Psyllid ID: psy7582

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------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-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-
LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRLK
ccccccHHccHHHHccccccHHHHHcHHHHHHHHHHHHHHccccEEEccccccccccccccccEEEEEcEEEEcccEEEcccccccccccHHHHcccccccccEEEEEEEEEEcccccccEEEEccEEEEccccEEcccccccccccHHHHHHccccccccccEEEEcccEEEEEEEccccccEEEEEEEccccccEEEEEEEEEcccccccEEEEEEEEEcccccccccccccEEEEEcccccccccHHHHHHHcccccHHHHHHHHHcccccHHHHHHHHccHHHHHccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHcccccEEccccccccHHHHHHHHHcccccHHccccccccccHHHHccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHcccccEEEccccccHHHHHHHHHcccccccccccccccccEEEEEccEEEEEEccHHHHHHHHHHHHHcccccccEEEEEEEccccEEEEEcccccccccEEEEEcccccccHHHHHHHHHcccccccHHHHHHcccEEEEEccccccEEEEEEHHccccccccccccccccccEEEEccccc
ccHHHHHHHHHHHHHHccHHHHHHccHHHHHHHHHHHHHHccccEEEcccccccccccccccEEEEEEEEEEEccccEEcccccccccccHHHHHHcccccccEEEEEEEEEEEccccccEEEcccEEEccEEEEEEccEEEcccccHHHHHHccccccccccEEEEEccHHEEEEHHHHcccEEEEEEccccccEEEEEEEEcccccccccEEEEEEEEccccccccccccccEEEEEcccccccccEEEEEEHccccccHHHHHHHccccccHHHHHHHcccHHHHHHHccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccEEEEEEcHHHHHHHHHHHHccccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHcccccccccccccccHcccccccEEcccccccccccHHHHHHHHHHEEccccccHHHHHHHHHcccccHHHccHHHccccEEEEEEcEEEEEcccHHHHHHHHHHHHHHcccccEEEEEEEEccccEEEEEcccccEEcEEEEEEcccEEEcHHHHHHHHHcccccccHHHHHHccEEEEEEccHHccEEEEEcHHHHHHHHccccccccccccEEEEccccc
LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIvedspqidLQAEAQhtstevetpprylLKFEQIYLskpthwekdgspspmmpnearlrnltysaplyvdITKTVVrqgeepvttqhqksfigkipIMLRSTYCLlngltdrdltelnecpldpggyfiinGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSclehssrptsTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHiiydfddpemmemvKPSLDEAFVIQEQNVALNFigargarpgvtkERRIKYAREILQkemlphvgvsdfcetKKAYFLGYMVHRLLLASLgrrelddrDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYslatgnwgdqkkahQARAGVSQVLNRLTFASSLshlrrvnspigrdgklakprqlhntlwgmicpaetpegaaVGLVKNLALMAYISvgsqpspiLEFLEEWSMENLEEIAPSAIADATKIFVNgcwvgihrdpeQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRihtdagricrPLLIAENGSLLLKKRhidnlkerdynnygwQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRLK
LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQhtstevetpprYLLKFEQIYLSKpthwekdgspspMMPNEARLRNLTYSAPLYVDITKTVVRqgeepvttqhqksfigkipiMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRsclehssrptsTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNfigargarpgvtkeRRIKYAREIlqkemlphvgvsdFCETKKAYFLGYMVHRLLLASLgrrelddrDHYVRMYAQKfidrgkdfNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFasslshlrrvnspigrdgklakPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLrrqmdiivsevsiirdirdreirihtdagricrplliaengsllLKKRHIDnlkerdynnygwQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLeeettmiamsprlk
LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSiirdirdreiriHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRLK
*WQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIV***********************RYLLKFEQIYLSK*******************LRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVN********LAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEE************
LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQ*****VETPPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQG****TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIR**************VNMMARGG****KSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGA**************YAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRR***************QLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPR**
LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQA**********TPPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNW************VSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRLK
LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAE****STEVETPPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLK*SAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPR**
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LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRLK
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query661 2.2.26 [Sep-21-2011]
P08266 1176 DNA-directed RNA polymera yes N/A 0.954 0.536 0.901 0.0
P30876 1174 DNA-directed RNA polymera yes N/A 0.977 0.550 0.846 0.0
Q8CFI7 1174 DNA-directed RNA polymera yes N/A 0.977 0.550 0.846 0.0
Q10578 1193 DNA-directed RNA polymera yes N/A 0.971 0.538 0.753 0.0
P38420 1188 DNA-directed RNA polymera yes N/A 0.945 0.526 0.619 0.0
Q42877 1191 DNA-directed RNA polymera N/A N/A 0.945 0.524 0.605 0.0
Q02061 1210 DNA-directed RNA polymera yes N/A 0.944 0.515 0.557 0.0
Q54J75 1170 DNA-directed RNA polymera yes N/A 0.931 0.526 0.585 0.0
A5DHT2 1236 DNA-directed RNA polymera N/A N/A 0.934 0.5 0.532 0.0
Q753Q4 1222 DNA-directed RNA polymera yes N/A 0.966 0.522 0.5 0.0
>sp|P08266|RPB2_DROME DNA-directed RNA polymerase II subunit RPB2 OS=Drosophila melanogaster GN=RpII140 PE=2 SV=2 Back     alignment and function desciption
 Score = 1226 bits (3173), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 592/657 (90%), Positives = 611/657 (92%), Gaps = 26/657 (3%)

Query: 1   LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
           LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSP I+LQAEAQHTS EVET
Sbjct: 22  LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVET 81

Query: 61  PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV 120
           PPR+ LKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKT   +G +PV
Sbjct: 82  PPRFSLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV 141

Query: 121 TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM 180
            TQHQK+FIGKIPIMLRSTYCLL+ LTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM
Sbjct: 142 ETQHQKTFIGKIPIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM 201

Query: 181 ATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAIL 240
           ATNTVYVFSMKD KYA+KTEIRSCLEHSSRPTSTLWVNMMARG Q++KKSAIGQRIIAIL
Sbjct: 202 ATNTVYVFSMKDGKYAFKTEIRSCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAIL 261

Query: 241 PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNF 300
           PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFV+QEQNVALNF
Sbjct: 262 PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNF 321

Query: 301 IGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRR 360
           IGARGARPGVTK++RIKYA+EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRR
Sbjct: 322 IGARGARPGVTKDKRIKYAKEILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRR 381

Query: 361 ELDDRDHY--------------------------VRMYAQKFIDRGKDFNLELAIKTKII 394
           ELDDRDHY                          VRMY QKFIDRGKDFNLELAIKT II
Sbjct: 382 ELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYTQKFIDRGKDFNLELAIKTNII 441

Query: 395 TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQ 454
           TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFAS+LSHLRRVNSPIGRDGKLAKPRQ
Sbjct: 442 TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPRQ 501

Query: 455 LHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSA 514
           LHNTLWGM+CPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSA
Sbjct: 502 LHNTLWGMLCPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSA 561

Query: 515 IADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGR 574
           IADATKIFVNGCWVGIHRDPEQLM TLRKLRRQMDIIVSEVS+IRDIRDREIRI+TDAGR
Sbjct: 562 IADATKIFVNGCWVGIHRDPEQLMATLRKLRRQMDIIVSEVSMIRDIRDREIRIYTDAGR 621

