
Sbjct: 35  PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 94
Query: 67  RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           R+GLIPL S + ++++ YSRDC C D C +CSV  TL      + T +V + DL      
Sbjct: 95  RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 149
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           V  +  RN    + +  E + +LI KLRKGQEL+L   AKKG  KEHAKW P A
Sbjct: 150 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 203

>pdb|3H0G|C Chain C, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 297

Iteration: 1
 Score =  137 bits (344), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 77/180 (42%), Positives = 109/180 (60%), Gaps = 17/180 (9%)
Query: 10  HIT--DLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
           HIT  +++  +V F + +T L+VANSLRRV +AE PT+AID V++  N++V+ DEF+A R
Sbjct: 6   HITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHR 65
Query: 68  IGLIPLTSDEVVDR----ILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL--K 121
           +G+IPL S  + +     + Y+R+C C  +C +CSVE  L+ KC  + T  +   DL   
Sbjct: 66  LGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVS 125
Query: 122 STDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
           S  +   P+      AD    G     LI KLRK QE+ LR  AKKG  KEHAKW+PT+ 
Sbjct: 126 SNSSLGHPIL-----ADPKSRGP----LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA 176

>pdb|2WAQ|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 265

Iteration: 1
 Score = 90.5 bits (223), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8   SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
           S+++    D+ +    E   L   N++RR  +   P M+ID V    N++ L DE +A R
Sbjct: 2   SINLLHKDDKRIDLVFEGYPLEFVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68  IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           + LIP TS+E +D   +  +C  C + C +C  +  ++ + + ++ + + + D+KS D  
Sbjct: 62  LALIPFTSEEALDTYRWPEECIDCTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           +VP++               DI IV L   Q++ L A  + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160

>pdb|2PA8|D Chain D, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE SULFOLOBUS Solfataricus Rna Polymerase Length = 265

Iteration: 1
 Score = 89.7 bits (221), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 87/174 (50%), Gaps = 16/174 (9%)
Query: 8   SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
           S+++    D  +    E   L   N++RR  +   P MA+D V    N++ L DE +A R
Sbjct: 2   SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61
Query: 68  IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           + LIP  S+E +D   +  +C  C + C +C  +  ++ +   ++ R + + D+KS D  
Sbjct: 62  LALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAE-APNEPRMIYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           VVP++               DI IV L   Q++ L A  + G+GKEHAK+ P +
Sbjct: 121 VVPISG--------------DIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVS 160

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	181
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	5e-46
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	1e-41
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	4e-39
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05

>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Length = 318

 Score =  152 bits (385), Expect = 5e-46
 Identities = 83/176 (47%), Positives = 112/176 (63%), Gaps = 5/176 (2%)

Query: 6   QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
            P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA
Sbjct: 5   GPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIA 64

Query: 66  SRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
            R+GLIPL S + ++++ YSRDC C D C +CSV  TL      + T +V + DL     
Sbjct: 65  HRLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS- 122

Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
               +  RN    + +  E + +LI KLRKGQEL+L   AKKG  KEHAKW P A 
Sbjct: 123 ---NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAA 175

>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 297

 Score =  140 bits (354), Expect = 1e-41
 Identities = 70/181 (38%), Positives = 106/181 (58%), Gaps = 11/181 (6%)

Query: 5   NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFI 64
           ++  + I +++  +V F + +T L+VANSLRRV +AE PT+AID V++  N++V+ DEF+
Sbjct: 3   SETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFL 62

Query: 65  ASRIGLIPLTSDEVVDRIL----YSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
           A R+G+IPL S  + +       Y+R+C C  +C +CSVE  L+ KC  + T  +   DL
Sbjct: 63  AHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDL 122

Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
             +    +               ++   LI KLRK QE+ LR  AKKG  KEHAKW+PT+
Sbjct: 123 VVSSNSSLGHPILADP-------KSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTS 175

Query: 181 G 181
            
Sbjct: 176 A 176

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D Length = 265

 Score =  133 bits (335), Expect = 4e-39
 Identities = 52/174 (29%), Positives = 87/174 (50%), Gaps = 16/174 (9%)

Query: 8   SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
           S+++    D  +    E   L   N++RR  +   P MA+D V    N++ L DE +A R
Sbjct: 2   SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61

Query: 68  IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
           + LIP  S+E +D   +  +C  C + C +C  +  ++ +   ++ R + + D+KS D  
Sbjct: 62  LALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEA-PNEPRMIYSKDIKSEDPS 120

Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
           VVP+              + DI IV L   Q++ L A  + G+GKEHAK+ P +
Sbjct: 121 VVPI--------------SGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVS 160

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

 Score = 42.1 bits (98), Expect = 5e-05
 Identities = 23/128 (17%), Positives = 45/128 (35%), Gaps = 24/128 (18%)

Query: 49  WVQLEANSTVLSDEFIASRIGLIPLTSDEVVD---RILYSRD-CTCV----DFCSECSVE 100
             Q++ N T  SD         I L    +     R+L S+    C+    +  +  +  
Sbjct: 206 LYQIDPNWTSRSDHSSN-----IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN 260

Query: 101 FTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYG----ETDDILIVKLR-K 155
              ++ C   +   +TT   + TD  +   T+ +   D +       E   +L+  L  +
Sbjct: 261 -AFNLSC---KIL-LTTRFKQVTDF-LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314

