Psyllid ID: psy5290

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530------
Protein Sequence
MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFLPQGLSTPESHPPVSPSIDTMLRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTANSVAQPNRKSSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSVQQESRGVTPGGDKTAADLPVYSYKGVPLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRPQPYSLPAGYGGVNERK
Secondary Structure (PSIPRED)
ccccccccccccHHHHcccHHHHHHHHcccccccccccccEEEEEEccccccccEEEEccccccccHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHHccccEEEEEEcccccccccccccccccccccHHHHHHHHHHHccccccccccHHccccHHHHHHccccccEEEEEccccHHHHHHHHcccEEEEEEEcccccEEcccccccccccccccccHHHHHHHHHHHHccEEEEEcccccccccccccccccccccccccccccccccEEEEEcccccccccccEEEEEcccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHcccEccHHHHcccHHHHHHHHccccccccccccccEEEEcccccccccEEEEEcccccccHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHccccccccEEEEEEHHHHcccHHHcccccEEEEccHHHHHHHHHHcEEEEEEEEEccccccccHHHHHEEccccccccccHccHcHHHHHHHcHHEEEEEccccccEEEcccccccccccccccccHHHHHHHHHHHccEEEEEccccccccEEEEccHHcccccccccccccccccEEEEEEHHHHHHcccHEEEEEcccEEEEccccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccEEEEccccEEcccccccccccccccccccccccccccccccccccccccccccccEEEEccccEEEccccccccccccccEEcccccccccccccccccccccccccccccEcccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mqlchdrgylvtqdELDQTLDQFKEqfgdkpsekrpaRSELIVLVahnddptdqmfvffpdepkigiKTIKTYCQRMQEETIHRAIIVVQtgmtpsakqslvdMAPKYILEYFLESELLInitehelvpehivltpEEKQELLTRYWRSCVTIFWtqkrtgeehflkecsfesatvksvypslkapIFQLLqqplfllvktsdranavflpqglstpeshppvspsiDTMLRSYEERHSLVFSlahfpfkhfkevtlgdfltngkslkqgvpltdipvmaFYTKHELDELKPFFKFFYMgdlevtansvaqpnrkssmetapampvpmqagyntgegyksvdgfkpdpvsgypyanrlpsshpqkhafflapvpvilpqpkpqehhhdgpgqhnilnrspsvqqesrgvtpggdktaadlpvysykgvplyiprgrqspsstvqptvespsgqksyypgensapagisstespgdigvsgftspgpqpyslpsglggtegvspheehvslvfpsspaprpqpyslpagyggvnerk
Flexible Loop (DISEMBL)
mqlchdrgylvtqdelDQTLDQFKEqfgdkpsekrpaRSELIVLVAHNDDPTDQMFvffpdepkiGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFlpqglstpeshppvSPSIDTMLRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTANSVAQPNRkssmetapampvpMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSVQQESRgvtpggdktaadlpvYSYKGVPLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFpsspaprpqpyslpagyggvnerk
Low Complexity Region (SEG)
MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIfqllqqplfllVKTSDRANAVFLPQGLSTPESHPPVSPSIDTMLRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTANSVAQPNRKSSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSVQQESRGVTPGGDKTAADLPVYSYKGVPLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRPQPYSLPAGYGGVNERK
Disordered region (IsUnstruct)
********YL******************************LIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFL***********************YEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTA***********************************************************HAFFLAPVPVIL******************************************LPVYSYKGVPLYI********************************************************************************************************
Disordered Region (DISOPRED)
MQLCHDRGYLVTQDELDQTLDQFKEQFGDKP*****A****IVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQK******FLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFLPQGLS******P**PSIDTMLRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTAN**********************************************************HAFFLAPVPVIL********************************************VYSYKGVPL******************************************************************************SLVFP*********YSLPAG*G******
Disordered Region (DISEMBL)
MQLCHDRGYLVTQDELDQTLDQFKEQ**********ARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFLPQGL**********PSIDTMLRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTANSV**********TAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFFLAPVPVILPQPK********PGQHNILNRS************GGDKTAADLPVYSYKGVPLYIPRGR*****************KSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRPQPYSLPAGYGGVNERK
Disordered Region (DISPRO)
MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFLPQGLSTPE*HPPVSPSIDTMLRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTANS***************MPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFFLAPVPVILPQPK**********************************TAADLPVYSYKGVPLYIPRG***********************************************SP***********************V**VFPSSPAPRPQPYSLPAGYG******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFLPQGLSTPESHPPVSPSIDTMLRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTNGKSLKQGVPLTDIPVMAFYTKHELDELKPFFKFFYMGDLEVTANSVAQPNRKSSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSVQQESRGVTPGGDKTAADLPVYSYKGVPLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRPQPYSLPAGYGGVNERK
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	536	2.2.26 [Sep-21-2011]
B0BNE2	210	DNA-directed RNA polymera	yes	N/A	0.272	0.695	0.828	5e-68
Q80UW8	210	DNA-directed RNA polymera	yes	N/A	0.272	0.695	0.828	5e-68
Q5R587	210	DNA-directed RNA polymera	yes	N/A	0.272	0.695	0.828	6e-68
P19388	210	DNA-directed RNA polymera	yes	N/A	0.272	0.695	0.828	3e-67
Q2T9T3	210	DNA-directed RNA polymera	yes	N/A	0.272	0.695	0.821	2e-66
Q9N5K2	211	DNA-directed RNA polymera	yes	N/A	0.272	0.691	0.753	1e-62
A8XGH1	211	DNA-directed RNA polymera	N/A	N/A	0.272	0.691	0.753	2e-62
Q54EH2	197	DNA-directed RNA polymera	yes	N/A	0.25	0.680	0.459	5e-28
Q09191	210	DNA-directed RNA polymera	yes	N/A	0.266	0.680	0.404	7e-24
Q757H7	215	DNA-directed RNA polymera	yes	N/A	0.257	0.641	0.406	2e-23

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

 Score =  259 bits (661), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 121/146 (82%), Positives = 132/146 (90%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKY+LE FL+ ELLI
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+V+T EE  ELL RY
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARY 163

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.
Rattus norvegicus (taxid: 10116)

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

 Score =  259 bits (661), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 121/146 (82%), Positives = 132/146 (90%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKY+LE FL+ ELLI
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+V+T EE  ELL RY
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARY 163

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Mus musculus (taxid: 10090)

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

 Score =  258 bits (660), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 121/146 (82%), Positives = 132/146 (90%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL++F+ QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+V+T EE  ELL RY
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARY 163

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Pongo abelii (taxid: 9601)

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

 Score =  256 bits (654), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 121/146 (82%), Positives = 131/146 (89%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL++FK Q GDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEEFKAQSGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+V+T EE  ELL RY
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARY 163

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Homo sapiens (taxid: 9606)

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

 Score =  253 bits (646), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 120/146 (82%), Positives = 130/146 (89%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQD LDQTL++FK QFG KPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct: 78  EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+V+T EE  ELL RY
Sbjct: 138 NITEHELVPEHVVMTKEEVTELLARY 163

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process.

Bos taurus (taxid: 9913)

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

 Score =  241 bits (614), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 110/146 (75%), Positives = 130/146 (89%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           +Q+ HDRGYLV QDELDQ L+ FK Q+GD+PSEK+PARS+L +LVAHNDDP DQMFVFFP
Sbjct: 19  LQMVHDRGYLVAQDELDQPLETFKVQYGDRPSEKKPARSDLTILVAHNDDPADQMFVFFP 78

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           ++ KIGIKTIK  CQ+MQE+ I RAIIVVQTGMTPSAKQS+ DMAPKY+LE+FLE+EL++
Sbjct: 79  EDAKIGIKTIKAICQQMQEQNISRAIIVVQTGMTPSAKQSIGDMAPKYMLEHFLEAELMV 138

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+V+T EEK ELL RY
Sbjct: 139 NITEHELVPEHVVMTAEEKAELLARY 164

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

Caenorhabditis elegans (taxid: 6239)

>sp|A8XGH1|RPAB1_CAEBR DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis briggsae GN=rpb-5 PE=3 SV=1

 Score =  240 bits (613), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 110/146 (75%), Positives = 130/146 (89%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           +Q+ HDRGYLV Q+ELDQ L+ FKE FGD+PSEK+PARS+L +LVAHNDDP DQMFVFFP
Sbjct: 19  LQMVHDRGYLVAQEELDQPLETFKETFGDRPSEKKPARSDLTILVAHNDDPADQMFVFFP 78