Query: 575 ICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAM 631
           ICRPLLI ENGSLLLKK H++ LKERDYNNY WQVLV SGVVEYIDTLEEET MIAM
Sbjct: 622 ICRPLLIVENGSLLLKKTHVEMLKERDYNNYSWQVLVASGVVEYIDTLEEETVMIAM 678
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 OS=Homo sapiens GN=POLR2B PE=1 SV=1 Back     alignment and function description
>sp|Q8CFI7|RPB2_MOUSE DNA-directed RNA polymerase II subunit RPB2 OS=Mus musculus GN=Polr2b PE=2 SV=2 Back     alignment and function description
>sp|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II subunit RPB2 OS=Caenorhabditis elegans GN=rpb-2 PE=2 SV=2 Back     alignment and function description
>sp|P38420|RPB2_ARATH DNA-directed RNA polymerase II subunit RPB2 OS=Arabidopsis thaliana GN=RPB135 PE=2 SV=2 Back     alignment and function description
>sp|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 PE=2 SV=1 Back     alignment and function description
>sp|Q02061|RPB2_SCHPO DNA-directed RNA polymerase II subunit RPB2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb2 PE=1 SV=2 Back     alignment and function description
>sp|Q54J75|RPB2_DICDI DNA-directed RNA polymerase II subunit rpb2 OS=Dictyostelium discoideum GN=polr2b PE=3 SV=1 Back     alignment and function description
>sp|A5DHT2|RPB2_PICGU DNA-directed RNA polymerase II subunit RPB2 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=RPB2 PE=3 SV=3 Back     alignment and function description
>sp|Q753Q4|RPB2_ASHGO DNA-directed RNA polymerase II subunit RPB2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB2 PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query661
324120648 1175 RNA polymerase II second largest subunit 0.954 0.537 0.933 0.0
324120650 1175 RNA polymerase II second largest subunit 0.954 0.537 0.931 0.0
324120622 1176 RNA polymerase II second largest subunit 0.954 0.536 0.919 0.0
324120628 1174 RNA polymerase II second largest subunit 0.954 0.537 0.917 0.0
324120604 1175 RNA polymerase II second largest subunit 0.954 0.537 0.917 0.0
324120610 1175 RNA polymerase II second largest subunit 0.954 0.537 0.916 0.0
324120606 1176 RNA polymerase II second largest subunit 0.954 0.536 0.914 0.0
324120608 1175 RNA polymerase II second largest subunit 0.954 0.537 0.914 0.0
324120652 1176 RNA polymerase II second largest subunit 0.954 0.536 0.914 0.0
324120630 1175 RNA polymerase II second largest subunit 0.954 0.537 0.913 0.0
>gi|324120648|dbj|BAJ78715.1| RNA polymerase II second largest subunit [Cryptotympana facialis] Back     alignment and taxonomy information
 Score = 1273 bits (3295), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 613/657 (93%), Positives = 625/657 (95%), Gaps = 26/657 (3%)

Query: 1   LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
           LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTS E+ET
Sbjct: 21  LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSGEIET 80

Query: 61  PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV 120
           PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKT+V++GE+P+
Sbjct: 81  PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTIVKEGEDPI 140

Query: 121 TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM 180
            TQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM
Sbjct: 141 ETQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM 200

Query: 181 ATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAIL 240
           ATNTVYVFSMKD K+AYK EIRSCLEHSSRPTSTLWVNMMARGGQS+KKSAIGQRIIAIL
Sbjct: 201 ATNTVYVFSMKDGKFAYKAEIRSCLEHSSRPTSTLWVNMMARGGQSIKKSAIGQRIIAIL 260

Query: 241 PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNF 300
           PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNF
Sbjct: 261 PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNF 320

Query: 301 IGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRR 360
           IGARGARPGVTKE+RIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLA+LGRR
Sbjct: 321 IGARGARPGVTKEKRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRR 380

Query: 361 ELDDRDHY--------------------------VRMYAQKFIDRGKDFNLELAIKTKII 394
           ELDDRDHY                          VRMYAQKFIDRGKDFNLELAIKTKII
Sbjct: 381 ELDDRDHYGNKRLDLAGPLLAFLFRGLFKNLMKEVRMYAQKFIDRGKDFNLELAIKTKII 440

Query: 395 TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQ 454
           TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFAS+LSHLRRVNSPIGRDGKLAKPRQ
Sbjct: 441 TDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRVNSPIGRDGKLAKPRQ 500

Query: 455 LHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSA 514
           LHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSA
Sbjct: 501 LHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSA 560

Query: 515 IADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGR 574
           IADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRI+TDAGR
Sbjct: 561 IADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIYTDAGR 620

Query: 575 ICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAM 631
           ICRPLLI ENGSLLLKKRHIDNLKERDYNNYGWQVLV SGVVEYIDTLEEETTMIAM
Sbjct: 621 ICRPLLIVENGSLLLKKRHIDNLKERDYNNYGWQVLVSSGVVEYIDTLEEETTMIAM 677

Source: Cryptotympana facialis

Species: Cryptotympana facialis

Genus: Cryptotympana

Family: Cicadidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|324120650|dbj|BAJ78716.1| RNA polymerase II second largest subunit [Anacanthocoris striicornis] Back     alignment and taxonomy information
>gi|324120622|dbj|BAJ78702.1| RNA polymerase II second largest subunit [Karoophasma biedouwense] Back     alignment and taxonomy information
>gi|324120628|dbj|BAJ78705.1| RNA polymerase II second largest subunit [Teleogryllus emma] Back     alignment and taxonomy information
>gi|324120604|dbj|BAJ78693.1| RNA polymerase II second largest subunit [Thermobia domestica] Back     alignment and taxonomy information
>gi|324120610|dbj|BAJ78696.1| RNA polymerase II second largest subunit [Mnais pruinosa pruinosa] Back     alignment and taxonomy information
>gi|324120606|dbj|BAJ78694.1| RNA polymerase II second largest subunit [Isolepisma japonica] Back     alignment and taxonomy information
>gi|324120608|dbj|BAJ78695.1| RNA polymerase II second largest subunit [Epiophlebia superstes] Back     alignment and taxonomy information
>gi|324120652|dbj|BAJ78717.1| RNA polymerase II second largest subunit [Bemisia tabaci] Back     alignment and taxonomy information
>gi|324120630|dbj|BAJ78706.1| RNA polymerase II second largest subunit [Oyamia lugubris] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query661
FB|FBgn0262955 1176 RpII140 "RNA polymerase II 140 0.556 0.312 0.934 2.6e-312
UNIPROTKB|A5PJW8 1174 POLR2B "DNA-directed RNA polym 0.556 0.313 0.891 1.2e-303
UNIPROTKB|E2RNN5 1174 POLR2B "DNA-directed RNA polym 0.556 0.313 0.891 1.2e-303
UNIPROTKB|C9J2Y9 1167 POLR2B "DNA-directed RNA polym 0.556 0.315 0.891 1.2e-303
UNIPROTKB|P30876 1174 POLR2B "DNA-directed RNA polym 0.556 0.313 0.891 1.2e-303
UNIPROTKB|I3LGP4 1167 POLR2B "DNA-directed RNA polym 0.556 0.315 0.891 1.2e-303
MGI|MGI:2388280 1174 Polr2b "polymerase (RNA) II (D 0.556 0.313 0.891 1.2e-303
RGD|1309477 1174 Polr2b "polymerase (RNA) II (D 0.556 0.313 0.891 1.2e-303
UNIPROTKB|F1NCB0 1174 POLR2B "DNA-directed RNA polym 0.556 0.313 0.885 6.8e-303
ZFIN|ZDB-GENE-041008-1 1117 polr2b "polymerase (RNA) II (D 0.556 0.329 0.888 2.9e-302
FB|FBgn0262955 RpII140 "RNA polymerase II 140kD subunit" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 1800 (638.7 bits), Expect = 2.6e-312, Sum P(2) = 2.6e-312
 Identities = 344/368 (93%), Positives = 357/368 (97%)

Query:     1 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
             LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSP I+LQAEAQHTS EVET
Sbjct:    22 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPAIELQAEAQHTSGEVET 81

Query:    61 PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV 120
             PPR+ LKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKT   +G +PV
Sbjct:    82 PPRFSLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTKNVEGLDPV 141

Query:   121 TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM 180
              TQHQK+FIGKIPIMLRSTYCLL+ LTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM
Sbjct:   142 ETQHQKTFIGKIPIMLRSTYCLLSQLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM 201

Query:   181 ATNTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAIL 240
             ATNTVYVFSMKD KYA+KTEIRSCLEHSSRPTSTLWVNMMARG Q++KKSAIGQRIIAIL
Sbjct:   202 ATNTVYVFSMKDGKYAFKTEIRSCLEHSSRPTSTLWVNMMARGSQNIKKSAIGQRIIAIL 261

Query:   241 PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNF 300
             PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFV+QEQNVALNF
Sbjct:   262 PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVVQEQNVALNF 321

Query:   301 IGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRR 360
             IGARGARPGVTK++RIKYA+EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRR
Sbjct:   322 IGARGARPGVTKDKRIKYAKEILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRR 381