Query: 156 GQELRLRA 163
            Q+L    
Sbjct: 315 PQDLPREV 322

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	181
3h0g_C	297	DNA-directed RNA polymerase II subunit RPB3; trans	100.0
2pa8_D	265	DNA-directed RNA polymerase subunit D; ferredoxin-	100.0
1twf_C	318	B44.5, DNA-directed RNA polymerase II 45 kDa polyp	100.0
1bdf_A	235	RNA polymerase alpha subunit; nucleotidyltransfera	100.0
2a6h_A	315	DNA-directed RNA polymerase alpha chain; RNA polym	100.0
3lu0_A	329	DNA-directed RNA polymerase subunit alpha; E. coli	100.0
2pa8_L	92	DNA-directed RNA polymerase subunit L; ferredoxin-	96.97
1xpp_A	115	TA1416, DNA-directed RNA polymerase subunit L; str	96.86
1twf_K	120	B13.6, DNA-directed RNA polymerase II 13.6 kDa pol	96.13
3h0g_K	123	DNA-directed RNA polymerase II subunit RPB11; tran	94.68

>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=3.5e-59  Score=399.09  Aligned_cols=168  Identities=42%  Similarity=0.773  Sum_probs=151.9

Q ss_pred             CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccc----
Q psy12829          5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVD----   80 (181)
Q Consensus         5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~----   80 (181)
                      ++|+|++.+.++++++|+++|+++|+||||||+|||||||+||+.|+|++|||+|+||+||||||||||+++++.+    
T Consensus         3 ~~p~I~i~~~~~~~~~F~l~g~~~tiaNALRRiLLSeVPt~AI~~V~I~~NtSvl~DE~laHrlglIP~v~edv~e~~~~   82 (297)
T 3h0g_C            3 SETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPV   82 (297)
T ss_dssp             -CCSBCCCCBCSSEEEEEECSCCHHHHHHHHHHHHSSCCEEEEEEEEEEEECSSSCHHHHHHHHHHSCBCCTTCSSCSSS
T ss_pred             CCCeEEEEEccCCEEEEEEECCChhHHHHHHHHHHHcCccceEEEEEEEeCCccccccceeeeeccCCcccccccccccc
Confidence            6799999999999999999999999999999999999999999999999999999999999999999999998643    


Q ss_pred             eEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCe--eeeccccCcCCCCCCccCCCCeEEEEeCCCCE
Q psy12829         81 RILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR--VVPVTSRNRDADMNEYGETDDILIVKLRKGQE  158 (181)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~--~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~  158 (181)
                      .|+|+.+|.|.+.|+.|+++|+|+++|+.+.+++|||+||++.+..  +.|+..         .++||||+||||++||+
T Consensus        83 ~l~~k~~c~~~~~~~~~~v~l~L~v~g~~~~~~~Vta~Dl~~~~~~~~~~pv~~---------~~~n~di~IakL~~gq~  153 (297)
T 3h0g_C           83 GLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILA---------DPKSRGPLICKLRKEQE  153 (297)
T ss_dssp             CCCCSSSCSSSSSCGGGSCEEEEEECCCCSSCEEEEGGGCBCCSCCSSCCBCCC---------STTSCCSEEEEECSSCC
T ss_pred             eeEeccccccccCCCCceEEEEEEEEeccCCCceEEcccccccCcccccccccc---------cCCCCCeEEEEECCCCE
Confidence            4889999999999999999999999998888999999999975432  223221         13689999999999999


Q ss_pred             EEEEEEEEeccccccceeccCCC
Q psy12829        159 LRLRAYAKKGFGKEHAKWNPTAG  181 (181)
Q Consensus       159 i~~e~~~~kG~G~~HAKw~pv~~  181 (181)
                      |+|+|+|+|||||+|||||||++
T Consensus       154 l~le~~a~kG~G~~HAKwsPv~~  176 (297)
T 3h0g_C          154 ISLRCIAKKGIAKEHAKWSPTSA  176 (297)
T ss_dssp             EEEEEEEEEECGGGCTTSCCBCC
T ss_pred             EEEEEEEECCEeccccccCcceE
Confidence            99999999999999999999984

>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D 2y0s_D

Probab=100.00  E-value=1.2e-57  Score=384.68  Aligned_cols=159  Identities=32%  Similarity=0.567  Sum_probs=149.1

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEee
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSR   86 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~   86 (181)
                      ++|++.+.++++++|.++|+++|+||||||+|||||||+||+.|+|++|||+|+||+++||||||||+++|+.|++.|+.
T Consensus         1 ~~i~i~~~~~~~~~f~l~g~~~t~~NalRRills~vp~~AI~~V~i~~Ntsvl~DE~v~Hr~~~Ip~~~edv~k~~~~~~   80 (265)
T 2pa8_D            1 MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPE   80 (265)
T ss_dssp             -CEEEEEECSSEEEEEEESSCHHHHHHHHHHHHHSCCEEEEEEEEEEEECSSSCHHHHHHHHTTSCBCCTTHHHHSCCGG
T ss_pred             CeEEEEEcCCCEEEEEEeCCCHHHHHHHHHHHHHcCccceEEEEEEEeCCCccccHHHHHhhcCCcCcccCchhhccccc
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999889999999