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           ++ KIGIKTIK  CQ+MQE+ I RAIIVVQTGMTPSAKQS+ DMAPKY+LE+FLE+EL++
Sbjct: 79  EDTKIGIKTIKAICQQMQEQNISRAIIVVQTGMTPSAKQSIGDMAPKYMLEHFLEAELMV 138

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+V+T EEK ELL RY
Sbjct: 139 NITEHELVPEHVVMTAEEKAELLARY 164

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

Caenorhabditis briggsae (taxid: 6238)

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

 Score =  126 bits (316), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 68/148 (45%), Positives = 91/148 (61%), Gaps = 14/148 (9%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           +Q+  DR Y++T  E             + P E   +R  L +     DDPTD ++VFFP
Sbjct: 15  LQMLSDREYIITAYE------------QEYPRESFVSRENLTMYCVKKDDPTDSIYVFFP 62

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMA--PKYILEYFLESEL 118
           D PK+G+  IK Y   M++   +RAIIVVQ  +TP AKQ+L + +   K  LE F E+EL
Sbjct: 63  DTPKVGVTQIKKYVDIMKDRQANRAIIVVQQNITPFAKQALAEFSQEKKITLEQFNEAEL 122

Query: 119 LINITEHELVPEHIVLTPEEKQELLTRY 146
           L+NIT H+LVP+HI+LT EEK ELLTRY
Sbjct: 123 LVNITHHQLVPKHILLTKEEKLELLTRY 150

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

Dictyostelium discoideum (taxid: 44689)

>sp|Q09191|RPAB1_SCHPO DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb5 PE=1 SV=1

 Score =  112 bits (280), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 59/146 (40%), Positives = 87/146 (59%), Gaps = 3/146 (2%)

Query: 2   QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVA-HNDDPTDQMFVFFP 60
           QL HDRGY V+Q ELD TLDQFK         +   R+ L       ND     +++ F 
Sbjct: 20  QLVHDRGYGVSQAELDLTLDQFKAMHCGMG--RNLDRTTLSFYAKPSNDSNKGTIYIEFA 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
            EP +GIK ++T+   + +      I++    MTPSA + +  +  ++ +E F ES+L++
Sbjct: 78  KEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIV 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NIT HELVP+HI+L+P+EK+ELL RY
Sbjct: 138 NITHHELVPKHILLSPDEKKELLDRY 163

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

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

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

 Score =  111 bits (277), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 63/155 (40%), Positives = 95/155 (61%), Gaps = 17/155 (10%)

Query: 2   QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQ------- 54
           ++  DRGY +TQ+E+D +L+ FK ++ D  S  RP R     +++   +PT++       
Sbjct: 21  EMVRDRGYFITQEEVDLSLEDFKAKYCD--SMGRPQRK----MMSFQSNPTEETLKKSPN 74

Query: 55  ---MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILE 111
              ++V F DEP +GIKT+K +   + E+     I + Q G+TPSA + L  +AP  I E
Sbjct: 75  MGSVWVEFCDEPSVGIKTMKNFVIHIGEKNFQTGIFIYQNGITPSALKLLPSVAPATI-E 133

Query: 112 YFLESELLINITEHELVPEHIVLTPEEKQELLTRY 146
            F E+ L++NIT HELVP+HI L+ EEK+ELL RY
Sbjct: 134 TFNETALVVNITHHELVPKHIKLSDEEKKELLKRY 168

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

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

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	536
156548548	210	PREDICTED: DNA-directed RNA polymerases	0.272	0.695	0.945	7e-76
66543279	179	PREDICTED: DNA-directed RNA polymerases	0.272	0.815	0.945	2e-75
48124579	210	PREDICTED: DNA-directed RNA polymerases	0.272	0.695	0.945	2e-75
357609342	210	hypothetical protein KGM_04074 [Danaus p	0.272	0.695	0.931	2e-75
350422012	210	PREDICTED: DNA-directed RNA polymerases	0.272	0.695	0.945	2e-75
332022832	210	DNA-directed RNA polymerases I, II, and	0.272	0.695	0.938	1e-74
383865249	210	PREDICTED: DNA-directed RNA polymerases	0.272	0.695	0.938	1e-74
322797006	211	hypothetical protein SINV_02648 [Solenop	0.272	0.691	0.931	1e-74
149287100	210	25-kDa subunit RNA polymerase [Ornithodo	0.272	0.695	0.924	2e-74
242247587	210	DNA-directed RNA polymerases I, II, and	0.272	0.695	0.938	2e-74

>gi|156548548|ref|XP_001604962.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Nasonia vitripennis]

 Score =  291 bits (744), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 138/146 (94%), Positives = 144/146 (98%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL+QFKEQFGDKPSEKRPARS+LIVLVAHNDDPTDQ+FVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEQFKEQFGDKPSEKRPARSDLIVLVAHNDDPTDQLFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE IHRAIIVVQ+GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 78  DEPKIGIKTIKTYCQRMQEEKIHRAIIVVQSGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EK+ELLTRY
Sbjct: 138 NITEHELVPEHIVLTPDEKEELLTRY 163

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66543279|ref|XP_623541.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Apis mellifera]

 Score =  290 bits (741), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 138/146 (94%), Positives = 143/146 (97%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL+QFKEQFGDKPSEKRPARS+LIVLVAHNDDPTDQ+FVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEQFKEQFGDKPSEKRPARSDLIVLVAHNDDPTDQLFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE IHRAIIVVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 78  DEPKIGIKTIKTYCQRMQEEKIHRAIIVVQQGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EK+ELLTRY
Sbjct: 138 NITEHELVPEHIVLTPDEKEELLTRY 163

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|48124579|ref|XP_396561.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Apis mellifera] gi|340724888|ref|XP_003400810.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Bombus terrestris] gi|380012055|ref|XP_003690105.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Apis florea]

 Score =  290 bits (741), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 138/146 (94%), Positives = 143/146 (97%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL+QFKEQFGDKPSEKRPARS+LIVLVAHNDDPTDQ+FVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEQFKEQFGDKPSEKRPARSDLIVLVAHNDDPTDQLFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE IHRAIIVVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 78  DEPKIGIKTIKTYCQRMQEEKIHRAIIVVQQGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EK+ELLTRY
Sbjct: 138 NITEHELVPEHIVLTPDEKEELLTRY 163

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357609342|gb|EHJ66401.1| hypothetical protein KGM_04074 [Danaus plexippus]

 Score =  290 bits (741), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 136/146 (93%), Positives = 141/146 (96%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPS+KRPARS+LIVLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSDKRPARSDLIVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DE KIGIKTIKTYC RMQEE IHRAI+VVQ GMTPSAKQSLVDMAPKYILE+FLESELLI
Sbjct: 78  DEAKIGIKTIKTYCTRMQEENIHRAIVVVQAGMTPSAKQSLVDMAPKYILEHFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EKQELL RY
Sbjct: 138 NITEHELVPEHIVLTPDEKQELLARY 163

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350422012|ref|XP_003493028.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Bombus impatiens]

 Score =  290 bits (741), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 138/146 (94%), Positives = 143/146 (97%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL+QFKEQFGDKPSEKRPARS+LIVLVAHNDDPTDQ+FVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEQFKEQFGDKPSEKRPARSDLIVLVAHNDDPTDQLFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE IHRAIIVVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 78  DEPKIGIKTIKTYCQRMQEEKIHRAIIVVQQGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EK+ELLTRY
Sbjct: 138 NITEHELVPEHIVLTPDEKEELLTRY 163

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022832|gb|EGI63105.1| DNA-directed RNA polymerases I, II, and III subunit RPABC1 [Acromyrmex echinatior]

 Score =  287 bits (734), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 137/146 (93%), Positives = 142/146 (97%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL+ FKEQFGDKPSEKRPARS+LIVLVAHNDDPTDQ+FVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLELFKEQFGDKPSEKRPARSDLIVLVAHNDDPTDQLFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE IHRAIIVVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 78  DEPKIGIKTIKTYCQRMQEEKIHRAIIVVQQGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EK+ELLTRY
Sbjct: 138 NITEHELVPEHIVLTPDEKEELLTRY 163

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383865249|ref|XP_003708087.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Megachile rotundata]