Query:   361 ELDDRDHY 368
             ELDDRDHY
Sbjct:   382 ELDDRDHY 389
GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;NAS;IDA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS;NAS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS
GO:0003677 "DNA binding" evidence=IEA
GO:0032549 "ribonucleoside binding" evidence=IEA
UNIPROTKB|A5PJW8 POLR2B "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RNN5 POLR2B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|C9J2Y9 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P30876 POLR2B "DNA-directed RNA polymerase II subunit RPB2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3LGP4 POLR2B "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:2388280 Polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1309477 Polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1NCB0 POLR2B "DNA-directed RNA polymerase" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-041008-1 polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

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) ?
Q8SR75RPB2_ENCCU2, ., 7, ., 7, ., 60.50830.92130.5337yesN/A
B0R8D6RPOB2_HALS32, ., 7, ., 7, ., 60.32220.68070.8604yesN/A
Q8CFI7RPB2_MOUSE2, ., 7, ., 7, ., 60.84670.97730.5502yesN/A
P08266RPB2_DROME2, ., 7, ., 7, ., 60.90100.95460.5365yesN/A
P30876RPB2_HUMAN2, ., 7, ., 7, ., 60.84670.97730.5502yesN/A
P38420RPB2_ARATH2, ., 7, ., 7, ., 60.61910.94550.5260yesN/A
Q10578RPB2_CAEEL2, ., 7, ., 7, ., 60.75330.97120.5381yesN/A
Q54J75RPB2_DICDI2, ., 7, ., 7, ., 60.58500.93190.5264yesN/A
Q02061RPB2_SCHPO2, ., 7, ., 7, ., 60.55760.94400.5157yesN/A
P0CX04RPOB2_HALSA2, ., 7, ., 7, ., 60.32220.68070.8604yesN/A
Q58444RPOB2_METJA2, ., 7, ., 7, ., 60.33580.69280.9196yesN/A
P41558RPOB2_METVS2, ., 7, ., 7, ., 60.32440.69740.9238yesN/A
O27123RPOB2_METTH2, ., 7, ., 7, ., 60.32220.69890.8901yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.963
4th Layer2.7.7.60.946

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query661
PRK08565 1103 PRK08565, PRK08565, DNA-directed RNA polymerase su 1e-175
COG0085 1060 COG0085, RpoB, DNA-directed RNA polymerase, beta s 1e-134
pfam04563394 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub 1e-129
PRK09606494 PRK09606, PRK09606, DNA-directed RNA polymerase su 1e-121
cd00653 866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 2e-64
cd00653 866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 2e-56
pfam04561185 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do 2e-49
pfam0456663 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, do 1e-29
pfam0456568 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do 1e-25
TIGR03670 599 TIGR03670, rpoB_arch, DNA-directed RNA polymerase 8e-25
PRK07225 605 PRK07225, PRK07225, DNA-directed RNA polymerase su 5e-24
PRK00405 1112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 5e-11
TIGR02013 1065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 2e-10
CHL00207 1077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 8e-09
pfam0456746 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, do 3e-08
CHL00001 1070 CHL00001, rpoB, RNA polymerase beta subunit 2e-07
pfam0456746 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, do 4e-07
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 2e-06
CHL00001 1070 CHL00001, rpoB, RNA polymerase beta subunit 4e-05
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 2e-04
TIGR02013 1065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 4e-04
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information 
 Score =  529 bits (1364), Expect = e-175
 Identities = 248/655 (37%), Positives = 355/655 (54%), Gaps = 73/655 (11%)

Query: 7   WIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLL 66
           W V+ AYF EKGLVRQ LDS+++FI+  +Q IV++  +I           + E P    +
Sbjct: 2   WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEI-----------KTEIPG-LKI 49

Query: 67  KFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQK 126
              +I + +P   E DGS  P+ P EARLRNLTY+APLY+ +    V  G E      ++
Sbjct: 50  VLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMI--PVENGIEYEP---EE 104

Query: 127 SFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVY 186
             IG +PIM++S  C L+GL+  +L E+ E P DPGGYFIINGSE+V+++QE +A N V 
Sbjct: 105 VKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVL 164

Query: 187 VFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQE 246
           V   K    +  T     +   +   + + V     G            I    P +  +
Sbjct: 165 V--DKGEAGSSITHTAKVISSRAGYRAQVTVERRKDG-----------TIYVSFPAVPGK 211

Query: 247 IPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAF-VIQEQNVALNFIGARG 305
           IP +I+ RALG   DRDI+  +     DPE+ + + PSL++A  +      AL++IG R 
Sbjct: 212 IPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASSIAATVEDALDYIGKRV 268

Query: 306 ARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDR 365
           A  G  +E RI+ A +IL K +LPH+G S     KKAYFLG M  +LL   LGRRE DD+
Sbjct: 269 A-IGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDK 327

Query: 366 DHY--------------------------VRMYAQKFIDRGKDFNLELAIKTKIITDGLR 399
           DHY                          ++   +K   RG+  +L   ++  IIT+ +R
Sbjct: 328 DHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIR 387

Query: 400 YSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTL 459
           ++LATGNW         R GVSQ+L+R  + S+LSHLRRV SP+ R     + R LH T 
Sbjct: 388 HALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQ 441

Query: 460 WGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADAT 519
           WG ICP ETPEG   GLVKNLALMA ISVG     + E L E  +  +EE         +
Sbjct: 442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWS 501

Query: 520 KIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSI--IRDIRDREIRIHTDAGRICR 577
           ++++NG  +G H D E+L   +R+LRR    I  EV++  I      E+ ++ D+GR+ R
Sbjct: 502 RVYLNGRLIGYHPDGEELAEKIRELRRSGK-ISDEVNVAYIETGEINEVYVNCDSGRVRR 560

Query: 578 PLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMW 632
           PL++ ENG   L + H++ LK+ +     +  LV+ GV+EY+D  EEE   +A+ 
Sbjct: 561 PLIVVENGKPKLTREHVEKLKKGELT---FDDLVKMGVIEYLDAEEEENAYVALD 612

Length = 1103
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated Back     alignment and domain information
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2 Back     alignment and domain information
>gnl|CDD|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4 Back     alignment and domain information
>gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3 Back     alignment and domain information
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B Back     alignment and domain information
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional Back     alignment and domain information
>gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5 Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5 Back     alignment and domain information
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 661
KOG0214|consensus 1141 100.0
PRK08565 1103 DNA-directed RNA polymerase subunit B; Provisional 100.0
PRK09606494 DNA-directed RNA polymerase subunit B''; Validated 100.0
KOG0216|consensus 1111 100.0
KOG0215|consensus 1153 100.0
COG0085 1060 RpoB DNA-directed RNA polymerase, beta subunit/140 100.0
CHL00001 1070 rpoB RNA polymerase beta subunit 100.0
TIGR02013 1065 rpoB DNA-directed RNA polymerase, beta subunit. Th 100.0
PRK00405 1112 rpoB DNA-directed RNA polymerase subunit beta; Rev 100.0
cd00653 866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 100.0
CHL00207 1077 rpoB RNA polymerase beta subunit; Provisional 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PF04563203 RNA_pol_Rpb2_1: RNA polymerase beta subunit; Inter 100.0
PF0456568 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; Int 99.95
PRK07225 605 DNA-directed RNA polymerase subunit B'; Validated 99.82
TIGR03670 599 rpoB_arch DNA-directed RNA polymerase subunit B. T 99.81
PF04561190 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; Int 99.76
PF0456663 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; Int 99.75
KOG0215|consensus 1153 99.3
PF0456748 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int 98.7
PF0688358 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do 97.83
PF0456748 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int 96.7
TIGR02013 1065 rpoB DNA-directed RNA polymerase, beta subunit. Th 85.11
>KOG0214|consensus Back     alignment and domain information 
Probab=100.00  E-value=9.5e-142  Score=1160.45  Aligned_cols=623  Identities=74%  Similarity=1.132  Sum_probs=573.8