Q ss_pred             cC-CCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEE
Q psy12829         87 DC-TCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYA  165 (181)
Q Consensus        87 ~~-~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~  165 (181)
                      +| .|+++|++|+++|+|+++| ++||+.|||+||++.+..++              ++||||+|+||++||+|+|+++|
T Consensus        81 ~~~~~~~~~~~~~~~~~l~~~~-~~g~~~V~a~Di~~~~~~v~--------------~~~~~i~I~~L~~g~~l~~e~~~  145 (265)
T 2pa8_D           81 ECIECTENCEKCYTKIYIEAEA-PNEPRMIYSKDIKSEDPSVV--------------PISGDIPIVLLGTNQKISLEARL  145 (265)
T ss_dssp             GCTTCCSSCTTTEEEEEEEEEC-CSSCEEEEGGGCEESSTTCC--------------BSCSCCEEEEECTTCEEEEEEEE
T ss_pred             cccccccCCCCcEEEEEEEEEe-cCCCcEEEhhhcccCCCCce--------------ecCCCcEEEEeCCCCEEEEEEEE
Confidence            98 7899999999999999999 67999999999997444444              67899999999999999999999


Q ss_pred             EeccccccceeccCC
Q psy12829        166 KKGFGKEHAKWNPTA  180 (181)
Q Consensus       166 ~kG~G~~HAKw~pv~  180 (181)
                      +||+||+||||+|++
T Consensus       146 ~~G~G~~~ak~~pv~  160 (265)
T 2pa8_D          146 RLGYGKEHAKFIPVS  160 (265)
T ss_dssp             EEECTTTCGGGCCEE
T ss_pred             ecCccccccCcccce
Confidence            999999999999985

>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ...

Probab=100.00  E-value=4.1e-58  Score=396.24  Aligned_cols=171  Identities=47%  Similarity=0.748  Sum_probs=152.4

Q ss_pred             CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccccceEEE
Q psy12829          5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILY   84 (181)
Q Consensus         5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~   84 (181)
                      ++|+|++.+.++++++|+|+|+++||||||||+|||||||+||+.|+|++|||+|+||+|+||||||||+++|+ |++.|
T Consensus         4 ~~p~I~i~~~~~~~~kF~leG~~~tlaNALRRiLLSevPg~AI~~V~I~~NTSvl~DE~vaHrlglIP~v~eDv-k~l~~   82 (318)
T 1twf_C            4 EGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEY   82 (318)
T ss_dssp             CSSBCCCSCCCSSEECCEEBSSCHHHHHHHHHHHHHCCCEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETTG-GGSCC
T ss_pred             cCCeEEEEEecCCEEEEEEEccChhHHHHHHHHHHHcCccceEEEEEEEeCCcccccceeEeecccCCCcccCh-hheEE
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999984 89999


Q ss_pred             eecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCC-ccCCCCeEEEEeCCCCEEEEEE
Q psy12829         85 SRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNE-YGETDDILIVKLRKGQELRLRA  163 (181)
Q Consensus        85 ~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~-~~~~~di~I~kL~~gq~i~~e~  163 (181)
                      +.+|.|+++|++|+++|+|+++|+.++++.|||+||++.+..   .+.  +..++.. .++||||+||||++||+|+|+|
T Consensus        83 ~~~~~~~~~c~~~~v~l~L~v~c~~~g~~~Vta~Di~~~~~~---~~~--~~~~p~v~ei~npdi~IakL~~gq~L~me~  157 (318)
T 1twf_C           83 SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNL---MGR--NIGHPIIQDKEGNGVLICKLRKGQELKLTC  157 (318)
T ss_dssp             TTTSSSSSCCTTTEEEEEEEEECCSSSCEEEEGGGEEECSCC---TTC--SEEEECCCSTTSCCSEEEEECTTCEEEEEE
T ss_pred             eeccccccCCCCceEEEEEEEEecCCCCeeEEhHhccccCcc---ccc--cccCCCccccCCCCeEEEEECCCCEEEEEE
Confidence            999999999999999999999999999999999999863310   010  0011122 2679999999999999999999


Q ss_pred             EEEeccccccceeccCCC
Q psy12829        164 YAKKGFGKEHAKWNPTAG  181 (181)
Q Consensus       164 ~~~kG~G~~HAKw~pv~~  181 (181)
                      +|+||+||+|||||||++
T Consensus       158 ~a~kG~G~~hAk~sPva~  175 (318)
T 1twf_C          158 VAKKGIAKEHAKWGPAAA  175 (318)
T ss_dssp             EEEEECTTTCGGGCCEEE
T ss_pred             EEEcCccccccccccccc
Confidence            999999999999999863

>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1

Probab=100.00  E-value=8.2e-42  Score=283.94  Aligned_cols=140  Identities=18%  Similarity=0.258  Sum_probs=126.2

Q ss_pred             CCCCCCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCcccccc
Q psy12829          2 PYANQPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDE   77 (181)
Q Consensus         2 ~~~~~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~   77 (181)
                      .|..+.+|++.+.++++++|.++    |++.|+||||||+||||+||+||+.|+|++         ++||||+|||+.||
T Consensus         7 ~~~~p~~i~i~~~~~~~~~F~l~Ple~G~~~tlgNaLRRiLLsevpg~AI~~V~Ie~---------v~He~~~Ipgv~Ed   77 (235)
T 1bdf_A            7 EFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVTEVEIDG---------VLHEYSTKEGVQED   77 (235)
T ss_dssp             CSCCCCEEEEEESSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCCEEEEEEEETT---------CCSTTCCCTTBSSC
T ss_pred             hhcCCceEEEEEccCCEEEEEEEecCCCCchHHHHHHHHHHHhcCCceEEEEEEEcc---------eeeccccCCCccCC
Confidence            46666679999999999999998    999999999999999999999999999954         99999999999998