 Score =  287 bits (734), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 137/146 (93%), Positives = 142/146 (97%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL+QFKEQFGDKPSEKRPARS+LIVLVAHNDDPTDQ+FVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEQFKEQFGDKPSEKRPARSDLIVLVAHNDDPTDQLFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE IHRAIIVVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 78  DEPKIGIKTIKTYCQRMQEEKIHRAIIVVQQGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EK+ELL RY
Sbjct: 138 NITEHELVPEHIVLTPDEKEELLGRY 163

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322797006|gb|EFZ19320.1| hypothetical protein SINV_02648 [Solenopsis invicta]

 Score =  286 bits (733), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 136/146 (93%), Positives = 142/146 (97%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQ L+QFKEQFGDKPSEK+PARS+LIVLVAHNDDPTDQ+FVFFP
Sbjct: 19  MQLCHDRGYLVTQDELDQDLEQFKEQFGDKPSEKKPARSDLIVLVAHNDDPTDQLFVFFP 78

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE IHRAIIVVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 79  DEPKIGIKTIKTYCQRMQEEKIHRAIIVVQQGMTPSAKQSLVDMAPKYILEQFLESELLI 138

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EK+ELLTRY
Sbjct: 139 NITEHELVPEHIVLTPDEKEELLTRY 164

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|149287100|gb|ABR23449.1| 25-kDa subunit RNA polymerase [Ornithodoros parkeri]

 Score =  286 bits (733), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 135/146 (92%), Positives = 140/146 (95%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTLDQFK+QFGDKPSE+RPARS+LIVLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLDQFKQQFGDKPSERRPARSDLIVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           DEPKIGIKTIKTYCQRMQEE I RAIIVVQ GMTPSAKQ+L DMAPKYILEYFLESELLI
Sbjct: 78  DEPKIGIKTIKTYCQRMQEENITRAIIVVQQGMTPSAKQALTDMAPKYILEYFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEH+VLTPEEK ELL RY
Sbjct: 138 NITEHELVPEHVVLTPEEKAELLARY 163

Source: Ornithodoros parkeri

Species: Ornithodoros parkeri

Genus: Ornithodoros

Family: Argasidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242247587|ref|NP_001156054.1| DNA-directed RNA polymerases I, II, and III subunit RPABC1-like [Acyrthosiphon pisum] gi|239793387|dbj|BAH72818.1| ACYPI000388 [Acyrthosiphon pisum]

 Score =  286 bits (731), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 137/146 (93%), Positives = 141/146 (96%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           MQLCHDRGYLVTQDELDQTL+QFKEQFGDKPSEKRP RS+LIVLVAHNDDPTDQMFVFFP
Sbjct: 18  MQLCHDRGYLVTQDELDQTLEQFKEQFGDKPSEKRPGRSDLIVLVAHNDDPTDQMFVFFP 77

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           +EPKIGIKTIKTYCQRMQEETI RAIIVVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct: 78  EEPKIGIKTIKTYCQRMQEETITRAIIVVQQGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NITEHELVPEHIVLTP+EKQELL RY
Sbjct: 138 NITEHELVPEHIVLTPDEKQELLCRY 163

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

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	536
FB|FBgn0033571	210	Rpb5 "Rpb5" [Drosophila melano	0.272	0.695	0.904	7.2e-68
ZFIN|ZDB-GENE-040801-83	210	polr2eb "polymerase (RNA) II (	0.272	0.695	0.849	1.2e-63
UNIPROTKB|F2Z4J4	210	POLR2E "DNA-directed RNA polym	0.272	0.695	0.835	3.3e-63
UNIPROTKB|E2R2E8	212	POLR2E "Uncharacterized protei	0.272	0.688	0.835	3.3e-63
UNIPROTKB|F6X571	210	POLR2E "Uncharacterized protei	0.272	0.695	0.835	3.3e-63
UNIPROTKB|I3LSI7	210	POLR2E "Uncharacterized protei	0.272	0.695	0.835	3.3e-63
UNIPROTKB|F1NHV9	215	POLR2E "Uncharacterized protei	0.272	0.679	0.835	4.2e-63
MGI|MGI:1913670	210	Polr2e "polymerase (RNA) II (D	0.272	0.695	0.828	4.2e-63
RGD|1589817	210	Polr2e "polymerase (RNA) II (D	0.272	0.695	0.828	4.2e-63
UNIPROTKB|Q5R587	210	POLR2E "DNA-directed RNA polym	0.272	0.695	0.828	6.9e-63

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

 Score = 689 (247.6 bits), Expect = 7.2e-68, P = 7.2e-68
 Identities = 132/146 (90%), Positives = 139/146 (95%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQL HDRGYLVTQDELDQTL+QFKE FGDKPSEKRPARS+LIVLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLSHDRGYLVTQDELDQTLEQFKEMFGDKPSEKRPARSDLIVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPKIGIKTIKTYC RMQEE IHRAI+VVQ GMTPSAKQSLVDMAPKYILE FLESELLI
Sbjct:    78 EEPKIGIKTIKTYCTRMQEENIHRAIVVVQGGMTPSAKQSLVDMAPKYILEQFLESELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EEKQELL+RY
Sbjct:   138 NITEHELVPEHVVMTVEEKQELLSRY 163

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

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

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

GO:0003677 "DNA binding" evidence=IEA

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

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

 Score = 649 (233.5 bits), Expect = 1.2e-63, P = 1.2e-63
 Identities = 124/146 (84%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTLD+F+ QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLDEFRSQFGDKPSEGRPRRNDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RAIIVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKMYCQRMQEENITRAIIVVQMGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEHIV+T EE  ELL RY
Sbjct:   138 NITEHELVPEHIVMTKEEVTELLARY 163

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

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

 Score = 645 (232.1 bits), Expect = 3.3e-63, P = 3.3e-63
 Identities = 122/146 (83%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   138 NITEHELVPEHVVMTKEEVTELLARY 163

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

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2R2E8 POLR2E "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 645 (232.1 bits), Expect = 3.3e-63, P = 3.3e-63
 Identities = 122/146 (83%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   138 NITEHELVPEHVVMTKEEVTELLARY 163

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F6X571 POLR2E "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 645 (232.1 bits), Expect = 3.3e-63, P = 3.3e-63
 Identities = 122/146 (83%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   138 NITEHELVPEHVVMTKEEVTELLARY 163

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LSI7 POLR2E "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 645 (232.1 bits), Expect = 3.3e-63, P = 3.3e-63
 Identities = 122/146 (83%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   138 NITEHELVPEHVVMTKEEVTELLARY 163

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

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

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 644 (231.8 bits), Expect = 4.2e-63, P = 4.2e-63
 Identities = 122/146 (83%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    23 MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 82

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct:    83 EEPKVGIKTIKMYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 142

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   143 NITEHELVPEHVVMTKEEVTELLARY 168

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

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

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

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

 Score = 644 (231.8 bits), Expect = 4.2e-63, P = 4.2e-63
 Identities = 121/146 (82%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKY+LE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   138 NITEHELVPEHVVMTKEEVTELLARY 163

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

 Score = 644 (231.8 bits), Expect = 4.2e-63, P = 4.2e-63
 Identities = 121/146 (82%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++FK QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKY+LE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYVLEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   138 NITEHELVPEHVVMTKEEVTELLARY 163

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=ISO;ISS

GO:0005634 "nucleus" evidence=IEA;ISO;ISS

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

 Score = 642 (231.1 bits), Expect = 6.9e-63, P = 6.9e-63
 Identities = 121/146 (82%), Positives = 132/146 (90%)

Query:     1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
             MQLCHDRGYLVTQDELDQTL++F+ QFGDKPSE RP R++L VLVAHNDDPTDQMFVFFP
Sbjct:    18 MQLCHDRGYLVTQDELDQTLEEFRAQFGDKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFP 77

Query:    61 DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
             +EPK+GIKTIK YCQRMQEE I RA+IVVQ GMTPSAKQSLVDMAPKYILE FL+ ELLI
Sbjct:    78 EEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLI 137

Query:   121 NITEHELVPEHIVLTPEEKQELLTRY 146
             NITEHELVPEH+V+T EE  ELL RY
Sbjct:   138 NITEHELVPEHVVMTKEEVTELLARY 163