Q ss_pred             cccchhhhhhcccCccchhHHHHHHHHHHHHhchhhhhccCCccccccccccCCCCCCCCCeEEEEEeEEEEcCCcccCC
Q psy7582           2 WQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTHWEK   81 (661)
Q Consensus         2 ~~~~~~~~i~~~f~~~~l~~~qi~SFn~Fi~~gl~~iv~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~i~i~~P~~~~~   81 (661)
                      +|+++|.+|++||+.+||+++|++||+.|++.++++|+++.|+|+.+....+.   .+...++.|+|+.|++.+|+..|.
T Consensus         1 ~qe~~w~vis~~f~ekglvrqQldsFdeFiq~~~qeiv~~~p~i~l~~~~qh~---~~~~~r~~l~f~qiylskP~~~e~   77 (1141)
T KOG0214|consen    1 TQEDCWDVISAYFEEKGLVRQQLDSFDEFIQQTLQEIVADSPKIELQDEAQHT---QENPARYQLFFEQIYLSKPTHTES   77 (1141)
T ss_pred             ChhHHHHHHHhhhcccchHHHHHHHHHHHHHHHHHHHHhcCCCceehhhhhhh---ccCccceEEEeeeEEEeccccccc
Confidence            47899999999999999999999999999999999999999999987655432   233467999999999999999999


Q ss_pred             CCCCCCCChHHHHhcCCCccceEEEEEEEEEEcCCCcceeeeeEEEEeeccceeeccCccccCCCChhhhhhcCCCCCCC
Q psy7582          82 DGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDP  161 (661)
Q Consensus        82 ~~~~~~l~P~ecR~r~~TYs~~l~v~v~~~~~~~~~~~~~~~~~~v~lG~iPiMv~S~~C~L~~~~~~el~~~~E~~~d~  161 (661)
                      ||...+++|+|||+|++|||+||||++...+.....+....+..+|++|+||||+||.+|.|+++++++|.+++|||+|+
T Consensus        78 dg~~~~m~p~eARlrnLTYSspLyVd~~k~~~~~~~~~~~~~~qkvfIGkIPiMlrS~~C~l~~~~d~dl~~l~eCp~Dq  157 (1141)
T KOG0214|consen   78 DGSTSTMFPNEARLRNLTYSSPLYVDATKIVKTSRDEVEDMQEQKVFIGKIPIMLRSSYCLLSGLTDKDLTELGECPYDQ  157 (1141)
T ss_pred             CCCccccCchhhHhhhcccccceEEEeEEEEeeccccccccccceeeEeccceeeehhhhhhcccchhhhhhccCCCcCC
Confidence            99999999999999999999999999998765443222223467899999999999999999999999999999999999


Q ss_pred             CceEEEcCeeeEEEeeeeeecCeEEEEEecC-CceeEEEEEEEeecCCCcCcceEEEEEEecCCccccccccccEEEEEe
Q psy7582         162 GGYFIINGSEKVLIAQEKMATNTVYVFSMKD-SKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAIL  240 (661)
Q Consensus       162 GGYFIInG~EkVii~q~~~~~n~i~~~~~~~-~~~~~~~~irs~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~i~~~~  240 (661)
                      ||||||||+|||+|+||++++|++|+++... +.+.|.++|||+.|.++++.+++|+++...+.       .+..|.+.+
T Consensus       158 gGyfIINGseKVlIAQe~matn~vyvf~k~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~-------~gq~i~~tl  230 (1141)
T KOG0214|consen  158 GGYFIINGSEKVLIAQEKMATNIVYVFKKAHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAG-------KGQEIIATL  230 (1141)
T ss_pred             CceEEEcCceeeeeehhhccCceEEEEecCCCCceeEeeeeehhhhccCCCcceeeeeeccccC-------CCceEEEEe
Confidence            9999999999999999999999999998776 77899999999999999999999998875432       256889999


Q ss_pred             cccccccchhhHHHHcCCCChHHHHHHhccCCCChHHHHhhhhhhhhhhhccCHHHHHHHHHhcCCCCCCChhhhHHHHH
Q psy7582         241 PYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIKYAR  320 (661)
Q Consensus       241 ~~~~~~IP~~illkALg~~sd~eI~~~i~~~~~~~~~~~~l~~~~~~~~~~~t~~~al~yig~~~~~~~~~~~~~~~~~~  320 (661)
                      ++.+++||+++|+||||+.+|+||++.|+|+++|.++.++++++++|++.+..+..||+|||++...++.++++.+++|+
T Consensus       231 pyikqeIPI~ilfrALG~v~dreILehIcYd~~D~em~e~lkpsieeafviq~qn~ALdfig~rga~~Gvtkekri~yak  310 (1141)
T KOG0214|consen  231 PYIKQEIPILILFRALGFVSDREILEHICYDFDDAEMFESLKPSIEEAFVIQEQNVALDFIGQRGACIGVTKEKRIKYAK  310 (1141)
T ss_pred             eeecccCcEEEEehhhcCCccHHHHHhhcCCCCcHHHHHHhhhhhhhhhhhhhhHHHHHHHHhcCCCCCCCcchhhHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999998888899999999999


Q ss_pred             HHHHhccCCCCccCCccchhHHHHHHHHHHHHHhhccCCcCCCChHHH---------------HHH-----------HHH
Q psy7582         321 EILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHY---------------VRM-----------YAQ  374 (661)
Q Consensus       321 ~~l~~~~l~Hig~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~---------------~k~-----------~~~  374 (661)
                      ++|++++|||++.....+++|++||+|||++|+.++.|++.+||+|||               +|.           ..+
T Consensus       311 diLqKe~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~lfR~lf~~l~rd~~~~mQ  390 (1141)
T KOG0214|consen  311 EILQKELLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKLFRSLFAKLLRDVTRYMQ  390 (1141)
T ss_pred             HHHHHHhccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999988888999999999999999999999999999999               222           334


Q ss_pred             HHHhhCCCCchHHHhhhhccccchhhhcccCcchhhhccccccccceEEecccchhhhhhhccccCCCCCCCCCCCCccc
Q psy7582         375 KFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQ  454 (661)
Q Consensus       375 ~~~~~~~~~~~~~~i~~~~it~~i~~~lsTGn~~~~~~~~~~~~G~sq~l~r~N~l~~lSh~Rrv~~~~~~~~k~~~~R~  454 (661)
                      +.++++..+++.-+++.++||++++|++|||||+..++.++.++||||||+|+||+++|||+||+++|.++++|.+.||+
T Consensus       391 k~le~~~dfni~~aika~iIt~gl~yslaTgnwgdq~ka~~~ragVsQVLnR~t~~sTLsHlRR~n~Pigr~GKlAkpRq  470 (1141)
T KOG0214|consen  391 KCLENGVDFNIELAIKAKIITNGLNYALATGNWGDQKKAMQGRAGVSQVLNRLNPLSTLSHLRRTNSPIGRTGKLAKPRQ  470 (1141)
T ss_pred             HHHhcCccceEEEEEEeeeecccceeeeccCCccchhHHhhccccHHHHhccccHHHHHHHHhhcCCccccccccCCccc
Confidence            55567788898888999999999999999999987888888999999999999999999999999999999999999999


Q ss_pred             cCCCcccccccCCCCCCcccccccccccceEEeecCCCchHHHHhhhhccccccccCccccccccccccCCeEEEeeCCh
Q psy7582         455 LHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDP  534 (661)
Q Consensus       455 Lhps~wG~iCPveTPEG~~cGLv~~La~~a~Vs~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~  534 (661)
                      |||||||++||+|||||++||||||||+||.|++|+.+.|+.++|++.||++++.+++..+.+.++||+||.|+|.+++|
T Consensus       471 lHnthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~~datkvfvNG~wvGlhrdp  550 (1141)
T KOG0214|consen  471 LHNSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPSPDATKVFVNGVWVGLHRDP  550 (1141)
T ss_pred             cCcccceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcCCCceEEEEcccEEEecCCH
Confidence            99999999999999999999999999999999999999999999999999999999988888999999999999999999


Q ss_pred             hhHHHHHHHHhhcCCcccceEEEEecCcCCceEEecCCCcccceeEEeeCCcccccHHHHHHhhhcccCCcCceEEeecc
Q psy7582         535 EQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSG  614 (661)
Q Consensus       535 ~~~~~~lr~~rr~~~~i~~~v~~~~~~~~~~i~i~s~~gRl~RP~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~kg  614 (661)
                      +.++.+||.+||+ ..++.||++++|...++++||||+||+|||||+|+|+++.++++|+.+|++++             
T Consensus       551 ~~l~~tlr~lRR~-~di~~Evs~vRDIr~kE~ri~tDaGR~~rPLliven~~l~~~k~hi~~L~~~~-------------  616 (1141)
T KOG0214|consen  551 EELVATLKRLRRQ-FDIIAEVSMVRDIRDKEIRIFTDAGRSLRPLLIVENAKLLIKKRHIRALKQSK-------------  616 (1141)
T ss_pred             HHHHHHHHHHHHh-hccchhhhhhccccccceeeeeccCccccceEEEechhhhhhhHHHHHHhhCc-------------
Confidence            9999999999999 77777999999999999999999999999999999999999999999886521             