Q ss_pred             c------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEE
Q psy12829         78 V------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIV  151 (181)
Q Consensus        78 ~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~  151 (181)
                      +      +|++.|+.++       .|++.++|+++    ||+.|||+||+. +..++              ++|||++||
T Consensus        78 v~~iilNlk~i~~~~~~-------~~~~~~~L~v~----gp~~VtA~Di~~-~~~v~--------------ivnpd~~Ia  131 (235)
T 1bdf_A           78 ILEILLNLKGLAVRVQG-------KDEVILTLNKS----GIGPVTAADITH-DGDVE--------------IVKPQHVIC  131 (235)
T ss_dssp             HHHHHHHHHTCCEECSS-------CSEEEEEEEEE----SSEEEEGGGBCC-CSSCE--------------ESCTTCEEE
T ss_pred             HHHHhhchheeEEeccC-------CceEEEEEEEe----cCeEEEhHhCCC-CCCCE--------------EcCCCeEEE
Confidence            6      5788888653       47899999998    999999999984 33243              678999999


Q ss_pred             EeCC-CCEEEEEEEEEecccccccee
Q psy12829        152 KLRK-GQELRLRAYAKKGFGKEHAKW  176 (181)
Q Consensus       152 kL~~-gq~i~~e~~~~kG~G~~HAKw  176 (181)
                      ||++ ||+|+|+|+|.||+||+||||
T Consensus       132 tL~~~g~~l~~e~~~~kG~Gy~~ak~  157 (235)
T 1bdf_A          132 HLTDENASISMRIKVQRGRGYVPAST  157 (235)
T ss_dssp             EECSTTCEEEEEEEEEECCSEECGGG
T ss_pred             EECCCCCEEEEEEEEEecccceeccc
Confidence            9999 999999999999999999999

>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* ...

Probab=100.00  E-value=2.1e-41  Score=291.76  Aligned_cols=140  Identities=21%  Similarity=0.300  Sum_probs=127.7

Q ss_pred             CCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCccccccc---
Q psy12829          6 QPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV---   78 (181)
Q Consensus         6 ~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~---   78 (181)
                      +|+|++.+.++++++|.++    |++.|+||||||+|||||||+||+.|+|++         ++||||+|||+.||+   
T Consensus         8 ~p~i~i~~~~~~~~~F~l~Ple~G~~~TlgNaLRRiLLsevpg~AI~~V~I~~---------v~He~~~Ipgv~Edv~eI   78 (315)
T 2a6h_A            8 APVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIED---------VLHEFSTIPGVKEDVVEI   78 (315)
T ss_dssp             CCEEEEEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHHTCEEEEEEEEEESS---------CCSTTCBCTTBSSBHHHH
T ss_pred             CCeEEEEEccCCEEEEEEEccCCCchhHHHHHHHHHHHhcCCceEEEEEEEec---------chhccCCCCCccCCHHHH
Confidence            4779999999999999997    999999999999999999999999999998         999999999999986   


Q ss_pred             ---cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCC
Q psy12829         79 ---VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRK  155 (181)
Q Consensus        79 ---~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~  155 (181)
                         +|++.|+.+|     |+.|++.++|+++    ||+.|||+||+. +..++              ++|||++||||++
T Consensus        79 ilNlk~i~~~~~~-----~~~~~~~~~L~v~----gp~~VtA~Di~~-~~~v~--------------ivnpd~~IatL~~  134 (315)
T 2a6h_A           79 ILNLKELVVRFLN-----PSLQTVTLLLKAE----GPKEVKARDFLP-VADVE--------------IMNPDLHIATLEE  134 (315)
T ss_dssp             HHHHHTCCEEECS-----TTCSBCCEEEEEE----SSCEEEGGGSCC-CTTEE--------------ESCTTCEEEEBCS
T ss_pred             hhhhheEEEeccc-----CCCCeEEEEEEEe----cCeeEEhhhCCc-CCCcE--------------EcCCCeEEEEECC
Confidence               5889998875     3468899999999    999999999985 33344              6789999999999


Q ss_pred             CCEEEEEEEEEeccccccceecc
Q psy12829        156 GQELRLRAYAKKGFGKEHAKWNP  178 (181)
Q Consensus       156 gq~i~~e~~~~kG~G~~HAKw~p  178 (181)
                      ||+|+|+|+|.+|+||+||||++
T Consensus       135 g~~l~me~~~~kG~Gy~~ak~~~  157 (315)
T 2a6h_A          135 GGRLNMEVRVDRGVGYVPAEKHG  157 (315)
T ss_dssp             SCEEEEEEEEEEEESEECHHHHC
T ss_pred             CCEEEEEEEEEecCCccccccCc
Confidence            99999999999999999999985

>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A

Probab=100.00  E-value=1.1e-35  Score=257.04  Aligned_cols=141  Identities=18%  Similarity=0.269  Sum_probs=122.5