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

---

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)
Q5R587	RPAB1_PONAB	No assigned EC number	0.8287	0.2723	0.6952	yes	N/A
Q80UW8	RPAB1_MOUSE	No assigned EC number	0.8287	0.2723	0.6952	yes	N/A
P19388	RPAB1_HUMAN	No assigned EC number	0.8287	0.2723	0.6952	yes	N/A
Q2T9T3	RPAB1_BOVIN	No assigned EC number	0.8219	0.2723	0.6952	yes	N/A
Q9N5K2	RPAB1_CAEEL	No assigned EC number	0.7534	0.2723	0.6919	yes	N/A
B0BNE2	RPAB1_RAT	No assigned EC number	0.8287	0.2723	0.6952	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	536
PLN03111	206	PLN03111, PLN03111, DNA-directed RNA polymerase II	4e-61
PTZ00061	205	PTZ00061, PTZ00061, DNA-directed RNA polymerase; P	3e-47
pfam03871	92	pfam03871, RNA_pol_Rpb5_N, RNA polymerase Rpb5, N-	3e-31
pfam01191	74	pfam01191, RNA_pol_Rpb5_C, RNA polymerase Rpb5, C-	3e-10
COG2012	80	COG2012, RPB5, DNA-directed RNA polymerase, subuni	2e-07
PRK09570	79	PRK09570, rpoH, DNA-directed RNA polymerase subuni	9e-07

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

 Score =  199 bits (509), Expect = 4e-61
 Identities = 72/146 (49%), Positives = 106/146 (72%), Gaps = 5/146 (3%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
           +++  DRGYLV+  EL+ TL +F+E+FG+KP      R +L +      DP+ ++ VFFP
Sbjct: 19  LEMLRDRGYLVSDSELNLTLSEFREKFGEKPK-----REDLRISAPKRSDPSKKILVFFP 73

Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
           +E K+G+KTIKTY +RM++E + RAI+V+Q+ +TP AKQ+L +   K+ +E F E+ELL+
Sbjct: 74  EEEKVGVKTIKTYAERMKDENVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLV 133

Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NIT+H LVP+H VLT EEK+ LL RY
Sbjct: 134 NITKHVLVPKHQVLTDEEKKTLLKRY 159

Length = 206

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

 Score =  163 bits (413), Expect = 3e-47
 Identities = 66/142 (46%), Positives = 98/142 (69%), Gaps = 5/142 (3%)

Query: 6   DRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDE-PK 64
           DRGY++T  E  +T   FKE+F     E    RS ++++ +H  DPT+++ V+F DE  K
Sbjct: 21  DRGYIITSQEKLETFATFKERF----EENERLRSRMLMVASHKTDPTNRIIVYFADETKK 76

Query: 65  IGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITE 124
            G+K I+   ++M+E  I RAI+V Q  +TP AK ++++ AP++I+E FLE+ELL+NIT+
Sbjct: 77  TGVKPIRELTEKMEEHDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITK 136

Query: 125 HELVPEHIVLTPEEKQELLTRY 146
           HELVP+HI LT +EK  LL RY
Sbjct: 137 HELVPKHIPLTDDEKLNLLQRY 158

Length = 205

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

 Score =  115 bits (291), Expect = 3e-31
 Identities = 33/78 (42%), Positives = 55/78 (70%), Gaps = 3/78 (3%)

Query: 1  MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFP 60
          M++  DRGYLVT++EL+ +L++FKE++        P RS+L       DDP+ +++VFF 
Sbjct: 18 MEMLRDRGYLVTEEELNLSLEEFKEKY---GDNGNPDRSKLTFSARPKDDPSGRIYVFFC 74

Query: 61 DEPKIGIKTIKTYCQRMQ 78
          +E K+G+KTI+T+ +RM+
Sbjct: 75 EEEKVGVKTIRTFVERMK 92

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

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

 Score = 56.0 bits (136), Expect = 3e-10
 Identities = 18/27 (66%), Positives = 24/27 (88%)

Query: 120 INITEHELVPEHIVLTPEEKQELLTRY 146
           +NIT+HELVP+H VL+ EEK++LL RY
Sbjct: 1   VNITKHELVPKHEVLSEEEKKKLLKRY 27

The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. Length = 74

>gnl|CDD|224923 COG2012, RPB5, DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 114 LESELLINITEHELVPEHIVLTPEEKQELLTRY 146
           +ES L  N+ +HELVPEH VL+ EE +E+L   
Sbjct: 1   MESMLKFNVLDHELVPEHEVLSEEEAKEVLKEL 33

Length = 80

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

 Score = 46.4 bits (111), Expect = 9e-07
 Identities = 13/27 (48%), Positives = 20/27 (74%)

Query: 120 INITEHELVPEHIVLTPEEKQELLTRY 146
            ++ +HELVPEH +L+ EE ++LL  Y
Sbjct: 4   FDVLDHELVPEHEILSEEEAKKLLKEY 30

Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	536
PTZ00061	205	DNA-directed RNA polymerase; Provisional	100.0
KOG3218|consensus	208		100.0
PLN03111	206	DNA-directed RNA polymerase II subunit family prot	100.0
PF03871	93	RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal do	99.87
PRK09570	79	rpoH DNA-directed RNA polymerase subunit H; Review	99.86
PF01191	74	RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal do	99.85
COG2012	80	RPB5 DNA-directed RNA polymerase, subunit H, RpoH/	99.84
PF04471	115	Mrr_cat: Restriction endonuclease; InterPro: IPR00	96.23

>PTZ00061 DNA-directed RNA polymerase; Provisional

Probab=100.00  E-value=8.8e-59  Score=438.30  Aligned_cols=173  Identities=38%  Similarity=0.642  Sum_probs=168.1

Q ss_pred             CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCC-CCCcchHHHHHHHHHHhh
Q psy5290           1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPD-EPKIGIKTIKTYCQRMQE   79 (536)
Q Consensus         1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpd-E~KVGVKtIRkyiErMkE   79 (536)
                      +|||+||||.|+++|++||+++|+++||+++    +.|++|+|++.+.+||+++|||||++ +++||+|+||+|+++|++
T Consensus        16 ~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~----~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~ir~~~~~~~~   91 (205)
T PTZ00061         16 CEMLEDRGYIITSQEKLETFATFKERFEENE----RLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKPIRELTEKMEE   91 (205)
T ss_pred             HHHHhccCCccCHHHHcCCHHHHHHHhccCc----ccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHHHHHHHHHHhh
Confidence            5999999999999999999999999999874    57999999999999999999999998 569999999999999999


Q ss_pred             cCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccC
Q psy5290          80 ETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKR  159 (536)
Q Consensus        80 ENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~t  159 (536)
                      +|++|+|||+|++|||+||++|.+++++++||+|+|+|||||||+|+|||||++||+|||++||++|+++++|||||+.+
T Consensus        92 ~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~~~qLPrI~~~  171 (205)
T PTZ00061         92 HDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRIQSA  171 (205)
T ss_pred             cCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCCHHHCCccccc
Confidence            99999999999999999999999999889999999999999999999999999999999999999999999999999999


Q ss_pred             CcccccccccCCccCcEEecC
Q psy5290         160 TGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       160 DPvavfvk~iGAKpGDVVrv~  180 (536)
                      ||+   ++++|+|+||||+|.
T Consensus       172 DPv---ary~g~k~G~vvkI~  189 (205)
T PTZ00061        172 DPV---ARYFGLSKGQVVKII  189 (205)
T ss_pred             Chh---hHhcCCCCCCEEEEE
Confidence            999   999999999999984

>KOG3218|consensus

Probab=100.00  E-value=1.2e-58  Score=436.16  Aligned_cols=173  Identities=54%  Similarity=0.866  Sum_probs=170.2

Q ss_pred             CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhc
Q psy5290           1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEE   80 (536)
Q Consensus         1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEE   80 (536)
                      |||||||||.|+++|++++|++|+++||+++    ++|++|+|+|.|++||+++|||||+++++||||+||.|+.+|+++
T Consensus        20 ~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~----p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~k~~~~~~~~~   95 (208)
T KOG3218|consen   20 MQMLRDRGYTVTQEELDLTLEEFKARYGDKM----PDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTMKTYVIQMQSE   95 (208)
T ss_pred             HHHHHhcCccccHHHhhhhHHHHHHHhccCC----cchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHHHHHHHHHHhc
Confidence            6999999999999999999999999999975    789999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCC
Q psy5290          81 TIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRT  160 (536)
Q Consensus        81 NI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tD  160 (536)
                      |++++|||+|++||++|++++.+++++|.||+|+|+||+||||+|+|||||++||+|||++||++|+++++|||+|+..|
T Consensus        96 ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~e~qLPRIq~~D  175 (208)
T KOG3218|consen   96 NIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLKETQLPRIQKKD  175 (208)
T ss_pred             CceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCCcccCCeeeccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccCCccCcEEecC
Q psy5290         161 GEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       161 Pvavfvk~iGAKpGDVVrv~  180 (536)
                      |+   ++++|+|-|+||+|-
T Consensus       176 pv---aRYyGLKrGqVVKI~  192 (208)
T KOG3218|consen  176 PV---ARYYGLKRGQVVKII  192 (208)
T ss_pred             hH---HhhhccccCcEEEEE
Confidence            99   999999999999984