Q ss_pred             eeeeecccchhhhhhhhhhhhhccchhhccccceeeeeEEEeccCC
Q psy7582         615 VVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRL  660 (661)
Q Consensus       615 ~Ie~ld~~E~~~~~ia~~~~~l~~g~~e~~d~eEeet~~i~m~~~~  660 (661)
                            .+      -..|..++.+|++||+|+|||||+||||+|++
T Consensus       617 ------~~------~~~w~~lv~~G~ie~idteeEEtvmiam~~~d  650 (1141)
T KOG0214|consen  617 ------PN------EYRWAHLLSSGEVEYIDTEEEETVMIAMGPKD  650 (1141)
T ss_pred             ------hh------hcchhhhccccceeeeccchhhhHHHhcCHHH
Confidence                  11      25688999999999999999999999999874

>PRK08565 DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated Back     alignment and domain information
>KOG0216|consensus Back     alignment and domain information
>KOG0215|consensus Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>CHL00001 rpoB RNA polymerase beta subunit Back     alignment and domain information
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit Back     alignment and domain information
>PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit Back     alignment and domain information
>CHL00207 rpoB RNA polymerase beta subunit; Provisional Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated Back     alignment and domain information
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B Back     alignment and domain information
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA Back     alignment and domain information
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>KOG0215|consensus Back     alignment and domain information
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2 Back     alignment and domain information
>PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA Back     alignment and domain information
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query661
3h0g_B 1210 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 0.0
1i3q_B 1224 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 0.0
2waq_B 1131 The Complete Structure Of The Archaeal 13-Subunit D 7e-97
2pmz_B 1124 Archaeal Rna Polymerase From Sulfolobus Solfataricu 6e-94
1i6v_C 1118 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 6e-10
1ynj_C 1119 Taq Rna Polymerase-Sorangicin Complex Length = 1119 6e-10
1hqm_C 1119 Crystal Structure Of Thermus Aquaticus Core Rna Pol 6e-10
1l9u_C 1118 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 6e-10
1iw7_C 1119 Crystal Structure Of The Rna Polymerase Holoenzyme 4e-09
3iyd_C 1342 Three-Dimensional Em Structure Of An Intact Activat 4e-05
3lu0_C 1342 Molecular Model Of Escherichia Coli Core Rna Polyme 1e-04
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 Back     alignment and structure 
Iteration: 1

 Score =  736 bits (1901), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/685 (54%), Positives = 471/685 (68%), Gaps = 61/685 (8%)
Query: 1   LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
           L QE CW VI+++F+E  L RQQL SFDEF+Q ++Q IV+D   + L   AQHT  + + 
Sbjct: 12  LTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDV 71
Query: 61  PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV 120
             RY + F QIYLS+PT  E DGS + M P EARLRNLTYS+PLYVD+ K V+   +  V
Sbjct: 72  TRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNV 131
Query: 121 ------------TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIIN 168
                         +  K FIGKIPIMLRST+C+LNG++D +L +LNECP D GGYFIIN
Sbjct: 132 PIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIIN 191
Query: 169 GSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSL 227
           GSEKV+IAQE+ A N V VF     S  AY  EIRS LE  SR  S++ + +MAR  ++ 
Sbjct: 192 GSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTEN- 250
Query: 228 KKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDE 287
                GQ I A LPYI+ +IPI+IVFRALG V DRDILEHI YD +D +M+EM+KP ++E
Sbjct: 251 ----SGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEE 306
Query: 288 AFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGY 347
           AFVIQ++++AL++IG RG+  GVT+E+R++YA +ILQKE+LPH+   +  ET+KA+FLGY
Sbjct: 307 AFVIQDKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGY 366
Query: 348 MVHRLLLASLGRRELDDRDHY--------------------------VRMYAQKFIDRGK 381
           M+HR+LL +L RRE DDRDH+                          V  Y QK ++  +
Sbjct: 367 MIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNR 426
Query: 382 DFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNS 441
           +FNL LA+K+ IIT+GLRYSLATGNWGDQK++   R GVSQVLNR TFAS+LSHLRR N+
Sbjct: 427 EFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT 486
Query: 442 PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEE 501
           PIGRDGKLAKPRQLHNT WGM+CPAETPEG A GLVKNL+LM+Y+SVGS  +PI+EFLEE
Sbjct: 487 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEE 546
Query: 502 WSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSXXXXX 561
           W +E LE+  PSA  +ATK+FVNG W+G+HRDP  L  TLR LRR++D I +EVS     
Sbjct: 547 WGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLD-ISAEVSIVRDI 605
Query: 562 XXXXXXXHTDAGRICRPLLIAEN-------GSLLLKKRHIDNLKERDYNNY--------G 606
                   TDAGRICRPL I +N       G L ++K HI  L E D + Y        G
Sbjct: 606 REKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIE-DKDRYDIDPEQRFG 664
Query: 607 WQVLVQSGVVEYIDTLEEETTMIAM 631
           W  LV SG++EY+D  EEET MIAM
Sbjct: 665 WTALVSSGLIEYLDAEEEETVMIAM 689
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 Back     alignment and structure
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131 Back     alignment and structure
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 Back     alignment and structure
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 Back     alignment and structure
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex Length = 1119 Back     alignment and structure
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1119 Back     alignment and structure
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 Back     alignment and structure
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1119 Back     alignment and structure
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1342 Back     alignment and structure
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query661
3h0g_B 1210 DNA-directed RNA polymerase II subunit RPB2; trans 0.0
1twf_B 1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 0.0
4ayb_B 1131 DNA-directed RNA polymerase; transferase, multi-su 0.0
2a6h_C 1119 DNA-directed RNA polymerase beta chain; RNA polyme 2e-10
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 3e-10
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 1e-05
3mlq_A188 DNA-directed RNA polymerase subunit beta; tudor, t 1e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-06
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-06
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210 Back     alignment and structure
 Score =  935 bits (2417), Expect = 0.0
 Identities = 379/685 (55%), Positives = 477/685 (69%), Gaps = 59/685 (8%)

Query: 1   LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
           L QE CW VI+++F+E  L RQQL SFDEF+Q ++Q IV+D   + L   AQHT  + + 
Sbjct: 12  LTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDV 71

Query: 61  PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGE--- 117
             RY + F QIYLS+PT  E DGS + M P EARLRNLTYS+PLYVD+ K V+   +   
Sbjct: 72  TRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNV 131

Query: 118 ---------EPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIIN 168
                    E    +  K FIGKIPIMLRST+C+LNG++D +L +LNECP D GGYFIIN
Sbjct: 132 PIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIIN 191

Query: 169 GSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSL 227
           GSEKV+IAQE+ A N V VF     S  AY  EIRS LE  SR  S++ + +MAR     
Sbjct: 192 GSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMAR----- 246

Query: 228 KKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDE 287
                GQ I A LPYI+ +IPI+IVFRALG V DRDILEHI YD +D +M+EM+KP ++E
Sbjct: 247 NTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEE 306

Query: 288 AFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGY 347
           AFVIQ++++AL++IG RG+  GVT+E+R++YA +ILQKE+LPH+   +  ET+KA+FLGY
Sbjct: 307 AFVIQDKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGY 366

Query: 348 MVHRLLLASLGRRELDDRDHY--------------------------VRMYAQKFIDRGK 381
           M+HR+LL +L RRE DDRDH+                          V  Y QK ++  +
Sbjct: 367 MIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNR 426

Query: 382 DFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNS 441
           +FNL LA+K+ IIT+GLRYSLATGNWGDQK++   R GVSQVLNR TFAS+LSHLRR N+
Sbjct: 427 EFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT 486

Query: 442 PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEE 501
           PIGRDGKLAKPRQLHNT WGM+CPAETPEG A GLVKNL+LM+Y+SVGS  +PI+EFLEE
Sbjct: 487 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEE 546

Query: 502 WSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDI 561
           W +E LE+  PSA  +ATK+FVNG W+G+HRDP  L  TLR LRR+   I +EVSI+RDI
Sbjct: 547 WGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRR-LDISAEVSIVRDI 605