Q ss_pred             CCCCCCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEeeCccccccceeeeeccCCcccccc
Q psy12829          2 PYANQPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDE   77 (181)
Q Consensus         2 ~~~~~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~   77 (181)
                      .|..+..+++.+.++.+++|.++    |++.|+||||||+||||+||+||+.|+|++         ++||||+|||+.||
T Consensus         7 ~~~~p~~~~v~~~~~~~~kF~l~PlerG~g~TlgNaLRRvLLssvpg~AIt~V~I~g---------v~Hefs~Ipgv~Ed   77 (329)
T 3lu0_A            7 EFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG---------VLHEYSTKEGVQED   77 (329)
T ss_dssp             TSSSCCCCCEEECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESS---------CSSTTCCCTTBSSC
T ss_pred             hccCCceEEEEEcCCCEEEEEEEecCCCChhHHHHHHHHHHHhcCCceEEEEEEEeC---------ccccccccccccCC
Confidence            36677788898899999999999    999999999999999999999999999976         99999999999998


Q ss_pred             cc------ceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEeccceeCCCeeeeccccCcCCCCCCccCCCCeEEE
Q psy12829         78 VV------DRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIV  151 (181)
Q Consensus        78 ~~------~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~  151 (181)
                      +.      |++.++.       |..|++.++|+++    ||+.|||+||.+ +..++              ++||+++||
T Consensus        78 v~eiilNlK~i~~k~-------~~~~~~~~~L~~~----Gp~~VtA~DI~~-~~~ve--------------ivnpd~~Ia  131 (329)
T 3lu0_A           78 ILEILLNLKGLAVRV-------QGKDEVILTLNKS----GIGPVTAADITH-DGDVE--------------IVKPQHVIC  131 (329)
T ss_dssp             HHHHHHHHHSCCCEE-------SSCSCEEEEECCC----SSSCEETTSSCC-CSSEE--------------CSCTTCEEE
T ss_pred             HHHHHhhhccceEec-------CCCceEEEEEEEe----CCeEEEeeeecc-CCCCE--------------EeCCCcEEE
Confidence            73      3443332       2457889999986    999999999986 33344              778999999


Q ss_pred             EeC-CCCEEEEEEEEEeccccccceec
Q psy12829        152 KLR-KGQELRLRAYAKKGFGKEHAKWN  177 (181)
Q Consensus       152 kL~-~gq~i~~e~~~~kG~G~~HAKw~  177 (181)
                      ||+ +||+|+|++++.+|+||++|.++
T Consensus       132 tL~~~~~~L~me~~i~~G~GY~~a~~~  158 (329)
T 3lu0_A          132 HLTDENASISMRIKVQRGRGYVPASTR  158 (329)
T ss_dssp             CBCSSCCCCCEEEEEEEESSEECTTTS
T ss_pred             EEccCCcEEEEEEEEECcccceechhc
Confidence            999 99999999999999999988754

>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymer assembly, transferase; 1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L

Probab=96.97  E-value=0.00093  Score=47.36  Aligned_cols=45  Identities=7%  Similarity=0.111  Sum_probs=37.2

Q ss_pred             CcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEE
Q psy12829          7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL   52 (181)
Q Consensus         7 ~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I   52 (181)
                      +++++.+.+++.++|.+.|=|+||||+||-.|+.. |..-+-...|
T Consensus         1 Meikvi~k~~n~~~f~i~~EDHTLgN~Lr~~L~~~-p~V~fagY~v   45 (92)
T 2pa8_L            1 MEIRILKSESNYLELEIEGEDHTLGNLIAGTLRRI-SGVSFASYYQ   45 (92)
T ss_dssp             CEEEEEEEETTEEEEEEETCCHHHHHHHHHHHHTS-TTEEEEEEEC
T ss_pred             CceEEEecCCCeEEEEEecCchhHHHHHHHHHhcC-CCeeEEEeec
Confidence            46899999999999999999999999999998874 6655444433

>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} SCOP: d.74.3.2

Probab=96.86  E-value=0.0013  Score=48.48  Aligned_cols=48  Identities=4%  Similarity=0.144  Sum_probs=38.8

Q ss_pred             CCCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEE
Q psy12829          4 ANQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQL   52 (181)
Q Consensus         4 ~~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I   52 (181)
                      .+++++++.+.+++.+.|.+.|=|+||||+||-.|+.. |..-+-...|
T Consensus         8 ~~kmeiki~~k~~n~~~f~i~~EDHTLgNlLr~~Llkd-p~V~fAgY~v   55 (115)
T 1xpp_A            8 TAESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKD-DQVDEARYYI   55 (115)
T ss_dssp             -CCCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTC-TTEEEEEEEC
T ss_pred             ccceEEEEEcCCCCEEEEEEeCCCchhHHHHHHHHhcC-CCeEEEEeec
Confidence            35688999999999999999999999999999998765 6554444433

>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...