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

Probab=100.00  E-value=1.7e-58  Score=436.60  Aligned_cols=172  Identities=43%  Similarity=0.733  Sum_probs=168.3

Q ss_pred             CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhc
Q psy5290           1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEE   80 (536)
Q Consensus         1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEE   80 (536)
                      +|||+||||.|+++|++||+++|+++||++     ++|++|+|++.+++|++++|||||+++++||+|+||+|+++|+++
T Consensus        19 ~eMl~DRGY~V~~~el~~s~~~F~~~~~~~-----~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgvk~ir~~~~~~~~e   93 (206)
T PLN03111         19 LEMLRDRGYLVSDSELNLTLSEFREKFGEK-----PKREDLRISAPKRSDPSKKILVFFPEEEKVGVKTIKTYAERMKDE   93 (206)
T ss_pred             HHHHhccCCccCHHHHcCCHHHHHHHHcCC-----cCHHHcEeeeecCCCCCCcEEEEeCCCCccCHHHHHHHHHHHhhc
Confidence            599999999999999999999999999986     579999999999999999999999999999999999999999999


Q ss_pred             CCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCC
Q psy5290          81 TIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRT  160 (536)
Q Consensus        81 NI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tD  160 (536)
                      |++|+|||+|++|||+||+++.++++.++||+|+|+|||||||+|+|||||++||+|||++||++|+++++|||||+.+|
T Consensus        94 ~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~i~~~qLPrI~~~D  173 (206)
T PLN03111         94 NVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRIQVSD  173 (206)
T ss_pred             CcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcCCCHHHCCcccccC
Confidence            99999999999999999999999988899999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccCCccCcEEecC
Q psy5290         161 GEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       161 Pvavfvk~iGAKpGDVVrv~  180 (536)
                      |+   ++++|+|+||||+|.
T Consensus       174 Pv---ary~g~k~G~vvkI~  190 (206)
T PLN03111        174 PI---ARYYGLKRGQVVKII  190 (206)
T ss_pred             hh---hHhcCCCCCCEEEEE
Confidence            99   999999999999984

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

Probab=99.87  E-value=2.5e-23  Score=174.67  Aligned_cols=76  Identities=50%  Similarity=1.109  Sum_probs=62.0

Q ss_pred             CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHh
Q psy5290           1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQ   78 (536)
Q Consensus         1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMk   78 (536)
                      +|||+||||.|+++|++||+++|+++||+++  +.++|++|+|.+.+.+||+++|+|||+++++||+|+||+|+++|+
T Consensus        18 ~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~--~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~kvgvk~Ir~~~~~m~   93 (93)
T PF03871_consen   18 MEMLRDRGYLVSEEELNMSLEEFKEKYGENP--GNPDRERLTISASKRDDPSDKIFVFFPEEPKVGVKTIRKYCERMK   93 (93)
T ss_dssp             CCCCCCCTEE--CCCCS--HHHHHHHCB-SS--SSB-GCCT-EEEEESCHT--EEEEEE-SSSCESCCCCHHHCHHH-
T ss_pred             HHHHhcCCCccChhhhcCCHHHHHHHHcccC--CCCCHHHeeeeccCCCCCCCeEEEEeCCCCCcCHHHHHHHHHhcC
Confidence            6999999999999999999999999999864  358999999999999999999999999999999999999999985

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

>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed

Probab=99.86  E-value=1.7e-22  Score=168.43  Aligned_cols=59  Identities=25%  Similarity=0.338  Sum_probs=57.5

Q ss_pred             eeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290         119 LINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       119 LVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      .+|||+|+|||+|++||+||+++||++|+++++|||||+.+||+   ++++|||+||||+|.
T Consensus         3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv---~r~~g~k~GdVvkI~   61 (79)
T PRK09570          3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPV---VKAIGAKPGDVIKIV   61 (79)
T ss_pred             ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceeccChh---hhhcCCCCCCEEEEE
Confidence            58999999999999999999999999999999999999999999   999999999999984

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

Probab=99.85  E-value=3.9e-22  Score=164.33  Aligned_cols=58  Identities=31%  Similarity=0.371  Sum_probs=49.8

Q ss_pred             eccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290         120 INITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       120 VNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      +|||+|+|||+|++||+||+++||++|+++++|||||+.+||+   ++++|||+||||+|.
T Consensus         1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv---~r~~g~k~GdVvkI~   58 (74)
T PF01191_consen    1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSSDPV---ARYLGAKPGDVVKII   58 (74)
T ss_dssp             S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHH---HHHTT--TTSEEEEE
T ss_pred             CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCcccccChh---hhhcCCCCCCEEEEE
Confidence            6999999999999999999999999999999999999999999   999999999999985

7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....

>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]

Probab=99.84  E-value=8.6e-22  Score=164.77  Aligned_cols=63  Identities=30%  Similarity=0.312  Sum_probs=60.8

Q ss_pred             ecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290         115 ESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       115 EsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      ++.+.+|+++|+|||+|++|++||++++|++|+|+++|||||+.+||+   ++++|||+||||+|-
T Consensus         2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPv---a~~lgak~GdvVkIv   64 (80)
T COG2012           2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPV---AKALGAKPGDVVKIV   64 (80)
T ss_pred             ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcccccChh---HHHccCCCCcEEEEE
Confidence            567899999999999999999999999999999999999999999999   999999999999984

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

Probab=96.23  E-value=0.013  Score=47.42  Aligned_cols=75  Identities=19%  Similarity=0.326  Sum_probs=42.0

Q ss_pred             EEEeecCCCCCCceEEEeCC-CCCcchHHHHHHHHHHhhcCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeeccee
Q psy5290          42 IVLVAHNDDPTDQMFVFFPD-EPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELL  119 (536)
Q Consensus        42 tfsashkdDPTdKIfVFFpd-E~KVGVKtIRkyiErMkEENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELL  119 (536)
                      -+.+.+.+....+++|.+-. ..+++.+.|+.++..+...+..++|||+.+.+|+.|++.+....   .|+++..++|.
T Consensus        37 Di~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~~~~~~~~~iivt~~~~t~~a~~~~~~~~---~I~l~d~~~L~  112 (115)
T PF04471_consen   37 DIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKAKKYGADKGIIVTSSGFTPEAKEFAEKFK---NIELIDGEDLQ  112 (115)
T ss_dssp             EEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHHGGGT-SEEEEE-SSEE-HHHHHHHH-----------------
T ss_pred             EEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhhhccCCCEEEEEECCcCCHHHHHHHHhhc---ccccccccccc
Confidence            34444433233467777643 35899999999999999999999999999999999998876542   57777776664

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	536
3h0g_E	210	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		5e-25
1dzf_A	215	Rpb5 From S.Cerevisiae Length = 215		3e-23

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

Iteration: 1
 Score =  112 bits (280), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 59/146 (40%), Positives = 87/146 (59%), Gaps = 3/146 (2%)
Query: 2   QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVA-HNDDPTDQMFVFFP 60
           QL HDRGY V+Q ELD TLDQFK         +   R+ L       ND     +++ F 
Sbjct: 20  QLVHDRGYGVSQAELDLTLDQFKAMHCGMG--RNLDRTTLSFYAKPSNDSNKGTIYIEFA 77
Query: 61  DEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLI 120
            EP +GIK ++T+   + +      I++    MTPSA + +  +  ++ +E F ES+L++
Sbjct: 78  KEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIV 137
Query: 121 NITEHELVPEHIVLTPEEKQELLTRY 146
           NIT HELVP+HI+L+P+EK+ELL RY
Sbjct: 138 NITHHELVPKHILLSPDEKKELLDRY 163