Query: 562 RDREIRIHTDAGRICRPLLIAEN-------GSLLLKKRHIDNLKER-------DYNNYGW 607
           R++E+R+ TDAGRICRPL I +N       G L ++K HI  L E            +GW
Sbjct: 606 REKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGW 665

Query: 608 QVLVQSGVVEYIDTLEEETTMIAMW 632
             LV SG++EY+D  EEET MIAM 
Sbjct: 666 TALVSSGLIEYLDAEEEETVMIAMS 690
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Length = 1224 Back     alignment and structure
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Length = 1131 Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 Back     alignment and structure
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} Length = 188 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query661
3h0g_B 1210 DNA-directed RNA polymerase II subunit RPB2; trans 100.0
1twf_B 1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 100.0
4ayb_B 1131 DNA-directed RNA polymerase; transferase, multi-su 100.0
2a6h_C 1119 DNA-directed RNA polymerase beta chain; RNA polyme 100.0
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 100.0
3mlq_A188 DNA-directed RNA polymerase subunit beta; tudor, t 99.97
3lti_A296 DNA-directed RNA polymerase subunit beta; BBM2, nu 98.51
3h0g_B 1210 DNA-directed RNA polymerase II subunit RPB2; trans 88.45
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=100.00  E-value=5.9e-144  Score=1278.09  Aligned_cols=636  Identities=60%  Similarity=0.989  Sum_probs=541.6

Q ss_pred             CcccchhhhhhcccCccchhHHHHHHHHHHHHhchhhhhccCCccccccccccCCCCCCCCCeEEEEEeEEEEcCCcccC
Q psy7582           1 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTHWE   80 (661)
Q Consensus         1 ~~~~~~~~~i~~~f~~~~l~~~qi~SFn~Fi~~gl~~iv~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~i~i~~P~~~~   80 (661)
                      +|++|+|.+|++||+.++|++|||||||+|+++||++|++++++++++.+.++.......+.++.|+|++++|++|++.+
T Consensus        12 ~~~ed~w~li~aff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~~e   91 (1210)
T 3h0g_B           12 LTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTMTE   91 (1210)
T ss_dssp             CCHHHHHHHHHHHHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCCBC
T ss_pred             CCHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHHhccCcEEecCccCcccccccCCceEEEEEEEEEEcCCceec
Confidence            46789999999999999999999999999999999999999999987653321111122345789999999999999998


Q ss_pred             CCCCCCCCChHHHHhcCCCccceEEEEEEEEEEcCCC---------c---ceeeeeEEEEeeccceeeccCccccCCCCh
Q psy7582          81 KDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGE---------E---PVTTQHQKSFIGKIPIMLRSTYCLLNGLTD  148 (661)
Q Consensus        81 ~~~~~~~l~P~ecR~r~~TYs~~l~v~v~~~~~~~~~---------~---~~~~~~~~v~lG~iPiMv~S~~C~L~~~~~  148 (661)
                      +++..+++||+|||+|++||+|||+|+|.+++.+..+         .   .......++.+|+|||||||++|||+++++
T Consensus        92 ~d~~~~~l~P~EcRlR~lTYsapl~Vdi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C~L~g~s~  171 (1210)
T 3h0g_B           92 ADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSD  171 (1210)
T ss_dssp             TTSCBCCCCTTTTTTTCCCCEEEEEEEEEC---------------------CCSSCCCEEEEEEECCSSSTTSSSSSCCH
T ss_pred             CCCcccccCHHHHHhcCCccceeEEEEEEEEEcCccccccccccccccccccccccceEEEecCCEEeCCCcccCCCCCH
Confidence            8888899999999999999999999999987643210         0   001123578999999999999999999999


Q ss_pred             hhhhhcCCCCCCCCceEEEcCeeeEEEeeeeeecCeEEEEEecC-CceeEEEEEEEeecCCCcCcceEEEEEEecCCccc
Q psy7582         149 RDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD-SKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSL  227 (661)
Q Consensus       149 ~el~~~~E~~~d~GGYFIInG~EkVii~q~~~~~n~i~~~~~~~-~~~~~~~~irs~~~~~~~~~~~~~l~~~~~g~~~~  227 (661)
                      +||+++||||+|+||||||||+||||++|+++|+|+++++.++. ++..+.|+|||++++.++....+.+++..++..  
T Consensus       172 ~eL~~~gEcp~D~GGYFIING~EKVII~qerla~N~~iv~~~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~~~~~~--  249 (1210)
T 3h0g_B          172 SELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE--  249 (1210)
T ss_dssp             HHHHHTTCCTTCCCCCBCGGGSCBCCCBCBCCCCSCCCCCCCCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCCCCCTT--
T ss_pred             HHHHhcCCCCCCCCCEEEEeCEEEEEEechhhccceEEEEeecCCCCceEEEEEEEEecCCccceeEEEEEEEecccc--
Confidence            99999999999999999999999999999999999999987654 344678899999987665544444555432210  


Q ss_pred             cccccccEEEEEecccccccchhhHHHHcCCCChHHHHHHhccCCCChHHHHhhhhhhhhhhhccCHHHHHHHHHhcCCC
Q psy7582         228 KKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGAR  307 (661)
Q Consensus       228 ~~~~~~~~i~~~~~~~~~~IP~~illkALg~~sd~eI~~~i~~~~~~~~~~~~l~~~~~~~~~~~t~~~al~yig~~~~~  307 (661)
                         ..++.+.+++++++.+||++++|||||.+||+||++.|+++..++.+.++|+++++++..++||++||+|||+++..
T Consensus       250 ---~~~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~~~i~tq~~aL~yIG~r~~~  326 (1210)
T 3h0g_B          250 ---NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGKRGST  326 (1210)
T ss_dssp             ---SCSCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTTSSCCSSHHHHHTTCCCSSS
T ss_pred             ---CCCceEEEEEeccccCCcHHHHHHHcCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHhhhcCCHHHHHHHHHHhccc
Confidence               02345778899999999999999999999999999999988889999999999999987789999999999999754


Q ss_pred             CCCChhhhHHHHHHHHHhccCCCCccCCccchhHHHHHHHHHHHHHhhccCCcCCCChHHH---------------HHHH
Q psy7582         308 PGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHY---------------VRMY  372 (661)
Q Consensus       308 ~~~~~~~~~~~~~~~l~~~~l~Hig~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~---------------~k~~  372 (661)
                      .+.+.+.++++|+++|++++|||+|....++.+|+.||++|+||||.++.|.+.+||+|||               +|..
T Consensus       327 ~~~~~~~~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~lfr~~  406 (1210)
T 3h0g_B          327 TGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRML  406 (1210)
T ss_dssp             CCCCHHHHHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHHHHHHH
T ss_pred             cCCCchhHHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHHHHHHHH
Confidence            4566777889999999999999999877777789999999999999999999999999999               2322


Q ss_pred             -----------HHHHHhhCCCCchHHHhhhhccccchhhhcccCcchhhhccccccccceEEecccchhhhhhhccccCC
Q psy7582         373 -----------AQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNS  441 (661)
Q Consensus       373 -----------~~~~~~~~~~~~~~~~i~~~~it~~i~~~lsTGn~~~~~~~~~~~~G~sq~l~r~N~l~~lSh~Rrv~~  441 (661)
                                 +++.+++.+.+++..+++.+.||++|+||||||||++.+++.++++||||+|+|+||+|+|||||||++
T Consensus       407 ~~~~~~~i~~~l~k~~~~~~~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~lShlRrv~~  486 (1210)
T 3h0g_B          407 FRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT  486 (1210)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHHHHHTTBBCC
T ss_pred             HHHHHHHHHHHHHHHhhcCCccCHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCCHHHHHHHHHhccC
Confidence                       223333556777778888889999999999999999899888999999999999999999999999999


Q ss_pred             CCCCCCCCCCccccCCCcccccccCCCCCCcccccccccccceEEeecCCCchHHHHhhhhccccccccCcccccccccc
Q psy7582         442 PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADATKI  521 (661)
Q Consensus       442 ~~~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~La~~a~Vs~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~~V  521 (661)
                      |+++++|+++||+||||||||+||+|||||++|||+||||++|.||++.+..||.++|.++||++++.+++....+.++|
T Consensus       487 p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le~~~~~~~~~~tkV  566 (1210)
T 3h0g_B          487 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSASPNATKV  566 (1210)
T ss_dssp             SCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCSCCCSSSSSSSCCC
T ss_pred             chhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHhCCcchhhcCcccCCCceEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999988777666788999