Probab=96.13  E-value=0.0044  Score=45.99  Aligned_cols=45  Identities=9%  Similarity=0.153  Sum_probs=36.0

Q ss_pred             CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEE
Q psy12829          5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWV   50 (181)
Q Consensus         5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V   50 (181)
                      +++.+++.+.+++.++|.+.|=|+||||+||-.|+.. |..-+-..
T Consensus        17 ~K~~~~~~~k~~n~~~f~i~~EDHTLgNlLr~~Llk~-p~V~fAgY   61 (120)
T 1twf_K           17 SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLND-RKVLFAAY   61 (120)
T ss_dssp             CSCCEEECSSSTTEEEEEEESCCHHHHHHHHHHHTTC-TTEEEEEE
T ss_pred             ceEEEEeccCCCCeEEEEEeCCCchHHHHHHHHHhhC-CCeeEEee
Confidence            4567777777889999999999999999999998864 65444443

>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=94.68  E-value=0.022  Score=42.37  Aligned_cols=34  Identities=12%  Similarity=0.270  Sum_probs=28.0

Q ss_pred             cEEEEEecCCeEEEEEEecCchhhHHHHHHHHhh
Q psy12829          8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAE   41 (181)
Q Consensus         8 ~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlse   41 (181)
                      .++.....++.+.|.+.|=|+||||+||-.|+..
T Consensus        19 ~~~~dtk~~n~~~f~i~~EDHTLgNlLr~~Llk~   52 (123)
T 3h0g_K           19 TYELDSKSPNAAVVTLEKEDHTLANMLANQLLSD   52 (123)
T ss_dssp             CEEECSSSTTEEEEEEESCCSSHHHHHHHTGGGS
T ss_pred             EEecCCCCCceEEEEEeCCCcchHHHHHHHHhcC
Confidence            3333455788999999999999999999998874

---

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	181
d1twfc2	131	d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharo	2e-48
d1twfc1	135	d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (S	9e-10

>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 131

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  151 bits (383), Expect = 2e-48
 Identities = 65/136 (47%), Positives = 86/136 (63%), Gaps = 5/136 (3%)

Query: 43  PTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFT 102
           PT+AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV  T
Sbjct: 1   PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLT 59

Query: 103 LDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLR 162
           L      + T +V + DL         +  RN    + +  E + +LI KLRKGQEL+L 
Sbjct: 60  LQAFGESESTTNVYSKDLVIVS----NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLT 115

Query: 163 AYAKKGFGKEHAKWNP 178
             AKKG  KEHAKW P
Sbjct: 116 CVAKKGIAKEHAKWGP 131

>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 135

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 52.1 bits (125), Expect = 9e-10
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 6  QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAID 48
           P V I + + +NV F + + +L++ANSLRRV IAE       
Sbjct: 3  GPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIAAAIEF 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	181
d1twfc2	131	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1bdfa2	126	RNA polymerase alpha subunit {Escherichia coli [Ta	99.75
d1smya2	123	RNA polymerase alpha subunit {Thermus thermophilus	99.73
d1twfc1	135	RPB3 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.49
d1bdfa1	105	RNA polymerase alpha {Escherichia coli [TaxId: 562	98.46
d1smya1	106	RNA polymerase alpha {Thermus thermophilus [TaxId:	97.6
d1xppa_	99	DNA-directed RNA polymerase subunit L, RpoL {Therm	97.04
d1twfk_	114	RPB11 {Baker's yeast (Saccharomyces cerevisiae) [T	94.06

>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=5e-43  Score=265.67  Aligned_cols=130  Identities=48%  Similarity=0.775  Sum_probs=111.7

Q ss_pred             CcceEEEEEEeeCccccccceeeeeccCCccccccccceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEecccee
Q psy12829         43 PTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKS  122 (181)
Q Consensus        43 Pt~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~di~~  122 (181)
                      |||||+.|+|++|||+|+||+|||||||||+.+++ .+.+.|..+|.|.+.|+.|++.|+|+++|+++++..|||+||++
T Consensus         1 PtlAid~V~I~~NTS~l~DE~iaHRLglIPi~~~~-~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~   79 (131)
T d1twfc2           1 PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI   79 (131)
T ss_dssp             CEEEEEEEEEEEECSSSCHHHHHHHHHTSCEEETT-GGGSCCTTTSSSSSCCTTTEEEEEEEEECCSSSCEEEEGGGEEE
T ss_pred             CeEEEEEEEEEECCcccchHHHHHhhcCceeeccC-hhhccccccccccCCCCCceEEEEeEcccCCCCCceEEhhheEE
Confidence            89999999999999999999999999999999876 46788888999999999999999999999999999999999986


Q ss_pred             CCCe-eeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEeccccccceecc
Q psy12829        123 TDAR-VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP  178 (181)
Q Consensus       123 ~~~~-~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAKw~p  178 (181)
                      .+.. +.+...+     ......+++|+|+||+|||+|+|+|+|+||+|++||||||
T Consensus        80 ~~~~~~~~~~~~-----~~~~~~~~~IlI~kL~pGQ~i~l~a~a~kG~Gk~HAK~sP  131 (131)
T d1twfc2          80 VSNLMGRNIGHP-----IIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGP  131 (131)
T ss_dssp             CSCCTTCSEEEE-----CCCSTTSCCSEEEEECTTCEEEEEEEEEEECTTTCGGGCC
T ss_pred             cCCccccccCCc-----cccCCcCCCCEEEEeCCCCEEEEEEEEEecccccCcEeCc
Confidence            4321 1111100     1112446899999999999999999999999999999998

>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RNA polymerase alpha subunit
species: Escherichia coli [TaxId: 562]