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

Iteration: 1
 Score =  106 bits (264), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 94/155 (60%), Gaps = 17/155 (10%)
Query: 2   QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQ------- 54
           ++  DRGY +TQ+E++  L+ FK ++ D  S  RP R     +++   +PT++       
Sbjct: 21  EMVKDRGYFITQEEVELPLEDFKAKYCD--SMGRPQRK----MMSFQANPTEESISKFPD 74
Query: 55  ---MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILE 111
              ++V F DEP +G+KT+KT+   +QE+     I V Q  +TPSA + LV   P   +E
Sbjct: 75  MGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMK-LVPSIPPATIE 133
Query: 112 YFLESELLINITEHELVPEHIVLTPEEKQELLTRY 146
            F E+ L++NIT HELVP+HI L+ +EK+ELL RY
Sbjct: 134 TFNEAALVVNITHHELVPKHIRLSSDEKRELLKRY 168

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	536
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	9e-46
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	1e-39
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	2e-10
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	3e-09
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	4e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

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

 Score =  159 bits (402), Expect = 9e-46
 Identities = 58/147 (39%), Positives = 86/147 (58%), Gaps = 3/147 (2%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQM-FVFF 59
            QL HDRGY V+Q ELD TLDQFK             R+ L      ++D      ++ F
Sbjct: 19  HQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLD--RTTLSFYAKPSNDSNKGTIYIEF 76

Query: 60  PDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELL 119
             EP +GIK ++T+   + +      I++    MTPSA + +  +  ++ +E F ES+L+
Sbjct: 77  AKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLI 136

Query: 120 INITEHELVPEHIVLTPEEKQELLTRY 146
           +NIT HELVP+HI+L+P+EK+ELL RY
Sbjct: 137 VNITHHELVPKHILLSPDEKKELLDRY 163

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

 Score =  142 bits (359), Expect = 1e-39
 Identities = 57/152 (37%), Positives = 88/152 (57%), Gaps = 9/152 (5%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDP------TDQ 54
            ++  DRGY +TQ+E++  L+ FK ++ D  S  RP R  +       ++          
Sbjct: 20  KEMVKDRGYFITQEEVELPLEDFKAKYCD--SMGRPQRKMMSFQANPTEESISKFPDMGS 77

Query: 55  MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFL 114
           ++V F DEP +G+KT+KT+   +QE+     I V Q  +TPSA + +    P   +E F 
Sbjct: 78  LWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLV-PSIPPATIETFN 136

Query: 115 ESELLINITEHELVPEHIVLTPEEKQELLTRY 146
           E+ L++NIT HELVP+HI L+ +EK+ELL RY
Sbjct: 137 EAALVVNITHHELVPKHIRLSSDEKRELLKRY 168

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

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 115 ESELLINITEHELVPEHIVLTPEEKQELLTRY 146
            S   I+   H LVP+H VL+ +E  ++L   
Sbjct: 4   SSNRKIDPRIHYLVPKHEVLSIDEAYKILKEL 35

>1eik_A RNA polymerase subunit RPB5; RPBH, OCSP, NESG, protein structure initiative, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.78.1.1 Length = 77

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 10/29 (34%), Positives = 17/29 (58%)

Query: 118 LLINITEHELVPEHIVLTPEEKQELLTRY 146
           +   I +H+LVPEH++L   E + +L   
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKEL 29

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

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 12/27 (44%), Positives = 20/27 (74%)

Query: 120 INITEHELVPEHIVLTPEEKQELLTRY 146
           + +T+H LVP+H ++  EE +E+L RY
Sbjct: 1   MKVTDHILVPKHEIVPKEEVEEILKRY 27

>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 = 58.3 bits (140), Expect = 5e-09
 Identities = 51/297 (17%), Positives = 93/297 (31%), Gaps = 80/297 (26%)

Query: 13  QDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTD-----QMFVFFPDEPKIGI 67
           +D L  T D +K    DK +      S L VL     +P +          FP    I  
Sbjct: 338 RDGLA-TWDNWKHVNCDKLTTII--ESSLNVL-----EPAEYRKMFDRLSVFPPSAHIPT 389

Query: 68  KTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPK----YILEYFLESELLI-NI 122
             +      + +         V   +    K SLV+  PK     I   +LE ++ + N 
Sbjct: 390 ILLSLIWFDVIKS-------DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE 442

Query: 123 TE-HELVPEHIVLTPEEKQELLT-----RYWRSCVTIFWTQKRTGEEHF---LKECSFES 173
              H  + +H  +      + L      +Y+      +         H    LK      
Sbjct: 443 YALHRSIVDHYNIPKTFDSDDLIPPYLDQYF------YS--------HIGHHLKNIE--- 485

Query: 174 ATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFLPQGL-STPESHPPVSPSIDTM-- 230
                     +  +F++    +FL        +  FL Q +     +       ++T+  
Sbjct: 486 -------HPERMTLFRM----VFL--------DFRFLEQKIRHDSTAWNASGSILNTLQQ 526

Query: 231 LRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTN-GKSLKQGVPLTDIPVMAFYTKHE 286
           L+ Y+      +   + P        + DFL    ++L      TD+  +A   + E
Sbjct: 527 LKFYKP-----YICDNDPKYERLVNAILDFLPKIEENLICS-KYTDLLRIALMAEDE 577

>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 = 55.2 bits (132), Expect = 4e-08
 Identities = 67/448 (14%), Positives = 124/448 (27%), Gaps = 150/448 (33%)

Query: 32  SEKRPARSELIVLVA--HNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIH-RAIIV 88
                  + L +L    +  DP            K+ I +I+   +R+ +   +   ++V
Sbjct: 190 KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249

Query: 89  VQTGMTPSAKQSLVDMAPKYILEYF-LESELLI--------------NITEHELVPEHIV 133
                       L+++        F L  ++L+                T   L    + 
Sbjct: 250 ------------LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297

Query: 134 LTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQ 193
           LTP+E + LL +         +   R  +   L     E   V +  P   + I + ++ 
Sbjct: 298 LTPDEVKSLLLK---------YLDCRPQD---LPR---E---VLTTNPRRLSIIAESIRD 339

Query: 194 PLFLLVKTSDRANAVFLPQGLSTPESHPPVSPSIDTMLRSYEERHSLVFSLAHFPFKHFK 253
            L     T D    V   +  +  ES      S++  L   E R  +   L+ FP     
Sbjct: 340 GL----ATWDNWKHVNCDKLTTIIES------SLNV-LEPAEYRK-MFDRLSVFP-PSAH 386

Query: 254 --EVTLG------------DFLT--NGKSL--KQGVPLTDIPVMAFYTKHELDELKPFFK 295
              + L               +   +  SL  KQ    T        +   +        
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST-------ISIPSI-------- 431

Query: 296 FFYMGDLEVTANSVAQPNRKSSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYA 355
             Y+ +L+V   +    +R             +   YN  + + S D   P  +  Y Y 
Sbjct: 432 --YL-ELKVKLENEYALHRS------------IVDHYNIPKTFDS-DDLIPPYLDQYFY- 474

Query: 356 NRLPSSHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSV-------QQESRG 408
                         +              HH         +     V       +Q+ R 
Sbjct: 475 ------------SHIG-------------HHLKNIEHPERMTLFRMVFLDFRFLEQKIRH 509

Query: 409 VTPGGDKTAADLPVYS----YKGVPLYI 432
            +   + + + L        YK    YI
Sbjct: 510 DSTAWNASGSILNTLQQLKFYKP---YI 534

>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 = 44.1 bits (103), Expect = 1e-04
 Identities = 40/237 (16%), Positives = 73/237 (30%), Gaps = 73/237 (30%)

Query: 103 DMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGE 162
           +   K + +          +++ E+  +HI+++ +      T        +FWT     E
Sbjct: 32  NFDCKDVQDMPKSI-----LSKEEI--DHIIMSKDAVSG--TLR------LFWTLLSKQE 76

Query: 163 E---HFLKECSFESATVKSVYPSLKAPIFQLLQQP---LFLLVKTSDR---ANAVFLPQG 213
           E    F++E       ++  Y  L +PI    +QP     + ++  DR    N VF    
Sbjct: 77  EMVQKFVEE------VLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130

Query: 214 LSTPESHPPVSPSIDTMLRS--YEERHS---LVF--------SLA-----------HFPF 249
           +S  + +          LR    E R +   L+          +A              F
Sbjct: 131 VSRLQPY--------LKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182