Q ss_pred             ccCCeEEEeeCChhhHHHHHHHHhhcCCcccceEEEEecCcCCceEEecCCCcccceeEEeeCC-------cccccHHHH
Q psy7582         522 FVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENG-------SLLLKKRHI  594 (661)
Q Consensus       522 ~lnG~~iG~~~~~~~~~~~lr~~rr~~~~i~~~v~~~~~~~~~~i~i~s~~gRl~RP~l~~~~~-------~~~~~~~~~  594 (661)
                      ||||+|+|++++|..|+++||.+||+ |.|+.+||+++|...++++||||+||+||||++|+|+       ++.++++|+
T Consensus       567 fvNG~wVGvh~dp~~Lv~~lR~lRR~-g~Is~eVSIvrdir~rE~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l~k~hi  645 (1210)
T 3h0g_B          567 FVNGVWLGVHRDPAHLTETLRSLRRR-LDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHI  645 (1210)
T ss_dssp             CSTTCCCCCCSCHHHHHHHHHHHHTT-TSSCTTCCCCCCTTTCCCCCCCSSCCBCCEEEECCCSSCSSSSCCCSSCHHHH
T ss_pred             EECCEEEEEeCCHHHHHHHHHHHhhc-CCCCCceEEEecCCCCeEEEecCCCcccceEEEEccCCcccccccccccHHHH
Confidence            99999999999999999999999999 9999999999999999999999999999999999986       899999999


Q ss_pred             HHhhhcccCCcCceEEeecceeeeecccchhhhhhhhhhhhhccchhhccccceeeeeEEEeccCC
Q psy7582         595 DNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRL  660 (661)
Q Consensus       595 ~~l~~~~~~~~~~~~ll~kg~Ie~ld~~E~~~~~ia~~~~~l~~g~~e~~d~eEeet~~i~m~~~~  660 (661)
                      ++|.++...  .              .++..  ....|.+++.+|+|||||||||||+||||+|++
T Consensus       646 ~~L~~~~~~--~--------------~~~~~--~~~~w~~Lv~~GvIEylDaeEEet~mIamtpeD  693 (1210)
T 3h0g_B          646 QQLIEDKDR--Y--------------DIDPE--QRFGWTALVSSGLIEYLDAEEEETVMIAMSPED  693 (1210)
T ss_dssp             HHHHHHHTC--C--------------CSCTT--CCCSSTTTTTTTSEEECCTTTGGGCCEESCHHH
T ss_pred             HHHhccccc--c--------------ccccc--ccCCHHHHHhCCCEEEecHhhhhceeEEecHHH
Confidence            888653110  0              01111  126799999999999999999999999999974
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Back     alignment and structure
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Back     alignment and structure
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Back     alignment and structure
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Back     alignment and structure
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} Back     alignment and structure
>3lti_A DNA-directed RNA polymerase subunit beta; BBM2, nucleotidyltransferase, transcription, transferase; HET: MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A Back     alignment and structure
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 661
d1twfb_ 1207 e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c 1e-179
d1smyc_ 1119 e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop 8e-73
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1207 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  539 bits (1390), Expect = e-179
 Identities = 343/688 (49%), Positives = 451/688 (65%), Gaps = 64/688 (9%)

Query: 1   LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
           +  E  W VI+A+F EKGLV QQLDSF++F+  ++Q I+ +   + L+  AQHT+     
Sbjct: 8   ITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNI 67

Query: 61  PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV 120
             +Y + F +IY++KP   E DG    + P EARLRNLTYS+ L+VD+ K      + P 
Sbjct: 68  SRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPG 127

Query: 121 --------------TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFI 166
                          ++  K FIG++PIMLRS  C L+  T+ DL +L ECP D GGYFI
Sbjct: 128 RELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFI 187

Query: 167 INGSEKVLIAQEKMATNTVYVF-SMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQ 225
           INGSEKVLIAQE+ A N V VF     S  ++  EIRS LE  SR  STL V +  R G 
Sbjct: 188 INGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGS 247

Query: 226 SLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSL 285
           S       + I A LPYIKQ+IPI+I+FRALG + D +ILEHI YD +D +M+EM+KP +
Sbjct: 248 S------ARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCV 301

Query: 286 DEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFL 345
           ++ FVIQ++  AL+FIG RG   G+ KE+RI+YA++ILQKE LPH+   +  E++KA+FL
Sbjct: 302 EDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFL 361

Query: 346 GYMVHRLLLASLGRRELDDRDHY--------------------------VRMYAQKFIDR 379
           GYM++RLLL +L R++ DDRDH+                          +  Y Q+ ++ 
Sbjct: 362 GYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEE 421

Query: 380 GKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRV 439
             DFN++LAI  K IT GL+Y+LATGNWG+QKKA  +RAGVSQVLNR T++S+LSHLRR 
Sbjct: 422 AHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRT 481

Query: 440 NSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFL 499
           N+PIGRDGKLAKPRQLHNT WG++CPAETPEG A GLVKNL+LM+ ISVG+ P PI+ FL
Sbjct: 482 NTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFL 541

Query: 500 EEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIR 559
            EW ME LE+  P    DAT++FVNG W G+HR+P +LM TLR LRR+ DI   EVS+IR
Sbjct: 542 SEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINP-EVSMIR 600

Query: 560 DIRDREIRIHTDAGRICRPLLIAEN------GSLLLKKRHIDNLKERDYNN--------- 604
           DIR++E++I TDAGR+ RPL I E+        L ++K HI  L   +Y +         
Sbjct: 601 DIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVE 660

Query: 605 -YGWQVLVQSGVVEYIDTLEEETTMIAM 631
            Y W  L+  G+VEYID  EEE+ +IAM
Sbjct: 661 EYTWSSLLNEGLVEYIDAEEEESILIAM 688
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query661
d1twfb_ 1207 RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyc_ 1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 100.0
>d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta
domain: RBP2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.8e-116  Score=1071.91  Aligned_cols=638  Identities=53%  Similarity=0.893  Sum_probs=500.6

Q ss_pred             CcccchhhhhhcccCccchhHHHHHHHHHHHHhchhhhhccCCccccccccccCCCCCCCCCeEEEEEeEEEEcCCcccC
Q psy7582           1 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTHWE   80 (661)
Q Consensus         1 ~~~~~~~~~i~~~f~~~~l~~~qi~SFn~Fi~~gl~~iv~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~i~i~~P~~~~   80 (661)
                      ++++|.|++|++||+.++|++|||+|||+||++||++|+++.+|+.+...............++.|+|++++|++|++.+
T Consensus         8 ~~~~d~w~~i~~~f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i~kP~~~e   87 (1207)
T d1twfb_           8 ITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNE   87 (1207)
T ss_dssp             CCTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEEEEEECC
T ss_pred             CCHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHCHHHHHHhcCCeEeeccccccccccCCCceEEEEEEEEEEcCCeEEc
Confidence            47889999999999999999999999999999999999999999987544332222223345788999999999999988


Q ss_pred             CCCCCCCCChHHHHhcCCCccceEEEEEEEEEEcCCC--------------cceeeeeEEEEeeccceeeccCccccCCC
Q psy7582          81 KDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGE--------------EPVTTQHQKSFIGKIPIMLRSTYCLLNGL  146 (661)
Q Consensus        81 ~~~~~~~l~P~ecR~r~~TYs~~l~v~v~~~~~~~~~--------------~~~~~~~~~v~lG~iPiMv~S~~C~L~~~  146 (661)
                      .++..+++||+|||+|++||+|+|+|+|++.+....+              .......++|++|+|||||+|++|||+++
T Consensus        88 ~~g~~~~l~P~EcR~r~lTYs~~l~v~i~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv~S~~C~L~~~  167 (1207)
T d1twfb_          88 SDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEA  167 (1207)
T ss_dssp             SSSCCEECCHHHHHHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTTSGGGTC
T ss_pred             CCCcccccCHHHHHhcCCccceEEEEEEEEEEEecccccccccceeecccccccceeeeeEEEEECCEEeCCCcccCCCc
Confidence            8888899999999999999999999999865321110              01122456899999999999999999999