Probab=99.75  E-value=2.4e-18  Score=128.61  Aligned_cols=98  Identities=16%  Similarity=0.178  Sum_probs=83.7

Q ss_pred             cceEEEEEEeeCccccccceeeeeccCCccccccc------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEe
Q psy12829         44 TMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTT  117 (181)
Q Consensus        44 t~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s  117 (181)
                      |.||+.|+|++         +.|+|..||++.||+      +|+++++.+.       .....++|+++    ||+.|||
T Consensus         1 G~AIt~vkI~G---------v~HEfsti~GV~EDV~~IiLNLK~i~~k~~~-------~~~~~~~l~~~----gp~~VtA   60 (126)
T d1bdfa2           1 GCAVTEVEIDG---------VLHEYSTKEGVQEDILEILLNLKGLAVRVQG-------KDEVILTLNKS----GIGPVTA   60 (126)
T ss_dssp             CEEEEEEEETT---------CCSTTCCCTTBSSCHHHHHHHHHTCCEECSS-------CSEEEEEEEEE----SSEEEEG
T ss_pred             CCCEEEEEECC---------cccccccCCCchhhHHHHHHhcccceEEecC-------CCceEEEEEec----CcccEEE
Confidence            68999999988         899999999999998      5788887542       35668889988    9999999


Q ss_pred             ccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeC-CCCEEEEEEEEEecccccccee
Q psy12829        118 ADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLR-KGQELRLRAYAKKGFGKEHAKW  176 (181)
Q Consensus       118 ~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~-~gq~i~~e~~~~kG~G~~HAKw  176 (181)
                      +||.... .++              ++|||.+||+|. ++.+|+||+++.+|+||..|-.
T Consensus        61 ~di~~~~-~ve--------------IvNpd~~Iatlt~~~~~l~mel~v~~GrGYv~ae~  105 (126)
T d1bdfa2          61 ADITHDG-DVE--------------IVKPQHVICHLTDENASISMRIKVQRGRGYVPAST  105 (126)
T ss_dssp             GGBCCCS-SCE--------------ESCTTCEEEEECSTTCEEEEEEEEEECCSEECGGG
T ss_pred             ecccCCC-CEE--------------EeCCceEEEEEecCCceEEEEEEEeCCCCeecccc
Confidence            9998632 233              889999999995 7999999999999999987753

>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RNA polymerase alpha subunit
species: Thermus thermophilus [TaxId: 274]

Probab=99.73  E-value=8.5e-19  Score=130.57  Aligned_cols=99  Identities=20%  Similarity=0.268  Sum_probs=83.3

Q ss_pred             cceEEEEEEeeCccccccceeeeeccCCccccccc------cceEEEeecCCCcCCCCCceEEEEEEEEecCCCceeEEe
Q psy12829         44 TMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV------VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTT  117 (181)
Q Consensus        44 t~AI~~V~I~~NtSvl~DE~laHRlglIP~~~~~~------~~~~~~~~~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s  117 (181)
                      |.||+.|+|.+         +.|+|+.||++.||+      +|++.++....     ...+..++|+++    ||+.|||
T Consensus         1 G~AIt~vkI~G---------v~HEfsti~GV~EDV~eIiLNLK~i~~~~~~~-----~~~~~~~~l~~~----Gp~~VtA   62 (123)
T d1smya2           1 GTAVTSVYIED---------VLHEFSTIPGVKEDVVEIILNLKELVVRFLNP-----SLQTVTLLLKAE----GPKEVKA   62 (123)
T ss_dssp             EEEEEEEEESS---------CCSTTCCCTTBSSCHHHHHHHHHHCCEEESST-----TCSEEEEEEEEC----SSBCCBG
T ss_pred             CcCEEEEEECC---------cccccccCCChhhhHHHHHHhhhhhheeeccc-----ccccEEEEEEec----CCCeEEe
Confidence            68999999998         899999999999998      57777764321     125677888887    9999999


Q ss_pred             ccceeCCCeeeeccccCcCCCCCCccCCCCeEEEEeCCCCEEEEEEEEEeccccccce
Q psy12829        118 ADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAK  175 (181)
Q Consensus       118 ~di~~~~~~~~p~~~~~~~~~~~~~~~~~di~I~kL~~gq~i~~e~~~~kG~G~~HAK  175 (181)
                      +||.... .++              ++|||.+||+|.++.+|+||+++.+|+||..|.
T Consensus        63 ~Di~~~~-~ve--------------IvNpd~~IaTl~~~~~l~mel~v~~GrGYv~ae  105 (123)
T d1smya2          63 RDFLPVA-DVE--------------IMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAE  105 (123)
T ss_dssp             GGSCCCT-TEE--------------ESCTTCBCCCBCTTCCEEEEEEEEEEESEECHH
T ss_pred             eeecCCC-cEE--------------EECCcEEEEEEcCCcEEEEEEEEcccccceEcc
Confidence            9998632 244              889999999999999999999999999998764

>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RPB3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.49  E-value=2.1e-15  Score=113.21  Aligned_cols=53  Identities=32%  Similarity=0.403  Sum_probs=50.4

Q ss_pred             CCCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcceEEEEEEeeCcc
Q psy12829          5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANST   57 (181)
Q Consensus         5 ~~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~AI~~V~I~~NtS   57 (181)
                      .+|+|++.+.+++.++|.|+|+++|+||||||+|||||||++++.+..++|++
T Consensus         2 ~~P~i~i~~~~~~~~~F~l~~~d~s~ANalRRi~iaeV~t~v~feyDp~N~lr   54 (135)
T d1twfc1           2 EGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIAAAIEFEYDPWNKLK   54 (135)
T ss_dssp             CSSBCCCSCCCSSEECCEEBSSCHHHHHHHHHHHHHCCEEEEEEEECSSTTSC
T ss_pred             CCCEEEEEEcCCCEEEEEEeCCCHHHHHHHHHHHHHhhhhheeeeeccccccc
Confidence            57999999999999999999999999999999999999999999999999854

>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RNA polymerase alpha
species: Escherichia coli [TaxId: 562]

Probab=98.46  E-value=1.1e-07  Score=67.74  Aligned_cols=53  Identities=19%  Similarity=0.321  Sum_probs=47.6

Q ss_pred             CCCCCCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEee
Q psy12829          2 PYANQPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEA   54 (181)
Q Consensus         2 ~~~~~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~   54 (181)
                      .+.++..+.+.+.++..++|.++    |++.++||++||+|+|++|..+...++|++
T Consensus         6 eil~P~~v~i~~~~~~~~k~~~eplErG~Gyt~gn~lr~~llSs~sPV~~V~y~Ve~   62 (105)
T d1bdfa1           6 EFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPPVERIAYNVEA   62 (105)
T ss_dssp             CSCCCCEEEEEESSSSEEEEEEEEEETTHHHHHHHHHHHHHTTSCCSEEEEEEECCB
T ss_pred             hhcCCCEEEEEecCCceEEEEEEEccCCcccccccccchhhhhcccceeEEEEeeee
Confidence            35666677888888889999987    999999999999999999999999999988

>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RNA polymerase alpha subunit dimerisation domain
domain: RNA polymerase alpha
species: Thermus thermophilus [TaxId: 274]

Probab=97.60  E-value=4.5e-05  Score=53.93  Aligned_cols=49  Identities=22%  Similarity=0.367  Sum_probs=42.4

Q ss_pred             CCcEEEEEecCCeEEEEEE----ecCchhhHHHHHHHHhhCCcceEEEEEEee
Q psy12829          6 QPSVHITDLTDENVKFQVE----DTELSVANSLRRVFIAETPTMAIDWVQLEA   54 (181)
Q Consensus         6 ~~~i~i~~~~~~~~~F~l~----g~~~siaNaLRRvLlsevPt~AI~~V~I~~   54 (181)
                      .|.+.+.+.+..+.+|..+    |++.++||++||+++|++|.++.....|++
T Consensus         8 ~p~~~~~~~~~~y~~~v~~p~erG~g~~~gn~l~~il~ss~~PV~kV~y~Ve~   60 (106)
T d1smya1           8 APVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVED   60 (106)
T ss_dssp             CCCCEEEECSSSCEEEEEEEECTTHHHHHHHHHHHHHHHTCECEEEEEEEEEE
T ss_pred             CceEEEeecCCceeEEEeeccCCCcccccccccceeehhcCChhhEEEEEecc
Confidence            4556666788889999987    999999999999999999998888888864

>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL {Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: DNA-directed RNA polymerase subunit L, RpoL
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=97.04  E-value=0.00035  Score=48.31  Aligned_cols=39  Identities=5%  Similarity=0.216  Sum_probs=34.7

Q ss_pred             CCcEEEEEecCCeEEEEEEecCchhhHHHHHHHHhhCCcc
Q psy12829          6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTM   45 (181)
Q Consensus         6 ~~~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLlsevPt~   45 (181)
                      +.++++.+.+++.++|.|+|-|+|+||+||..|+.. |.+
T Consensus         2 ~~~ikvi~~~~n~~~~~i~~EdHTlgn~L~~~L~~~-~~V   40 (99)
T d1xppa_           2 ESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKD-DQV   40 (99)
T ss_dssp             CCEEEEEEECSSEEEEEEESCCHHHHHHHHHHHTTC-TTE
T ss_pred             CceEEEEecCCCEEEEEEeCCCchHHHHHHHHHhcC-CCe
Confidence            457899999999999999999999999999999964 553

>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: DCoH-like
superfamily: RBP11-like subunits of RNA polymerase
family: RBP11/RpoL
domain: RPB11
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.06  E-value=0.021  Score=39.91  Aligned_cols=33  Identities=12%  Similarity=0.224  Sum_probs=27.1

Q ss_pred             cEEEEEecCCeEEEEEEecCchhhHHHHHHHHh
Q psy12829          8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIA   40 (181)
Q Consensus         8 ~i~i~~~~~~~~~F~l~g~~~siaNaLRRvLls   40 (181)
                      .++.....++...|.++|-|+|+||+||..|+.
T Consensus        20 ~i~~~~~~~n~~~~~i~~EdhTlGnlL~~~L~~   52 (114)
T d1twfk_          20 KIDPDTKAPNAVVITFEKEDHTLGNLIRAELLN   52 (114)
T ss_dssp             CEEECSSSTTEEEEEEESCCHHHHHHHHHHHTT
T ss_pred             EEEecCCCCceEEEEEeCCCchHHHHHHHHHhc
Confidence            333333457899999999999999999999986