Query: 250 KHF-----KEVTLGDFLTNGKSL-----KQGVPLTDIPVMAFYTKHEL-DELKPFFK 295
           K F        +    L   + L           +D         H +  EL+   K
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	536
3h0g_E	210	DNA-directed RNA polymerases I, II, and III subuni	100.0
1dzf_A	215	DNA-directed RNA polymerases I, II, and III 27 KD	100.0
1eik_A	77	RNA polymerase subunit RPB5; RPBH, OCSP, NESG, pro	99.89
1hmj_A	78	RPB5, protein (subunit H); RNA polymerase, archaea	99.86
4ayb_H	84	DNA-directed RNA polymerase; transferase, multi-su	99.85

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

Probab=100.00  E-value=6.8e-58  Score=431.70  Aligned_cols=176  Identities=34%  Similarity=0.557  Sum_probs=171.0

Q ss_pred             CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCC-CCceEEEeCCCCCcchHHHHHHHHHHhh
Q psy5290           1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDP-TDQMFVFFPDEPKIGIKTIKTYCQRMQE   79 (536)
Q Consensus         1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDP-TdKIfVFFpdE~KVGVKtIRkyiErMkE   79 (536)
                      +|||+||||.|+++|++||+++|+++||+++  +.++|++|+|.+.+++|| +++|||||+++++||+|+||+|+++|++
T Consensus        19 ~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~--~~~~r~~l~~~~~~~~dp~~~~i~VfF~~~~~vgvk~Ir~~~~~~~~   96 (210)
T 3h0g_E           19 HQLVHDRGYGVSQAELDLTLDQFKAMHCGMG--RNLDRTTLSFYAKPSNDSNKGTIYIEFAKEPSVGIKEMRTFVHTLGD   96 (210)
T ss_dssp             SSTTTTTTEECCTTTTSCCHHHHHHHSCCSS--SSCCCSSCCCEEEESSCSSCCCEEEECCCSSSCCTTTTGGGTHHHHH
T ss_pred             HHHhcCCCCccCHHHHhCCHHHHHHHhcccC--CCCCchheEEEEEcCCCCccCeEEEEECCCCccChHHHHHHHHHHHH
Confidence            6999999999999999999999999999874  458999999999999999 9999999999999999999999999999


Q ss_pred             cCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccC
Q psy5290          80 ETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKR  159 (536)
Q Consensus        80 ENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~t  159 (536)
                      +|++|+|||+|+++|++||+++.+++++++||+|+|+|||||||+|+|||+|++||+|||++||++|+|+++|||||+.+
T Consensus        97 en~~~~IiV~q~~~t~~A~~~l~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eE~~~lL~~y~i~~~qLP~I~~~  176 (210)
T 3h0g_E           97 HNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQLPRIQLA  176 (210)
T ss_dssp             TTCSEEEECCSSCCCSHHHHTTTTTCTTCEECCCCSSSSCSCTTSBTTBCCEECCCHHHHHHHHHHTCCCTTTSCCCCTT
T ss_pred             cCCceEEEEECCCCCHHHHHHHHHhCcCcEEEEEeehHeeEecccccccCcEEEcCHHHHHHHHHHcCCCHHHCCccccc
Confidence            99999999999999999999999999889999999999999999999999999999999999999999999999999999


Q ss_pred             CcccccccccCCccCcEEecCC
Q psy5290         160 TGEEHFLKECSFESATVKSVYP  181 (536)
Q Consensus       160 DPvavfvk~iGAKpGDVVrv~~  181 (536)
                      ||+   ++++|||+||||+|.-
T Consensus       177 DPv---~~~~g~k~GdVvkI~R  195 (210)
T 3h0g_E          177 DPV---ARYLGLKRGEVVKIVR  195 (210)
T ss_dssp             CHH---HHHHTCCTTCEEEEEC
T ss_pred             Ccc---hhhhCCCCCCEEEEEe
Confidence            999   9999999999999853

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

Probab=100.00  E-value=6.9e-57  Score=426.21  Aligned_cols=174  Identities=33%  Similarity=0.561  Sum_probs=168.7

Q ss_pred             CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCce------EEEeCCCCCcchHHHHHHH
Q psy5290           1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQM------FVFFPDEPKIGIKTIKTYC   74 (536)
Q Consensus         1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKI------fVFFpdE~KVGVKtIRkyi   74 (536)
                      +|||+||||.|+++|++||+++|+++||+.+  |.++|++|+|++.+++|+++++      ||||+++++||+|+||+|+
T Consensus        20 ~eMl~DRGY~v~~~e~~~sl~~F~~~~~~~~--g~p~r~~L~~~~~~~~d~~~k~~~~~~~~VfF~~~~~vgvk~ir~~~   97 (215)
T 1dzf_A           20 KEMVKDRGYFITQEEVELPLEDFKAKYCDSM--GRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFV   97 (215)
T ss_dssp             HHHHHHTTBCCCHHHHTCCHHHHHHHHBCTT--SCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECSSSEECHHHHHHHH
T ss_pred             HHHHhcCCCccCHhHhcCCHHHHHHHHcccc--CCCchhheEEEecCCCChhhhhccCCceEEEecCCCccchHHHHHHH
Confidence            5899999999999999999999999999853  5689999999999999999998      9999999999999999999


Q ss_pred             HHHhhcCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCcc
Q psy5290          75 QRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIF  154 (536)
Q Consensus        75 ErMkEENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLP  154 (536)
                      ++|+++|++|+|||+|+++||+||+++.++++ ++||+|+|+||+||||+|+|||||++||+|||++||++|+|+++|||
T Consensus        98 ~~~~~e~~~~~IlV~q~~itp~Ak~~l~~~~~-~~iE~F~e~eL~vni~~H~lVP~H~~l~~eE~~~lL~~y~i~~~qLP  176 (215)
T 1dzf_A           98 IHIQEKNFQTGIFVYQNNITPSAMKLVPSIPP-ATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLP  176 (215)
T ss_dssp             HHHHHTTCSEEEEEESSEECHHHHTTTTSSTT-CEEEEEEHHHHSSCGGGSTTSCEEEECCHHHHHHHHHHTTCCGGGSC
T ss_pred             HHHHhcCCceEEEEECCCCChHHHHHHHHhcC-ceEEEeehHHheeccccceeccceEEccHHHHHHHHHHcCCCHHHCC
Confidence            99999999999999999999999999999988 89999999999999999999999999999999999999999999999


Q ss_pred             ccccCCcccccccccCCccCcEEecC
Q psy5290         155 WTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       155 kIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      ||+.+||+   ++++|||+||||+|.
T Consensus       177 ~I~~~DPv---ar~~g~k~G~vvkI~  199 (215)
T 1dzf_A          177 RIQRADPV---ALYLGLKRGEVVKII  199 (215)
T ss_dssp             EECTTCHH---HHHHTCCTTCEEEEE
T ss_pred             ceeccChh---hHHhCCcCCCEEEEE
Confidence            99999999   999999999999984

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

Probab=99.89  E-value=5.4e-24  Score=175.49  Aligned_cols=60  Identities=18%  Similarity=0.243  Sum_probs=58.6

Q ss_pred             eeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290         118 LLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       118 LLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      |++|||+|+|||+|++||+|||++||++|+++++|||||+.+||+   ++++|||+||||+|-
T Consensus         1 l~vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLP~I~~~DPv---ar~~G~k~GdVvkI~   60 (77)
T 1eik_A            1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPV---AKAIGAKRGDIVKII   60 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTTSHH---HHGGGCCTTCEEEEE
T ss_pred             CcccCccceecCCEEEcCHHHHHHHHHHcCCCHHHCCeeeCcCHh---hHHhCCCCCCEEEEE
Confidence            789999999999999999999999999999999999999999999   999999999999984

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

Probab=99.86  E-value=5.6e-23  Score=169.87  Aligned_cols=58  Identities=26%  Similarity=0.358  Sum_probs=56.8

Q ss_pred             eccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290         120 INITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       120 VNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      ||||+|+|||+|++||+|||++||++|+++++|||||+.+||+   ++++|||+||||+|-
T Consensus         1 vnIt~H~LVPkH~iLs~eEk~~lL~~y~i~~~qLPrI~~~DPv---ar~~G~k~GdVvkI~   58 (78)
T 1hmj_A            1 MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPV---IQEIGAKEGDVVRVI   58 (78)
T ss_pred             CCccceeeCCCeEECCHHHHHHHHHHcCCCHHHCCeeeCcCHh---hHHhCCCCCCEEEEE
Confidence            7999999999999999999999999999999999999999999   999999999999984

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

Probab=99.85  E-value=1.4e-22  Score=168.83  Aligned_cols=63  Identities=19%  Similarity=0.237  Sum_probs=58.0

Q ss_pred             ecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290         115 ESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       115 EsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      .++++||||+|+|||+|++||+||+++||++|+|+.+|||+|+.+||+   ++++|+++||||+|.
T Consensus         4 ~~~~~~Ni~~H~LVPkH~vLs~eE~~~ll~~y~i~~~qLP~I~~~DPv---a~~~g~k~GdVvkI~   66 (84)
T 4ayb_H            4 SSNRKIDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPV---ARSINAKPGDIIRII   66 (84)
T ss_dssp             ----CCCCSSSSSCCEEEECCHHHHHHHHHHHTCCGGGSCCEESSSHH---HHHHTCCTTCEEEEE
T ss_pred             cccceecccccccCCCeEECCHHHHHHHHHHhcCCHhHCCeecccCHh---HHhhCCCCCCEEEEE
Confidence            467999999999999999999999999999999999999999999999   999999999999985

---

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	536
d1dzfa1	139	c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal doma	5e-49
d1eika_	77	d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA pol	1e-08
d1dzfa2	72	d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal do	3e-08

>d1dzfa1 c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 139

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Eukaryotic RPB5 N-terminal domain
family: Eukaryotic RPB5 N-terminal domain
domain: Eukaryotic RPB5 N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  163 bits (415), Expect = 5e-49
 Identities = 42/127 (33%), Positives = 68/127 (53%), Gaps = 9/127 (7%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDP------TDQ 54
            ++  DRGY +TQ+E++  L+ FK ++ D  S  RP R  +       ++          
Sbjct: 16  KEMVKDRGYFITQEEVELPLEDFKAKYCD--SMGRPQRKMMSFQANPTEESISKFPDMGS 73

Query: 55  MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFL 114
           ++V F DEP +G+KT+KT+   +QE+     I V Q  +TPSA + LV   P   +E F 
Sbjct: 74  LWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMK-LVPSIPPATIETFN 132

Query: 115 ESELLIN 121
           E+ L++N
Sbjct: 133 EAALVVN 139

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

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

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 10/29 (34%), Positives = 17/29 (58%)

Query: 118 LLINITEHELVPEHIVLTPEEKQELLTRY 146
           +   I +H+LVPEH++L   E + +L   
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKEL 29

>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 72

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: Eukaryotic RPB5 C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 48.5 bits (116), Expect = 3e-08
 Identities = 17/25 (68%), Positives = 21/25 (84%)

Query: 122 ITEHELVPEHIVLTPEEKQELLTRY 146
           IT HELVP+HI L+ +EK+ELL RY
Sbjct: 1   ITHHELVPKHIRLSSDEKRELLKRY 25

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	536
d1dzfa1	139	Eukaryotic RPB5 N-terminal domain {Baker's yeast (	100.0
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	99.82
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	99.75
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	99.52

>d1dzfa1 c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Eukaryotic RPB5 N-terminal domain
family: Eukaryotic RPB5 N-terminal domain
domain: Eukaryotic RPB5 N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.8e-35  Score=258.60  Aligned_cols=118  Identities=33%  Similarity=0.617  Sum_probs=110.0

Q ss_pred             CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCC------CCCceEEEeCCCCCcchHHHHHHH
Q psy5290           1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDD------PTDQMFVFFPDEPKIGIKTIKTYC   74 (536)
Q Consensus         1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdD------PTdKIfVFFpdE~KVGVKtIRkyi   74 (536)
                      +|||+||||.|+++|+++|+++|+++||+++  +.++|+.|+|.+.+.++      .+++|||||+++++||+|+||+|+
T Consensus        16 ~EMl~DRGY~V~~~el~~s~~~F~~~~~~~~--~~p~r~~l~~~~~~~~~~~~k~~~~~~I~V~F~~~~kvgvk~ir~~~   93 (139)
T d1dzfa1          16 KEMVKDRGYFITQEEVELPLEDFKAKYCDSM--GRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFV   93 (139)
T ss_dssp             HHHHHHTTBCCCHHHHTCCHHHHHHHHBCTT--SCBCGGGTCEEECBCHHHHHHCTTCCCEEEEECSSSEECHHHHHHHH
T ss_pred             HHHHhcCCCcCCHHHHcCCHHHHHHHHcccc--CCcCHHHhcccCCCchhhhhccCCCCeEEEEECCCCccCHHHHHHHH
Confidence            5999999999999999999999999999875  46999999999988654      467899999999999999999999


Q ss_pred             HHHhhcCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeec
Q psy5290          75 QRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLIN  121 (536)
Q Consensus        75 ErMkEENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVN  121 (536)
                      ++|+++|++|||||+|++|||+|+++|.++.+ ++||+|+|+|||||
T Consensus        94 ~~m~~~~~~r~IlV~q~~iTp~Ak~~i~~~~~-~~iE~F~e~eLLVN  139 (139)
T d1dzfa1          94 IHIQEKNFQTGIFVYQNNITPSAMKLVPSIPP-ATIETFNEAALVVN  139 (139)
T ss_dssp             HHHHHTTCSEEEEEESSEECHHHHTTTTSSTT-CEEEEEEHHHHSSC
T ss_pred             HHHHhcCCceEEEEECCCCCHHHHHHHHhccC-ceEEEechhhcccC
Confidence            99999999999999999999999999987754 89999999999998

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

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

Probab=99.82  E-value=2.7e-21  Score=156.30  Aligned_cols=60  Identities=18%  Similarity=0.243  Sum_probs=58.3

Q ss_pred             eeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290         118 LLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY  180 (536)
Q Consensus       118 LLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~  180 (536)
                      |.+||++|+|||+|++||+||++++|++|+++.+|||+|+.+||+   ++++|+++||||+|.
T Consensus         1 l~~NI~~H~lVPkH~il~~ee~~~~l~~~~i~~~qLP~I~~~DPv---a~~~g~k~GdvvkI~   60 (77)
T d1eika_           1 MKREILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPV---AKAIGAKRGDIVKII   60 (77)
T ss_dssp             CCCCCCSSSSCCEEEEECHHHHHHHHHHTTCCTTTSCCCBTTSHH---HHGGGCCTTCEEEEE
T ss_pred             CCccccccccCCCeEEcCHHHHHHHHHHhcCCHHHCCeecccCHh---hhhhCCcCCcEEEEE
Confidence            679999999999999999999999999999999999999999999   999999999999985

>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: Eukaryotic RPB5 C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.75  E-value=1.3e-19  Score=144.79  Aligned_cols=57  Identities=33%  Similarity=0.421  Sum_probs=55.1

Q ss_pred             cccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecCC
Q psy5290         122 ITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYP  181 (536)
Q Consensus       122 ITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~~  181 (536)
                      ||+|+|||+|++|++||++++|++|+++.+|||+|+.+||+   ++++|+++||||+|.-
T Consensus         1 It~H~lVPkH~~l~~eE~~~il~~y~i~~~qLP~I~~~DPv---a~~~g~~~GdvikI~R   57 (72)
T d1dzfa2           1 ITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPV---ALYLGLKRGEVVKIIR   57 (72)
T ss_dssp             GGGSTTSCEEEECCHHHHHHHHHHTTCCGGGSCEECTTCHH---HHHHTCCTTCEEEEEC
T ss_pred             CCcCccCCCeEEcCHHHHHHHHHHhCCCHhHCCeecccCHh---hhhcCCCCCCEEEEEE
Confidence            79999999999999999999999999999999999999999   9999999999999853

>d1hmja_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.52  E-value=1.4e-15  Score=120.24  Aligned_cols=50  Identities=22%  Similarity=0.261  Sum_probs=48.5

Q ss_pred             CceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecCC
Q psy5290         129 PEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYP  181 (536)
Q Consensus       129 PKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~~  181 (536)
                      |+|++||+||+++||++|+++.+|||+|+.+||+   ++++|+++||||+|.-
T Consensus         1 PkH~il~~eE~~~ll~~y~i~~~qLP~I~~~DPv---a~~~g~k~GdvvkI~R   50 (68)
T d1hmja_           1 PKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPV---IQEIGAKEGDVVRVIR   50 (68)
T ss_pred             CCCEECCHHHHHHHHHHhCCCHHHCCcccccCHH---HHHhCCCCCcEEEEEE
Confidence            8999999999999999999999999999999999   9999999999999864