Q ss_pred             ChhhhhhcCCCCCCCCceEEEcCeeeEEEeeeeeecCeEEEEEecC-CceeEEEEEEEeecCCCcCcceEEEEEEecCCc
Q psy7582         147 TDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKD-SKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQ  225 (661)
Q Consensus       147 ~~~el~~~~E~~~d~GGYFIInG~EkVii~q~~~~~n~i~~~~~~~-~~~~~~~~irs~~~~~~~~~~~~~l~~~~~g~~  225 (661)
                      +++++++.||||+|+||||||||+||||++|++.++|+++++..+. +++.+.++|||+.+++.+...++.+.+...   
T Consensus       168 ~~~~l~~~gEc~~D~GGYFIING~EKVIi~Q~r~~~n~~~v~~~~~~~~~~~~~~irS~~~~~~~~~~~~~~~~~~~---  244 (1207)
T d1twfb_         168 TESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGR---  244 (1207)
T ss_dssp             CHHHHHHTTCCTTCCCCSEEETTEEEEECEEEEECSSCCEEEECCTTSSEEEEEEEECCCSSSCCCCCEEEEEEESC---
T ss_pred             CHHHHHHcCCCCCCCCcEEEECCEEEEEEEEEecCCCeEEEEEcCCCCceEEEEEEEEEeCCCCceeEEEEEEEEEc---
Confidence            9999999999999999999999999999999999999999988654 456788999999987766655555544321   


Q ss_pred             cccccccccEEEEEecccccccchhhHHHHcCCCChHHHHHHhccCCCChHHHHhhhhhhhhhhhccCHHHHHHHHHhcC
Q psy7582         226 SLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARG  305 (661)
Q Consensus       226 ~~~~~~~~~~i~~~~~~~~~~IP~~illkALg~~sd~eI~~~i~~~~~~~~~~~~l~~~~~~~~~~~t~~~al~yig~~~  305 (661)
                         .......+.+.+++.+.+||+++||||||..+|+||++.++++..+..+.+.+..+++++..+.|+++||.|||+++
T Consensus       245 ---~~~~~~~i~~~~~~~~~~IPl~illrALG~~sD~eI~~~i~~~~~~~~~~~~l~~~~~~~~~~~t~e~al~yig~~~  321 (1207)
T d1twfb_         245 ---EGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRG  321 (1207)
T ss_dssp             ---SSCSSCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHTTTCCSHHHHHHHHHHTT
T ss_pred             ---CCccceEEEEEeehhcccchHHHHHHHhCCcchhhhhhhcccCchhhHHHHHHHHHHhhccchhhHHHHHHHHHhhc
Confidence               11122357788898888999999999999999999999999887787888888888888778899999999999986


Q ss_pred             CCCCCChhhhHHHHHHHHHhccCCCCccCCccchhHHHHHHHHHHHHHhhccCCcCCCChHHH---------------HH
Q psy7582         306 ARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGRRELDDRDHY---------------VR  370 (661)
Q Consensus       306 ~~~~~~~~~~~~~~~~~l~~~~l~Hig~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~---------------~k  370 (661)
                      .....+.+...+.++++|.+++|||++....+...|+.+|++|++||+.+..|.+.+||+|||               +|
T Consensus       322 ~~~~~~~~~~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~~~fr  401 (1207)
T d1twfb_         322 TALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFK  401 (1207)
T ss_dssp             SCTTSCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHHHHHH
T ss_pred             cccCCCccchHHHHHHHHHhhhccccccccchhhhHHHHHHHHHHHHHHhhhcccCCcchhhhccchhhhHHHHHHHHHH
Confidence            544445566788999999999999999766666789999999999999999999999999999               33


Q ss_pred             HHHHHHHh-----------hCCCCchHHHhhhhccccchhhhcccCcchhhhccccccccceEEecccchhhhhhhcccc
Q psy7582         371 MYAQKFID-----------RGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRV  439 (661)
Q Consensus       371 ~~~~~~~~-----------~~~~~~~~~~i~~~~it~~i~~~lsTGn~~~~~~~~~~~~G~sq~l~r~N~l~~lSh~Rrv  439 (661)
                      ..+++...           +.+.+++...++.+.||++|++||+||||++....+++++|+||+|+|+||+|++||+|||
T Consensus       402 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~it~~i~~~~~TGn~~~~~~~~~~~~G~sq~l~r~n~l~~lSh~Rrv  481 (1207)
T d1twfb_         402 TLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRT  481 (1207)
T ss_dssp             HHHHHHHHHHHHHHHSCCC--------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSSHHHHHHHHTEE
T ss_pred             HHHHHHHHHHHhhhccccccccccChhhhhccCcHHHHHHHHHhcCcccccccccccccchhhhhhhcCHHHHHHhhhcc
Confidence            33333321           1122334444566789999999999999987766667999999999999999999999999


Q ss_pred             CCCCCCCCCCCCccccCCCcccccccCCCCCCcccccccccccceEEeecCCCchHHHHhhhhccccccccCcccccccc
Q psy7582         440 NSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIAPSAIADAT  519 (661)
Q Consensus       440 ~~~~~~~~k~~~~R~Lhps~wG~iCPveTPEG~~cGLv~~La~~a~Vs~~~~~~~i~~~l~~~g~~~~~~~~~~~~~~~~  519 (661)
                      |+++++++|+++||+||||||||+||||||||+||||+||||++|+|+.+.+..++.+++..+|+.++.........+..
T Consensus       482 ~~~~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~  561 (1207)
T d1twfb_         482 NTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDAT  561 (1207)
T ss_dssp             ECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTTCEEGGGCCGGGCTTCE
T ss_pred             cCCcccccccchhhhcchhhccceeeeeCCCCCcccceeccceeeeeccccccceeeEEeeccCcccceeeeeccccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999887665555556778


Q ss_pred             ccccCCeEEEeeCChhhHHHHHHHHhhcCCcccceEEEEecCcCCceEEecCCCcccceeEEeeCCc------ccccHHH
Q psy7582         520 KIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENGS------LLLKKRH  593 (661)
Q Consensus       520 ~V~lnG~~iG~~~~~~~~~~~lr~~rr~~~~i~~~v~~~~~~~~~~i~i~s~~gRl~RP~l~~~~~~------~~~~~~~  593 (661)
                      +||+||.|+|+++++..+++.+|.+||. |.++.++++.++....+++|+||+||++|||+.++|+.      ..+.+.+
T Consensus       562 ~V~~nG~~~G~~~~~~~l~~~lr~~R~~-g~i~~~~s~~~~~~~~~i~i~td~Gr~~rPlfi~~nd~~~~~~~~~mqrq~  640 (1207)
T d1twfb_         562 RVFVNGVWHGVHRNPARLMETLRTLRRK-GDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGH  640 (1207)
T ss_dssp             EEEETTEEEEEESCHHHHHHHHHHHHHH-TSSCTTCEEEEETTTTEEEEECCSCCEEEEEEEEECCCTTSSCEESCCHHH
T ss_pred             eeeeeeeEEEEEcchheeehheeeeeec-cCccceeeeeeeccccceEEEecCccccCCceeecchhhhcccceeeeHhh
Confidence            9999999999999999999999999999 99999999999988999999999999999988877753      2244444


Q ss_pred             HHHhhhcccCCcCceEEeecceeeeecccchhhhhhhhhhhhhccchhhccccceeeeeEEEeccCC
Q psy7582         594 IDNLKERDYNNYGWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTMIAMSPRL  660 (661)
Q Consensus       594 ~~~l~~~~~~~~~~~~ll~kg~Ie~ld~~E~~~~~ia~~~~~l~~g~~e~~d~eEeet~~i~m~~~~  660 (661)
                      +..|...+.              ..++...+ ......|...+.+|+|||+|++|++.++||++|+.
T Consensus       641 v~~l~~~e~--------------~~v~~~~e-~~~~~~~~~~~~~g~ieyid~~E~~~~~Ia~~~~~  692 (1207)
T d1twfb_         641 IAKLMATEY--------------QDIEGGFE-DVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPED  692 (1207)
T ss_dssp             HHHHHHHHH--------------CC----------CCCHHHHHHTTSEEEEEHHHHTTCCEESSGGG
T ss_pred             Hhhhhcccc--------------cccccccc-chhhccccccccCCceeeecchhcceEEEEecccc
Confidence            443322111              01111111 11123466777889999999999999999988753
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure