Citrus Sinensis ID: 002545

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 (MEMSAT_SVM) ?
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-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910
MARKKSADFEPLRELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKEE
cccccccccHHHHcccccccccHHHHHHHHHHHHHHHHHHcccccccEEEEEEEEEEEcccccEEEEEEEEccccEEEcccccccccccHHHHHHccccccccccEEEEccccccccccHHHccccccccEEEEEEcccccEEEEEEEEEEEcccccEEEEEEEEEEcccEEEEEEEcccccccHHHHHHHHcccccHHHHHHHHccccccHHHHHccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccHHHHHHHHHHcccccccccccccccccEEEEcccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHcccEEEcccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEEEEccEEEEEEEccHHHHHHHHHHHcccccccccccccEEEEEEccccccccEEEEEEccccccccEEEccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccHHcccccccccccccccccccccccccccEEEEEEEcccccccHHHHHcccccccccEEEEEEEEEEEEEcccccccccccccccccccccccccccccccccccccEEcccccEEEEEccccccEEEEEEcccccEEEEEEEEEEcccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccEEEccccccccccHHHHHHHHHcccc
cHHHHHHHHHHHHccHHHHHHHHHHHHHcccccccHHHHHccccccccEEEEEEEEEEccccEEEEEEEEEcccEEEEEccccccccccHHHHHHccccccccccEEEEccHHHHHHHHHHHHHcccccEEEEEEcccccccEEEEEEEEEEccccccEEEEEEEEccccEEEEEEEccccccccEEEEEEHcccccHHHHHHHHHccccHHccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccEcccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHccccHHHHHHHHHHHcccccccccccHHHHccHHHHHHHHHHHHHHHHHHHHccHHHHcccccccHHHHccccccEEcccccccccccHHHHHHHHEEEEEccccccHHHHHHHHHcccHHHHHHHcccccccHccccccccccEEEEEccEEEEEcccHHHHHHHHHHHHHcccccccccccEEEEEEcccccccccEEEEEcccccEEEEEEEEcccccccccEEEcccEEEEEEEEEcccccccccccccccEEEEEcHHHHHHHHHccccccccccccccHHHHHHHHHHccccHHHHHHHccccEEEEEccccccEccHHHHHcccccccccccEEEEEEEEccccHHHEEEEEHHHHHccccEEEEEEEEEEEEccccccccccccccccccccccHHHHccccccccccEEEccccEEEEEEccccccccEEEEccccccEEEEEEEEEcccccccEEEEEEEEEccccccccccccccccccEEEEEEccccccccccccccccEEEcccccccHHHHHHHHHHHHcccc
markksadfepLRELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFqyldagspvvrerfnfgqfpvMLKTrrchlqgadsqKLVSLKEEAAEMGGYFILNGLERVFrsvilpkqnypmsmvrssfrdrregytdkaVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTccydekykkekgavgsplVSERVKIILAEVQDLSLTTRLQCLQHIGEhfqpvidglqsesYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLvdhtsvsdnpdslqnqeillPGHLITIYLKEKLEDWLRKGKKLIQDEIEnngkkfdffnLANIKKVmeknpskqigTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHrgasfaglrTTSVRKllpeswgflcpvhtpdgepcgllnhmtstcrvasyydsrgnirdfSKMRTSILRVLIGvgmipslpklvksgppavLSVLLdgrvvgvipsSEIEKVVAHLRRLKVSaasvipddlevgyvplslggaypglylftsppkfvrpvrnislpseesqnieligpfeQVFMeircpdggdggrrnafpatheeihptgmLSVVanltpysdhnqsprnmyqcqmakqtMGFSVQALKFRAdqklyhlqtpqtpivrtntytkygideyptgTNAIVAVLAYTgydmedamilnkssvdrgmchgqiyqtetidlsddgnkvdrgqklfrrnkdakslhsvidsdglpyvgqmihpgepycsiydkttnswrtnsrkgsesVFVDYVAVdmknsknlpqkanirfrhtrnpiigdkfssrhgqkgvcsqlwpdidmpfsgvtgmrpdliinphafpsRMTIAMLLESVAAKEE
markksadfeplrELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVIlpkqnypmsmvrssfrdrregytdkavvircvrkdqssvtlKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDekykkekgavgsplVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQdeienngkkfdffNLANIKKVmeknpskqigtSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYdsrgnirdfSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVsaasvipddleVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKlyhlqtpqtpivrtNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQtetidlsddgnkVDRGQKLfrrnkdakslhsvidsdglPYVGQMIHPGEPYCSIYDKTTNswrtnsrkgseSVFVDYVAVdmknsknlpqkanirfrhtRNPIigdkfssrhgqKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKEE
MARKKSADFEPLRELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKEE
************RELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSV******LQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVM*********TSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL******NIELIGPFEQVFMEIRCPDG***************IHPTGMLSVVANLTP**********MYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDL***********************HSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRT******ESVFVDYVAVDMK********ANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLL********
******A**EPLRELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDK*****************LYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHR***********VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTET**************************HSVIDSDGLPYVGQMIHPGEPYCSIYDKTT******SRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK**
*********EPLRELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKEE
MARKKSADFEPLRELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDD***VDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK**
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MARKKSADFEPLRELVRHHIESFDYMLDEGLSEMFDHCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKEE
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 ?
Query910 2.2.26 [Sep-21-2011]
Q9P7X8 1174 Probable DNA-directed RNA yes no 0.896 0.695 0.434 0.0
Q75DS1 1196 DNA-directed RNA polymera yes no 0.917 0.698 0.448 0.0
O74633 1234 DNA-directed RNA polymera N/A no 0.914 0.674 0.430 0.0
P22138 1203 DNA-directed RNA polymera yes no 0.917 0.694 0.436 0.0
Q54BM1 1130 DNA-directed RNA polymera yes no 0.956 0.769 0.400 0.0
P70700 1135 DNA-directed RNA polymera yes no 0.935 0.749 0.408 0.0
Q9H9Y6 1135 DNA-directed RNA polymera yes no 0.942 0.755 0.405 0.0
Q5REE8 1136 DNA-directed RNA polymera yes no 0.942 0.755 0.407 0.0
O54888 1135 DNA-directed RNA polymera yes no 0.918 0.736 0.381 1e-175
P28365 1166 DNA-directed RNA polymera N/A no 0.946 0.738 0.376 1e-172
>sp|Q9P7X8|RPA2_SCHPO Probable DNA-directed RNA polymerase I subunit RPA2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpa2 PE=3 SV=2 Back     alignment and function desciption
 Score =  733 bits (1893), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 393/905 (43%), Positives = 557/905 (61%), Gaps = 89/905 (9%)

Query: 38  CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLK 97
            R+   +Y  +L+  ++F +   G P   E    G  P+M+++ RCHL+G    +L++ K
Sbjct: 106 ARERLTTYKSRLV--LKFSWSVNGGPRQSEMREVGMIPIMVRSNRCHLEGLSPAELIAHK 163

Query: 98  EEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQS 157
           EE+ EMGGYFI+NG+E++ R +ILPK+N+P +++R SF +R   Y+   + IRCVR DQS
Sbjct: 164 EESEEMGGYFIVNGIEKLIRMLILPKRNHPTAIIRPSFANRGTSYSQYGLSIRCVRPDQS 223

Query: 158 SVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEK 217
           S+T  L+YL NG     F  +  EYL+P  ++LKAL++T+D EIF  +            
Sbjct: 224 SLTNTLHYLNNGVTMFRFHWRKNEYLIPSMMILKALLETSDKEIFEGIV----------G 273

Query: 218 GAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD 277
             +G+  +++RV+++L   +   L ++ + LQ++G  F+ V+   +  +   V   +++ 
Sbjct: 274 KDLGNTFLTDRVELMLRAYKSYGLYSQTETLQYLGSKFRVVLGVAEDLTDVEVGRFLLQK 333

Query: 278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLE 337
            + VHL +  DKF LL+FM++KL++LV     +DNPDS Q+QEILL G L    LKEK+E
Sbjct: 334 VVLVHLREAKDKFRLLLFMIRKLYALVAGECCADNPDSPQHQEILLGGFLYGQILKEKIE 393

Query: 338 DWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGL 397
           DWL   +  I  ++  +    DF +   + +V  K  +  IGT ++  L TG L + TGL
Sbjct: 394 DWLNSIRAQINLDVRRSAPGVDFSDRKYLTRVFSK-INNDIGTKLQYFLSTGNLVSNTGL 452

Query: 398 DLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDG 457
           DLQQ  GYTV AE+LNF RF+S FR VHRGA FA L+TT+VRKLLPE+WGF+CPVHTPDG
Sbjct: 453 DLQQATGYTVVAEKLNFYRFLSHFRMVHRGAFFAELKTTTVRKLLPEAWGFMCPVHTPDG 512

Query: 458 EPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL 517
            PCGLLNH+   C + ++                       V  IPSL   +   PP+V+
Sbjct: 513 SPCGLLNHLARKCEIVTHPSD--------------------VSQIPSLLLSLGVDPPSVV 552

Query: 518 S-------VLLDGRVVGVIPSSEIEKVVAHLRRLKVSAA-----------SVIPDDLEVG 559
                   V LDG++VG       + V   LR +K+  A           + +P DLE+G
Sbjct: 553 GHESGWGCVQLDGKIVGWCTYKLAKHVADVLRLMKIEYAVKLRNGTATEPAKVPLDLEIG 612

Query: 560 YVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDG 619
           YVP S  G YPGLYLF++P + VRPV++IS     +  ++++GPFEQV+M+I C      
Sbjct: 613 YVPPSHNGQYPGLYLFSNPARMVRPVKHIS-----TGELDMLGPFEQVYMDIAC------ 661

Query: 620 GRRNAFP-------ATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQ 672
                FP       +TH E  PT +LS+VAN+TP+SD NQSPRNMYQCQM KQTMG    
Sbjct: 662 -----FPKEIVPKVSTHVEYSPTNVLSIVANMTPFSDFNQSPRNMYQCQMGKQTMGTPGT 716

Query: 673 ALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNK 732
           AL++R D KLY LQT QTP+VR   +  YG+D YP GTNA+VAV++YTGYDMEDAMILNK
Sbjct: 717 ALRYRTDNKLYRLQTGQTPVVRPKLHNTYGLDHYPNGTNAVVAVISYTGYDMEDAMILNK 776

Query: 733 SSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDA------KSLHSVIDSDGLPY 786
           S+ +RG  +G +Y+ E+ DLS    K  RG+ +      A      +     +D+DGLP+
Sbjct: 777 SAHERGFGYGTVYKGESFDLS---QKRRRGEPVVHHFGFAPGSTPRREWLQKLDADGLPF 833

Query: 787 VGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAV---DMKNSKNLPQKANIRFR 843
           +G  +  G+P  + YD++T      +  G+E  FVD V +   D+ +S+   Q+ +++ R
Sbjct: 834 IGIKLEDGDPIVAYYDESTGQNFIETYHGTEPGFVDEVRLLGNDVGDSEC--QQIHVKLR 891

Query: 844 HTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLE 903
            TR+PIIGDKFSSRHGQKG+CSQ WP +DMPF+  +GM+PD+IINPHAFPSRMTI M +E
Sbjct: 892 ITRSPIIGDKFSSRHGQKGICSQKWPTVDMPFT-ESGMQPDIIINPHAFPSRMTIGMFIE 950

Query: 904 SVAAK 908
           S+A K
Sbjct: 951 SLAGK 955
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6
>sp|Q75DS1|RPA2_ASHGO DNA-directed RNA polymerase I subunit RPA2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPA2 PE=3 SV=2 Back     alignment and function description
>sp|O74633|RPA2_NEUCR DNA-directed RNA polymerase I subunit RPA2 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=acr-2 PE=1 SV=2 Back     alignment and function description
>sp|P22138|RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPA135 PE=1 SV=1 Back     alignment and function description
>sp|Q54BM1|RPA2_DICDI DNA-directed RNA polymerase I subunit rpa2 OS=Dictyostelium discoideum GN=polr1b PE=3 SV=1 Back     alignment and function description
>sp|P70700|RPA2_MOUSE DNA-directed RNA polymerase I subunit RPA2 OS=Mus musculus GN=Polr1b PE=2 SV=2 Back     alignment and function description
>sp|Q9H9Y6|RPA2_HUMAN DNA-directed RNA polymerase I subunit RPA2 OS=Homo sapiens GN=POLR1B PE=1 SV=2 Back     alignment and function description
>sp|Q5REE8|RPA2_PONAB DNA-directed RNA polymerase I subunit RPA2 OS=Pongo abelii GN=POLR1B PE=2 SV=1 Back     alignment and function description
>sp|O54888|RPA2_RAT DNA-directed RNA polymerase I subunit RPA2 OS=Rattus norvegicus GN=Polr1b PE=1 SV=1 Back     alignment and function description
>sp|P28365|RPA2_EUPOC DNA-directed RNA polymerase I subunit RPA2 OS=Euplotes octocarinatus GN=RPA2 PE=3 SV=2 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 ?
Query910
255578257 1159 DNA-directed RNA polymerase I subunit, p 0.986 0.774 0.758 0.0
359487166 1142 PREDICTED: DNA-directed RNA polymerase I 0.985 0.785 0.766 0.0
296087844 1113 unnamed protein product [Vitis vinifera] 0.952 0.778 0.791 0.0
449458081 1173 PREDICTED: DNA-directed RNA polymerase I 0.990 0.768 0.722 0.0
356548837 1175 PREDICTED: DNA-directed RNA polymerase I 0.986 0.764 0.721 0.0
356563684 1175 PREDICTED: DNA-directed RNA polymerase I 0.986 0.764 0.722 0.0
297851416 1188 hypothetical protein ARALYDRAFT_313639 [ 0.983 0.753 0.685 0.0
224053240 1109 predicted protein [Populus trichocarpa] 0.969 0.795 0.725 0.0
79356046 1178 nuclear RNA polymerase A2 [Arabidopsis t 0.982 0.758 0.683 0.0
12324162 1114 DNA-directed RNA polymerase subunit, put 0.961 0.785 0.701 0.0
>gi|255578257|ref|XP_002529996.1| DNA-directed RNA polymerase I subunit, putative [Ricinus communis] gi|223530519|gb|EEF32401.1| DNA-directed RNA polymerase I subunit, putative [Ricinus communis] Back     alignment and taxonomy information
 Score = 1488 bits (3852), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 702/925 (75%), Positives = 803/925 (86%), Gaps = 27/925 (2%)

Query: 7   ADFEPLRELVRHHIESFDYMLDEGLSEMFDH-----------------CRQAKISYTGKL 49
            D+  L+EL RHHI+SFDYM++ GL  M D+                 CRQAKISYTGK 
Sbjct: 16  GDYSALQELTRHHIDSFDYMIERGLEIMLDNIKPESSRTKHKRLLPFECRQAKISYTGKF 75

Query: 50  MADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFIL 109
            ADV F+Y   G  V+RE++NFGQ P+MLK+R CHL G DSQ+LVS  EE+AEMGGYFIL
Sbjct: 76  EADVCFEY--HGKAVIREKYNFGQLPIMLKSRLCHLYGVDSQQLVSFNEESAEMGGYFIL 133

Query: 110 NGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRK------DQSSVTLKL 163
           NGLERV R +I+PK+NYPMS VR SFRDRREGYTDKAVVIRCVR+      DQSSV++KL
Sbjct: 134 NGLERVVRLLIMPKRNYPMSTVRGSFRDRREGYTDKAVVIRCVREYQSSLTDQSSVSVKL 193

Query: 164 YYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSP 223
           YYL +GS RLGFW+QG+EYLLP GIVLKAL +T D EI+  LTCCYDEKY+K KGAVGS 
Sbjct: 194 YYLRSGSARLGFWIQGREYLLPAGIVLKALAETTDREIYEKLTCCYDEKYEKAKGAVGSQ 253

Query: 224 LVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHL 283
           LV ER KIIL EV+DLSL T+ +CL+HIGEHFQPV+DGL+ E++  VA  V++DYIFVHL
Sbjct: 254 LVGERAKIILDEVRDLSLFTQSECLRHIGEHFQPVMDGLEKETFSNVAHAVLKDYIFVHL 313

Query: 284 NDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKG 343
           N+ +DKFNLLIFMLQKLFSLVD TSV DNPDSLQNQE+LLPGHL+TIYLKEKLE+WLRK 
Sbjct: 314 NNYDDKFNLLIFMLQKLFSLVDQTSVVDNPDSLQNQEVLLPGHLVTIYLKEKLEEWLRKA 373

Query: 344 KKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRA 403
           KK++Q+EI  N   F+F ++ ++KKV++KNPS  I  ++E MLKTGRL TQTGLDLQQRA
Sbjct: 374 KKVLQEEIAKN-NNFNFLSVLDVKKVIDKNPSTTISLAVENMLKTGRLVTQTGLDLQQRA 432

Query: 404 GYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLL 463
           GYTVQAERLNFLRF+SFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLL
Sbjct: 433 GYTVQAERLNFLRFLSFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLL 492

Query: 464 NHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDG 523
           NHMT +CR+ SY+DS+G ++DF  +R SIL VL  +GM  SLPKLV++GPP VLSVLLDG
Sbjct: 493 NHMTRSCRITSYFDSQGAVKDFFDIRKSILGVLTSLGMTSSLPKLVQAGPPQVLSVLLDG 552

Query: 524 RVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVR 583
           RVVG IPSS++EKVV HLRRLKV+A+SVIPDDLEVGYVPLS+GGA+PGLYLFTSP +F+R
Sbjct: 553 RVVGSIPSSQVEKVVVHLRRLKVAASSVIPDDLEVGYVPLSMGGAFPGLYLFTSPSRFIR 612

Query: 584 PVRNISLPSEESQNIELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVAN 643
           PV+NIS+P+ E +NIELIGPFEQVFMEIRCPDGG+GGR +AFPATHEEIHPT MLSVVAN
Sbjct: 613 PVKNISIPAGEGENIELIGPFEQVFMEIRCPDGGNGGRSDAFPATHEEIHPTDMLSVVAN 672

Query: 644 LTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGI 703
           LTP+SDHNQSPRNMYQCQMAKQTM FS+Q+L+FRADQKLYHLQTPQTPIVRT++YTKY +
Sbjct: 673 LTPWSDHNQSPRNMYQCQMAKQTMAFSLQSLRFRADQKLYHLQTPQTPIVRTSSYTKYCV 732

Query: 704 DEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQ 763
           DEYPTGTNAIVAVLAYTGYDMEDAMILNKSSV+RGMCHGQIYQTETIDLS++G++ DR Q
Sbjct: 733 DEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVERGMCHGQIYQTETIDLSEEGSRSDRAQ 792

Query: 764 KLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDY 823
           ++FRR+   KSLHSVIDSDGLPYVGQMIHP EPYCSIY++ TN+ RTN+RKGS+ V VDY
Sbjct: 793 RMFRRSNIDKSLHSVIDSDGLPYVGQMIHPNEPYCSIYNEITNTTRTNNRKGSDPVIVDY 852

Query: 824 VAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883
           VA+D KN K+L QK NIRFRH RNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP
Sbjct: 853 VAIDTKNKKHL-QKVNIRFRHPRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 911

Query: 884 DLIINPHAFPSRMTIAMLLESVAAK 908
           DLIINPHAFPSRMTIAMLLES+AAK
Sbjct: 912 DLIINPHAFPSRMTIAMLLESLAAK 936

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359487166|ref|XP_002263835.2| PREDICTED: DNA-directed RNA polymerase I subunit RPA2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|296087844|emb|CBI35100.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449458081|ref|XP_004146776.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|356548837|ref|XP_003542805.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like [Glycine max] Back     alignment and taxonomy information
>gi|356563684|ref|XP_003550091.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA2-like [Glycine max] Back     alignment and taxonomy information
>gi|297851416|ref|XP_002893589.1| hypothetical protein ARALYDRAFT_313639 [Arabidopsis lyrata subsp. lyrata] gi|297339431|gb|EFH69848.1| hypothetical protein ARALYDRAFT_313639 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|224053240|ref|XP_002297732.1| predicted protein [Populus trichocarpa] gi|222844990|gb|EEE82537.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|79356046|ref|NP_564341.2| nuclear RNA polymerase A2 [Arabidopsis thaliana] gi|332193031|gb|AEE31152.1| nuclear RNA polymerase A2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|12324162|gb|AAG52049.1|AC022455_3 DNA-directed RNA polymerase subunit, putative; 8546-1198 [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.70.766
4th Layer2.7.7.60.824

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
fgenesh1_pm.C_scaffold_1002419
annotation not avaliable (1188 aa)
(Arabidopsis lyrata)
Predicted Functional Partners:
fgenesh2_kg.5__2208__AT3G57660.1
annotation not avaliable (1678 aa)
  ••••• 0.962
fgenesh2_kg.5__2151__AT3G57150.1
annotation not avaliable (561 aa)
   •• • 0.849
fgenesh2_kg.8__1958__AT5G60040.1
annotation not avaliable (1376 aa)
• •• •• 0.831
scaffold_101731.1
annotation not avaliable (895 aa)
   •    0.756
fgenesh1_pm.C_scaffold_7002163
annotation not avaliable (187 aa)
   •  • 0.733
fgenesh2_kg.3__2374__AT3G21540.1
annotation not avaliable (954 aa)
   •    0.720
fgenesh2_kg.6__3261__AT4G04940.1
annotation not avaliable (911 aa)
   •    0.708
Al_scaffold_0007_3549
annotation not avaliable (52 aa)
   •••• 0.699
fgenesh1_pm.C_scaffold_6001142
annotation not avaliable (587 aa)
   •    0.695
scaffold_200152.1
annotation not avaliable (534 aa)
   •    0.685

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query910
COG0085 1060 COG0085, RpoB, DNA-directed RNA polymerase, beta s 1e-134
cd00653 866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 1e-116
pfam00562373 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do 1e-101
PRK08565 1103 PRK08565, PRK08565, DNA-directed RNA polymerase su 1e-91
TIGR03670 599 TIGR03670, rpoB_arch, DNA-directed RNA polymerase 1e-64
PRK07225 605 PRK07225, PRK07225, DNA-directed RNA polymerase su 2e-62
cd00653866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 6e-50
pfam04563394 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub 1e-29
cd00653866 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun 1e-26
PRK09606494 PRK09606, PRK09606, DNA-directed RNA polymerase su 2e-22
pfam0456568 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do 3e-22
pfam0688358 pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 9e-16
CHL00207 1077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 1e-14
pfam04561185 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do 7e-11
TIGR02013 1065 TIGR02013, rpoB, DNA-directed RNA polymerase, beta 3e-09
PRK09603 2890 PRK09603, PRK09603, bifunctional DNA-directed RNA 2e-08
CHL00207 1077 CHL00207, rpoB, RNA polymerase beta subunit; Provi 6e-08
PRK14844 2836 PRK14844, PRK14844, bifunctional DNA-directed RNA 7e-08
PRK00405 1112 PRK00405, rpoB, DNA-directed RNA polymerase subuni 2e-07
CHL00001 1070 CHL00001, rpoB, RNA polymerase beta subunit 7e-06
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information 
 Score =  427 bits (1100), Expect = e-134
 Identities = 214/996 (21%), Positives = 333/996 (33%), Gaps = 212/996 (21%)

Query: 3   RKKSADFEPLRELVRHHIESFDYMLDEGLSEMFD-------------------------- 36
             K  +F  L  LV   ++S++    EGL E+F                           
Sbjct: 15  FGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESYNGNTELEYGSYRLGEPPK 74

Query: 37  ----HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQK 92
                CR   ++Y+  L   +     + G  +  +    G  P+M +             
Sbjct: 75  FYPEECRLRGLTYSAPLYVKLRLVVNETGEEIKEQEVYMGDIPLMTR------------- 121

Query: 93  LVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCV 152
                      GGYFI+NG ERV  S                           A VI   
Sbjct: 122 -----------GGYFIINGTERVIVSQEHRSPGVIF---VEKKDKTGSKVLYVARVIPY- 166

Query: 153 RKDQSSVTL--KLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYD 210
           R          K    +    +           +PV I+L+AL    D EI        D
Sbjct: 167 RGSWLEFEFDPKDNLYVRIDRK---------RKIPVTILLRALGLETDEEIIEAF--GGD 215

Query: 211 EKYKKEKGAVGSPLVSERVKIILAEVQDLSLT--TRLQCLQHIGEHFQPVIDGLQSESYY 268
           E            +  E  + +L   ++      T    L+ IG     V      E  Y
Sbjct: 216 ELTD--------LVPPEGEEALLEIYEEAKGEKITARNALELIGSRVFVVKRYDAKEGRY 267

Query: 269 AVAETVIRDYIFVHLNDNNDKFNL--------LIFMLQKLFSLVDHTSVSDNPDSLQNQE 320
             A+ V+   +  HL +  ++++L        +I M++ L  L       D+ D L N+ 
Sbjct: 268 KRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRR 327

Query: 321 ILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKN------- 373
           + L G L+    +  L    R                       ++K+ +EK        
Sbjct: 328 LRLVGELLENLFRVGLSRMER-----------------------DVKERLEKADKRDTLV 364

Query: 374 PSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGL 433
           P   I       L TG            R+  +   ++ N L  +S  R +         
Sbjct: 365 PQDLINAKPIHALITGFFG---------RSQLSQFMDQTNPLSELSHKRRLSALGLSRER 415

Query: 434 RTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSIL 493
               VR + P  +G +CP+ TP+G   GL+  +    R+        N   F +  T   
Sbjct: 416 AGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARI--------NEYGFLE--TPYR 465

Query: 494 RVLIGV-GMIPSLPKLVKSGPPAVLSVLLDGRVVGVI--PSSEIEKVVAHLRRLKVSAAS 550
           +VL G   +       ++        V + G+  G +  P   +E++V   RR      S
Sbjct: 466 KVLDGSLVVDE-----IEYLSADEEDVYVIGQANGTLDEPGELVEELV-ECRRGGSGEVS 519

Query: 551 VIPDD------------LEVGYVPLSLGGAYPGL-YLFTSPPKFVRPVRNISLPSEESQN 597
           V   +            + VG   +           L  S  +        +        
Sbjct: 520 VADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPLVGTG 579

Query: 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNM 657
           +E +   +     I     G          TH EI P  +L + A+L PY +HNQSP N+
Sbjct: 580 MEYLDAEDSGAAVI-AKRPGVV--------THVEISPIVILGIEASLIPYPEHNQSPYNL 630

Query: 658 YQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVL 717
           Y+   + Q  G + + L  R D     L     P V T         E   G NA+VA +
Sbjct: 631 YKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFM 682

Query: 718 AYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRR--NKDAKSL 775
            + GY+ EDA+I+++ SV+R +      +    +  D       G +  R   N   ++L
Sbjct: 683 PWNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKL----GPEEIRDIPNVSEEAL 738

Query: 776 HSVIDSDGLPYVGQMIHPGEPYCSIYDKTT------------------NSWRTNSRK--G 815
              +D DG+  +G  +  G+       K T                     R  S +   
Sbjct: 739 -RNLDEDGIIRIGAEVKGGDILVG---KVTPKGETELTPEERLLRIFGEKVRDTSLRVPH 794

Query: 816 SESVFVDYVAVDMKNSKNLP---QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDID 872
            E   VD V V        P   +   +     R P IGDK + RHG KGV S++ P  D
Sbjct: 795 GEEGIVDDVQV-FTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQED 853

Query: 873 MPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908
           MPF    G  PD+I+NP   PSRM I  +LE+   K
Sbjct: 854 MPFL-EDGTPPDIILNPLGVPSRMNIGQILETHLGK 888

Length = 1060
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6 Back     alignment and domain information
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional 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|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit Back     alignment and domain information
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, 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|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated 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|219216 pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 specific domain Back     alignment and domain information
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional 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|233685 TIGR02013, rpoB, DNA-directed 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|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional 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|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|214330 CHL00001, rpoB, 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 910
KOG0216 1111 consensus RNA polymerase I, second largest subunit 100.0
PRK08565 1103 DNA-directed RNA polymerase subunit B; Provisional 100.0
KOG0214 1141 consensus RNA polymerase II, second largest subuni 100.0
KOG0215 1153 consensus RNA polymerase III, second largest subun 100.0
COG0085 1060 RpoB DNA-directed RNA polymerase, beta subunit/140 100.0
cd00653 866 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po 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
CHL00001 1070 rpoB RNA polymerase beta subunit 100.0
CHL00207 1077 rpoB RNA polymerase beta subunit; Provisional 100.0
PRK09603 2890 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK14844 2836 bifunctional DNA-directed RNA polymerase subunit b 100.0
PRK07225 605 DNA-directed RNA polymerase subunit B'; Validated 100.0
TIGR03670 599 rpoB_arch DNA-directed RNA polymerase subunit B. T 100.0
PRK09606494 DNA-directed RNA polymerase subunit B''; Validated 100.0
PF00562386 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int 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 99.94
PF04561190 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; Int 99.85
PF0456663 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; Int 99.48
PF0688358 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do 99.12
PF0456748 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int 98.53
COG0085 1060 RpoB DNA-directed RNA polymerase, beta subunit/140 97.65
KOG0215 1153 consensus RNA polymerase III, second largest subun 97.17
KOG0214 1141 consensus RNA polymerase II, second largest subuni 95.63
PHA03394865 lef-8 DNA-directed RNA polymerase subunit beta-lik 93.79
>KOG0216 consensus RNA polymerase I, second largest subunit [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=2.3e-226  Score=1891.78  Aligned_cols=867  Identities=53%  Similarity=0.891  Sum_probs=819.3

Q ss_pred             CCCCcCCccCchhhHHHHHHHHHHHHHHhHHHHH--------------------------------------------HH
Q 002545            2 ARKKSADFEPLRELVRHHIESFDYMLDEGLSEMF--------------------------------------------DH   37 (910)
Q Consensus         2 ~~~~~~~~~~~~~Lv~~hi~SFn~Fi~~gl~~i~--------------------------------------------~e   37 (910)
                      |+.+...+..+++++++|++|||...+.||....                                            .|
T Consensus         5 ~~k~~p~fp~l~~a~~pHi~sfnal~~~gll~~~v~~~~ek~~~~~g~kis~~ve~i~iakP~l~~~~~ss~~r~lyPaE   84 (1111)
T KOG0216|consen    5 PPKDYPSFPELQDAASPHIDSFNALTNGGLLNAGVAGIAEKVPLKAGDKISMKVESIQIAKPMLSDKVHSSDTRKLYPAE   84 (1111)
T ss_pred             CcccCccchhhhhhhhhhhccccchhhhhHHHHHhhchhhhcccccCCceeEEEEEEEecCCCCCccccccccccccchh
Confidence            4555566778999999999999999998887664                                            89


Q ss_pred             HHHcCCeeeeEEEEEEEEEEecCCCceeeeEeeecccceeecCCCccCCCCChHHHHhcccccccCCcEEEEcCceeEEE
Q 002545           38 CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFR  117 (910)
Q Consensus        38 cR~r~~TY~~~l~v~i~~~~~~~~~~~~~~~v~iG~iPIMv~S~~C~L~~~~~~el~~~~E~~~D~GGYFIInG~EKVIr  117 (910)
                      ||+|.+||+|.+.|++.|.+|  ++........+|.+||||+|++|||.|++++||++.+|++.|+||||||||+|||||
T Consensus        85 cRqR~~TY~Gkl~v~v~wsVN--g~~~~~e~~dlG~vPIMlrSklChL~g~sp~eLV~hkEe~~EmGGYFIvNGIEKvIR  162 (1111)
T KOG0216|consen   85 CRQRGLTYKGKLVVRVSWSVN--GGHVVIEKRDLGHVPIMLRSKLCHLNGASPKELVKHKEESSEMGGYFIVNGIEKVIR  162 (1111)
T ss_pred             HhhccceecceEEEEEEEEEC--CeeeeeeeeecCccceEEeccccccCCCChHHHhhccCchhhcCcEEEEcChHHhhh
Confidence            999999999999999999999  888878889999999999999999999999999999999999999999999999999


Q ss_pred             EEEeecCCccEEEEeccccCCCCcceeeEEEEEeeecCCCceEEEEEEEeCCeEEEEEEeecccccccHHHHHHhccCCC
Q 002545          118 SVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTN  197 (910)
Q Consensus       118 ~qi~~~~N~~~~~~r~~~~~~~~~~t~~~v~~r~~~~~~~~~~~~l~y~~~g~~~l~~~~~~~~~~IPi~ilLkALg~~s  197 (910)
                      ++|+++||+|+++.|++|++||..||+|++++|||++|+++.+++|||+.||.+.++|.++|.+|.+|++++||||...|
T Consensus       163 mLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRcVReDqSsvtn~LHYLnnGtv~~~F~~rK~eylvPv~lILKAL~~ts  242 (1111)
T KOG0216|consen  163 MLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRCVREDQSSVTNVLHYLNNGTVMFRFSHRKREYLVPVVLILKALTNTT  242 (1111)
T ss_pred             hheeccCCCceEEechhhhhcCCCccccceEEEEeccccccceeEEEEecCCcEEEEEEEeeeeehhhHHHHHHHHhccC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccccchhhcccCCCCChhhHHHHHHHHHHHHhcccccHHHHHHHHhhcccccccCCCCccHHHHHHHHHHh
Q 002545          198 DLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRD  277 (910)
Q Consensus       198 D~EI~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~t~~~al~yLg~~fr~~~~~~~~~~~~~~g~~~L~~  277 (910)
                      |+|||+.++          +++..++|+.++++.||+++++++++|+++|++|||++||+.+...+.+++.++|+++|++
T Consensus       243 DeEIf~~lv----------~g~~gdqfl~~rv~~mLr~v~ee~l~trtqcl~yLGs~FRaVl~~v~~~~D~evg~fILr~  312 (1111)
T KOG0216|consen  243 DEEIFEGLV----------GGDEGDQFLTSRVELMLREVQEENLFTRTQCLQYLGSRFRAVLDFVPEQPDLEVGRFILRE  312 (1111)
T ss_pred             HHHHHHHHh----------CCccCceeHHHHHHHHHHHHhhcccccHHHHHHHHhhhhhhhhcCCCCCchHHHHHHHHHh
Confidence            999999997          4778899999999999999999999999999999999999877655569999999999999


Q ss_pred             HhccCCCCCcchHHHHHHHHHHHHhhcCCCCCCCCcccccccEEcccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Q 002545          278 YIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK  357 (910)
Q Consensus       278 ~ll~Hl~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~l~NkRv~l~G~Ll~~lf~~~~~~~l~~~~~~i~~~~~~~~~~  357 (910)
                      +++.||+++.+||.+|++|++||++++.|+|.+||+|+.+|||++++|+|++.+|+|++++|+..++.++++.+.+.+.+
T Consensus       313 ~VlvHLd~~~DKF~lLifmiqKL~slv~ge~~~dnpDs~q~qEil~~ghl~~~~LkEriEe~l~~~~~~vr~~l~~~~~~  392 (1111)
T KOG0216|consen  313 YVLVHLDSDEDKFNLLIFMIQKLYSLVDGECTPDNPDSPQNQEILLPGHLYGSILKERIEEWLRFISAQVRRDLYKLGFK  392 (1111)
T ss_pred             heEEEecccHHHHHHHHHHHHHHHHHhcCCcCCCCCCChhhhhcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999886667


Q ss_pred             ccccchHHHHHHHhcCCCcchHHHHHhHhcccCcccccccccccccceEEEccccchhhHhhhhcccccCCccccccccc
Q 002545          358 FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS  437 (910)
Q Consensus       358 ~~~~~~~~~~~~~~~~~~~~It~~i~~~~sTGnw~~~~~~~~~q~sGvsqvleRln~~~~lSH~Rrv~rg~~~~~~k~t~  437 (910)
                      .++.+..++.+++.+.+ ..|+++|++||||||++++++++++|++|++++|||+|++|||||||.||||++|++|++|+
T Consensus       393 ~~~~~~~~i~~~~~r~~-~~Ig~~me~fLsTGnl~s~sgldLqQ~sG~tv~AEriNf~RflShFRavhRGa~f~~mrTTt  471 (1111)
T KOG0216|consen  393 EDFLDISAIRKVFMRTN-GNIGRKMEYFLSTGNLVSRSGLDLQQTSGYTVVAERINFYRFLSHFRAVHRGAFFAEMRTTT  471 (1111)
T ss_pred             chhHhHHHHHHHHhhcc-ccHHHHHHHHHhcCCeeeccchhhHhhcCcEEehhhhhHHHHHHHHHHHhcccchhheeehh
Confidence            77777788888998876 49999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCccccccCCCCCCccccccccccceeEEeeecCCCCcccccchhhHHHHHHHHhcCCeecCCccccCCCCcee
Q 002545          438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVL  517 (910)
Q Consensus       438 vR~Lhps~wG~iCPveTPEG~~cGLv~~LA~~~~Is~~~~~~~~~~~~~~~~~~i~~~L~~lG~~~~~~~~~~~~~~~~~  517 (910)
                      +|||.|++|||+||||||||+||||+||||..|+|++..++.+          .+..+|.++||.|... .... ....|
T Consensus       472 vRKLlPEsWGFlCPVHTPDG~PCGlLnH~t~~c~I~t~~dd~s----------~ip~~L~~~Gm~p~~~-~~~~-G~~l~  539 (1111)
T KOG0216|consen  472 VRKLLPESWGFLCPVHTPDGAPCGLLNHMTRTCRIVTRPDDVS----------FIPSILFELGMVPSSH-LVEA-GEPLY  539 (1111)
T ss_pred             hHhhCchhhcccccccCCCCCchhHHHhhhhheeEeecCcchh----------hhhHHHHhcCCCchhc-cccC-CCcee
Confidence            9999999999999999999999999999999999999887753          3899999999998732 2222 23479


Q ss_pred             EEEECCEEEeeecCccHHHHHHHHHHHHHhcCCCCCCCceEEEEEcCCCCCCCceEeecCCCceeceEEeecCCCCCCCc
Q 002545          518 SVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISLPSEESQN  597 (910)
Q Consensus       518 ~V~lnG~~iG~~~~~~~~~~~~~lr~~k~~~~~~i~~~~eI~~v~~~~~~~~~~i~i~td~gR~~RPv~~~~~~~~~~g~  597 (910)
                      +|++||+++|+++...+..+++.||++|......||.++||+||+.+.+++||++||++++||++|||.+++.+     .
T Consensus       540 ~VlldGk~vG~~s~~~a~~i~~~lR~~Kv~~p~~iP~~leIg~Vp~s~~gqyPglyi~s~~aR~~RpV~nl~~~-----~  614 (1111)
T KOG0216|consen  540 PVLLDGKVVGWVSSPLAKKIVDYLRYYKVEAPAVIPNDLEIGYVPTSTNGQYPGLYIFSGPARMIRPVKNLSLD-----S  614 (1111)
T ss_pred             EEEECCEEEEeeccHHHHHHHHHHHHHhhcCcccCCCcceEeeeecCCCCCCceeEEecCchhhhhehhccccC-----c
Confidence            99999999999999999999999999999877789999999999999999999999999999999999999887     8


Q ss_pred             eeeeCccceeeeeeecCCCCCCCCCCCCCceecccCCCccccceeecccCCCCCCcchhhhhhhccccccccceeEEEEe
Q 002545          598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFR  677 (910)
Q Consensus       598 iE~i~~~Eq~~~~Ia~~~~~~~~~~~~~~~th~EI~p~~~ls~~asliPF~~hNqspRn~yq~~M~KQaig~~~~n~~~R  677 (910)
                      +||||++||+++.||+.++++.+..    +||.|++|+.+||++|+||||+|||||||||||||||||+||+|.++|..|
T Consensus       615 ~e~iG~fEQvym~i~~~~~e~~~~v----~th~E~~pt~~ls~~anliP~sD~NQSPRNmYQCQMgKQtmg~p~~a~~~r  690 (1111)
T KOG0216|consen  615 VEWIGPFEQVYMNIAIDPKEIFPDV----TTHVELHPTGILSIVANLIPFSDHNQSPRNMYQCQMGKQTMGTPGHALRTR  690 (1111)
T ss_pred             hhhcccHHHhhhhhccchhhcCCCc----ceeEEecccchHhHhhcCccccccCCCchhHHHhhhhhhhcCCccccchhc
Confidence            9999999999999999999998875    899999999999999999999999999999999999999999999999999


Q ss_pred             ccCceeecCCCCeeeEecccccccCccccCCCceeeEEEEeccCCCcccceeeeccccccCcceeeEEEEEEEEeeccCC
Q 002545          678 ADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN  757 (910)
Q Consensus       678 ~D~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~~~~~  757 (910)
                      +|+|+|+|++||.|+|++..++.+++|++|.|+||+|||+|||||||||||||||+|+||||+++++||++.++|.++..
T Consensus       691 adnklYrlqt~qsP~vr~~~y~~y~~d~yp~GtNaiVAVisyTgyDMeDAmiiNK~s~eRGf~~G~vykte~i~L~~~~~  770 (1111)
T KOG0216|consen  691 ADNKLYRLQTPQSPIVRPELYDTYGMDDYPNGTNAIVAVISYTGYDMEDAMIINKSSYERGFAYGTVYKTEKIDLSKKRS  770 (1111)
T ss_pred             ccCceEEecCCCCceeecccccccccccCCCCcceEEEEEeecccChhhhhhhchhhhhccccceeEEeeeeechhhccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999866553


Q ss_pred             CcCccceeecc-CCCChhhhcccCCCCCcccCceecCCCcEEEeeccCCCceeeeeecCCCceEEEEEEEEecCCCCCCe
Q 002545          758 KVDRGQKLFRR-NKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVAVDMKNSKNLPQ  836 (910)
Q Consensus       758 ~~~~~~~~f~~-~~~~~~~~~~ld~dG~~~~g~~v~~gd~l~~~~~~~~~~~~~~~~~~~e~g~v~~v~~~~~~~~~~~~  836 (910)
                      +    ...|.. |...+  .++||+||||.+|+++..||++++.|+...++++..+|++.|+|+||.|++..++.|+..+
T Consensus       771 r----~~~F~~~p~~~~--~~~ld~dgLP~~G~kl~~~dp~~~y~d~~t~~~~~~~~~~~ep~~vd~vr~~~~~~~~~~k  844 (1111)
T KOG0216|consen  771 R----SKHFGRSPGEPE--LKKLDADGLPSIGQKLEYGDPYYAYFDEETGKTRIKKYHGTEPGIVDEVRVLGNDMGDQEK  844 (1111)
T ss_pred             c----eeeeeeCCCCcc--ccccCCCCCCCCcccccCCCcEEEEEcccCCceEEEEecCCCCeeeEEEEEccccCCCccc
Confidence            2    445654 33333  6889999999999999999999999999999999999999999999999999998876558


Q ss_pred             EEEEEEeeeeCCCcccceeccCCCccEEeeeecCcCcCccCCCCCcCcEEeCCCCccccccHHHHHHHhhccc
Q 002545          837 KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKE  909 (910)
Q Consensus       837 ~v~i~~r~~R~p~iGDKf~sRHGqKGv~s~i~~~~dMPf~~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gK~  909 (910)
                      .+.|++|.+|+|.||||||||||||||||..||.+||||| ++|++|||||||||||||||||||+|+||||+
T Consensus       845 ~~~i~~Ri~R~p~IGDKFsSRhGQKGicS~~wP~~dmPFt-esGm~PDii~NPH~FPSRMTIgM~iEs~AgK~  916 (1111)
T KOG0216|consen  845 CATITLRIPRNPIIGDKFSSRHGQKGICSQKWPTIDMPFT-ESGMVPDIIINPHAFPSRMTIGMLIESMAGKA  916 (1111)
T ss_pred             eEEEEEEecCCCcccchhhhhccccccccccCCCCCCCcc-ccCcCcceeeCCCCCcccccHHHHHHHHhchh
Confidence            8999999999999999999999999999999999999999 99999999999999999999999999999996

>PRK08565 DNA-directed RNA polymerase subunit B; Provisional Back     alignment and domain information
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] Back     alignment and domain information
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] Back     alignment and domain information
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>cd00653 RNA_pol_B_RPB2 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
>CHL00001 rpoB RNA polymerase beta subunit Back     alignment and domain information
>CHL00207 rpoB RNA polymerase beta subunit; Provisional Back     alignment and domain information
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed Back     alignment and domain information
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional 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
>PRK09606 DNA-directed RNA polymerase subunit B''; Validated Back     alignment and domain information
>PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 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
>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
>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
>COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] Back     alignment and domain information
>KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] Back     alignment and domain information
>KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] Back     alignment and domain information
>PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional 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 ?
Query910
2waq_B 1131 The Complete Structure Of The Archaeal 13-Subunit D 1e-60
2pmz_B 1124 Archaeal Rna Polymerase From Sulfolobus Solfataricu 2e-60
3h0g_B 1210 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 3e-45
1i3q_B 1224 Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio 1e-43
1iw7_C 1119 Crystal Structure Of The Rna Polymerase Holoenzyme 8e-11
1ynj_C 1119 Taq Rna Polymerase-Sorangicin Complex Length = 1119 4e-10
1hqm_C 1119 Crystal Structure Of Thermus Aquaticus Core Rna Pol 4e-10
1l9u_C 1118 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 4e-10
1i6v_C 1118 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 4e-10
3lu0_C 1342 Molecular Model Of Escherichia Coli Core Rna Polyme 2e-07
3iyd_C 1342 Three-Dimensional Em Structure Of An Intact Activat 2e-07
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131 Back     alignment and structure 
Iteration: 1

 Score =  231 bits (590), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 231/889 (25%), Positives = 386/889 (43%), Gaps = 116/889 (13%)
Query: 67  ERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126
           E    G  P+MLK+    +      KL+ + E+  + GGYFI+NG ERV    I+ +++ 
Sbjct: 115 EEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERV----IVTQEDL 170
Query: 127 PMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGF-WLQGKEYLLP 185
             + V           T  A +I      +  VT++   L +G+  + F  + GK   +P
Sbjct: 171 APNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTIE--RLKDGTFHVSFPAVPGK---IP 225
Query: 186 VGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRL 245
             I+++AL    D +I        D + + E      P + +   I  A V D       
Sbjct: 226 FVILMRALGILTDRDIV--YAVSLDPEIQNEL----FPSLEQASSI--ANVDD------- 270
Query: 246 QCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHL----NDNNDKFNLLIFMLQKLF 301
             L  IG     V  G + E+    A+ +I  Y   HL    +D   K   L + + K+ 
Sbjct: 271 -ALDFIGSR---VAIGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVI 326
Query: 302 SLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFF 361
            L       D+ D   N+ + L G L     +   + +++     ++   +  G+K    
Sbjct: 327 ELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKS-KVRGRKLALK 385
Query: 362 NLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFF 421
            L     V E+                 R A  TG  +  R G +   +R N+L  +S  
Sbjct: 386 ALVRPDIVTERI----------------RHALATGNWVGGRTGVSQLLDRTNWLSMLSHL 429
Query: 422 RAVHRGASFA-GLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRG 480
           R V   +S A G      R L    WG +CP  TP+G   GL+ ++    ++A   + + 
Sbjct: 430 RRVI--SSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEK- 486
Query: 481 NIRDFSKMRTSILRVLIGVGMIPS---LPKLVKSGPP-----AVLSVLLDGRVVGVI-PS 531
                      + + L  +G++P    + ++ + G           V+L+GR+VG     
Sbjct: 487 ----------IVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYRDG 536
Query: 532 SEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL- 590
            E+ K +   RR        I D++ VG++          +++     +  RP+  +S  
Sbjct: 537 EELAKKIRERRR-----KGEISDEVNVGHIVTDFINE---VHVNCDSGRVRRPLIIVSNG 588
Query: 591 -PSEESQNIELIGP----FEQVFMEIRCPDGGDGGRRNAFPA----------THEEIHPT 635
            P    ++IE +      F+ +  + +          NA+ A          TH EI   
Sbjct: 589 NPLVTREDIEKLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEHTHLEIWSP 648
Query: 636 GMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRT 695
            +L + A++ PY +HNQSPRN YQ  MAKQ +G      + R D + + L  PQ P+V+T
Sbjct: 649 AILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQT 708
Query: 696 NTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHG---QIYQTETID- 751
                 G    P G NAI+AV+++TGY+MED++I+N+SSV+RGM      ++Y TE +  
Sbjct: 709 RALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKY 768
Query: 752 ---------LSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYD 802
                    + + G +  +G++ +R  +D   +   ++  G   +   + P        +
Sbjct: 769 PGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKE 828
Query: 803 KTTNSWRTNSR---KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHG 859
            +    + ++    +  E   VD V +      N  +   +R R  R P IGDKF+SRHG
Sbjct: 829 LSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGN--KLVKVRVRDLRIPSIGDKFASRHG 886
Query: 860 QKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908
           QKGV   L P +DMP++ V G+ PD+I+NPHA PSRMT+  ++E +A K
Sbjct: 887 QKGVIGMLIPQVDMPYT-VKGVVPDVILNPHALPSRMTLGQIMEGIAGK 934
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 Back     alignment and structure
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 Back     alignment and structure
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 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|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|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 Back     alignment and structure
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query910
4ayb_B 1131 DNA-directed RNA polymerase; transferase, multi-su 0.0
1twf_B 1224 DNA-directed RNA polymerase II 140 kDa polypeptid; 1e-129
3h0g_B 1210 DNA-directed RNA polymerase II subunit RPB2; trans 3e-66
3h0g_B 1210 DNA-directed RNA polymerase II subunit RPB2; trans 2e-51
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-12
2a6h_C 1119 DNA-directed RNA polymerase beta chain; RNA polyme 4e-08
3lu0_C 1342 DNA-directed RNA polymerase subunit beta; E. coli 9e-07
>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
 Score =  715 bits (1846), Expect = 0.0
 Identities = 221/985 (22%), Positives = 377/985 (38%), Gaps = 161/985 (16%)

Query: 12  LRELVRHHIESFDYMLDEGLSEMFD----------------------------------- 36
            + LVR H++S++  +   L E+ D                                   
Sbjct: 23  SKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEIPGLKVRLGKIRIGKPRVRESDRGERE 82

Query: 37  ----HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQK 92
                 R   ++Y   L   +    ++       E    G  P+MLK+    +      K
Sbjct: 83  ISPMEARLRNLTYAAPLWLTMI--PVENNIEAEPEEVYIGDLPIMLKSAIDPISQYTLDK 140

Query: 93  LVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCV 152
           L+ + E+  + GGYFI+NG ERV  +      N     V           T  A +I   
Sbjct: 141 LIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNR----VLVDTGKTGSNITHTAKIISST 196

Query: 153 RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEK 212
              +  VT++   L +G+  + F        +P  I+++AL    D +I   +    D +
Sbjct: 197 AGYRVPVTIE--RLKDGTFHVSF--PAVPGKIPFVILMRALGILTDRDIVYAV--SLDPE 250

Query: 213 YKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAE 272
            + E              +  +  Q  S+      L  IG        G + E+    A+
Sbjct: 251 IQNE--------------LFPSLEQASSIANVDDALDFIGSRVAI---GQKRENRIEKAQ 293

Query: 273 TVIRDYIFVHL----NDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLI 328
            +I  Y   HL    +D   K   L + + K+  L       D+ D   N+ + L G L 
Sbjct: 294 QIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLF 353

Query: 329 TIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKT 388
               +   + +++     ++       K      L  + +         +   I   L T
Sbjct: 354 ASLFRVAFKAFVKDLTYQLEKSKVRGRK----LALKALVR------PDIVTERIRHALAT 403

Query: 389 GRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGF 448
           G         +  R G +   +R N+L  +S  R V    +         R L    WG 
Sbjct: 404 GNW-------VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQ-PNFEARDLHGTQWGR 455

Query: 449 LCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVGMIP----- 503
           +CP  TP+G   GL+ ++    ++A   +              + + L  +G++P     
Sbjct: 456 MCPFETPEGPNSGLVKNLALMAQIAVGINE-----------KIVEKTLYEMGVVPVEEVI 504

Query: 504 ---SLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGY 560
              +     ++       V+L+GR+VG     + E++   +R  +      I D++ VG+
Sbjct: 505 RRVTEGGEDQNEYLKWSKVILNGRLVGYY--RDGEELAKKIRERRRKG--EISDEVNVGH 560

Query: 561 VPLSLGGAYPGLYLFTSPPKFVRPVRNIS-------------LPSEE--------SQNIE 599
           +          +++     +  RP+  +S             L S             IE
Sbjct: 561 IVTDFINE---VHVNCDSGRVRRPLIIVSNGNPLVTREDIEKLDSGSITFDDLVRQGKIE 617

Query: 600 LIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQ 659
            +   E+    +                TH EI    +L + A++ PY +HNQSPRN YQ
Sbjct: 618 YLDAEEEENAYVALEP-----SDLTPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTYQ 672

Query: 660 CQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAY 719
             MAKQ +G      + R D + + L  PQ P+V+T      G    P G NAI+AV+++
Sbjct: 673 SAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISF 732

Query: 720 TGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGN-KVDRGQKLFRRNKDAKS--LH 776
           TGY+MED++I+N+SSV+RGM     ++  + +       + D+        +  K    +
Sbjct: 733 TGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYY 792

Query: 777 SVIDSDGLPYVGQMIHPGEPYCSIYDKTTN-----------SWRTNSR--KGSESVFVDY 823
            +++ +G+      +  G+                      + R  S   +  E   VD 
Sbjct: 793 RLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDL 852

Query: 824 VAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRP 883
           V +    +    +   +R R  R P IGDKF+SRHGQKGV   L P +DMP++ V G+ P
Sbjct: 853 VLIT--ETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYT-VKGVVP 909

Query: 884 DLIINPHAFPSRMTIAMLLESVAAK 908
           D+I+NPHA PSRMT+  ++E +A K
Sbjct: 910 DVILNPHALPSRMTLGQIMEGIAGK 934
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 910
d1twfb_ 1207 e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c 1e-119
d1smyc_ 1119 e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop 3e-75
>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 =  388 bits (997), Expect = e-119
 Identities = 229/1027 (22%), Positives = 376/1027 (36%), Gaps = 169/1027 (16%)

Query: 15   LVRHHIESFDYMLDEGLSEMFD-------------------------------------- 36
            LV   ++SF+  +D  L ++                                        
Sbjct: 26   LVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMV 85

Query: 37   -------------HCRQAKISYTGKLMADVEFQYLDA-----------------GSPVVR 66
                           R   ++Y+  L  DV+ +  +A                       
Sbjct: 86   NESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSES 145

Query: 67   ERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126
             +   G+ P+ML+++ C+L  A    L  LKE   +MGGYFI+NG E+V  +      N 
Sbjct: 146  GKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNI 205

Query: 127  PMSMVRSSFRDRREGYTDKAVVIRCVRKDQS----SVTLKLYYLLNGSVR-LGFWLQGKE 181
                    F+            IR   +  S    ++ +KLY     S R +   L   +
Sbjct: 206  VQV-----FKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIK 260

Query: 182  YLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSL 241
              +P+ I+ +AL    D EI  H   CYD    +               +         +
Sbjct: 261  QDIPIVIIFRALGIIPDGEILEH--ICYDVNDWQML-----------EMLKPCVEDGFVI 307

Query: 242  TTRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHL----NDNNDKFNLLIFML 297
              R   L  IG     +  G++ E     A+ +++     H+       + K   L +M+
Sbjct: 308  QDRETALDFIGRRGTAL--GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMI 365

Query: 298  QKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357
             +L          D+ D    + + L G L+    K   +   +       D      + 
Sbjct: 366  NRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTK-------DIFRYMQRT 418

Query: 358  FDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRF 417
             +  +  N+K  +    +K I + ++  L TG    Q    +  RAG +    R  +   
Sbjct: 419  VEEAHDFNMKLAI---NAKTITSGLKYALATGNWGEQKK-AMSSRAGVSQVLNRYTYSST 474

Query: 418  ISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYD 477
            +S  R  +      G +    R+L    WG +CP  TP+G+ CGL+ +++    + S   
Sbjct: 475  LSHLRRTNTPIGRDG-KLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCI-SVGT 532

Query: 478  SRGNIRDFSKMR----------------TSILRVLIGVGMIPSLPKLVKSGPPAVLSVLL 521
                I  F                    T +    +  G+  +  +L+++         +
Sbjct: 533  DPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDI 592

Query: 522  DGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPP-- 579
            +  V  +    E E  +            ++ DD  +G+  L +   +    + T     
Sbjct: 593  NPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDI 652

Query: 580  --KFVRPVRNISLPSEESQNIELIGPFEQVFMEIRC-------------------PDGGD 618
               F                +E I   E+  + I                     P    
Sbjct: 653  EGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRI 712

Query: 619  GGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRA 678
                +A   TH EIHP+ +L V A++ P+ DHNQSPRN YQ  M KQ MG  +     R 
Sbjct: 713  RVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRM 772

Query: 679  DQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738
            D     L  PQ P+  T         E P G NAIVA+  Y+GY+ ED+MI+N+SS+DRG
Sbjct: 773  DTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRG 832

Query: 739  MCHGQIYQTETIDLSDDGNKVDRGQKLFRRNKDAKSLHSV---IDSDGLPYVGQMIHPGE 795
            +     +++        G  +    +  +R    +  H     +D DGL   G  +   +
Sbjct: 833  LFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGED 892

Query: 796  PYCSIYDKTT------------NSWRTNSR--KGSESVFVDYVAVDMKNSKNLPQKANIR 841
                     +            +S R  S   + +E+  VD V   +  +++  +   +R
Sbjct: 893  VIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVL--VTTNQDGLKFVKVR 950

Query: 842  FRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAML 901
             R T+ P IGDKF+SRHGQKG     +   DMPF+   G+ PDLIINPHA PSRMT+A L
Sbjct: 951  VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA-EGIVPDLIINPHAIPSRMTVAHL 1009

Query: 902  LESVAAK 908
            +E + +K
Sbjct: 1010 IECLLSK 1016
>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 ?
Query910
d1twfb_ 1207 RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta 100.0
d1smyc_ 1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 100.0
d1smyc_ 1119 RNA-polymerase beta {Thermus thermophilus [TaxId: 97.88
>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=0  Score=1674.56  Aligned_cols=841  Identities=27%  Similarity=0.407  Sum_probs=708.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHH---------------------------------------------------HHH
Q ss_conf             37033499999979999997699999---------------------------------------------------999
Q 002545           10 EPLRELVRHHIESFDYMLDEGLSEMF---------------------------------------------------DHC   38 (910)
Q Consensus        10 ~~~~~lv~~hi~SFn~Fi~~gl~~ii---------------------------------------------------~ea   38 (910)
                      ...++|++|||||||+||++||++|+                                                   +||
T Consensus        21 f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i~kP~~~e~~g~~~~l~P~Ec  100 (1207)
T d1twfb_          21 FREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEA  100 (1207)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEEEEEEECCSSSCCEECCHHHH
T ss_pred             HCCCCCCHHHHHHHHHHHHHCHHHHHHHCCCEEEECCCCCCCCCCCCCCEEEEEEEEEEECCCEEECCCCCCCCCCHHHH
T ss_conf             68998608989999999987879999850975763155555544678856999998999838837707886265698999


Q ss_pred             HHCCCEEEEEEEEEEEEEEECC-----------------CCCEEEEEEEECCCCEEECCCCCCCCCCCHHHHHHCCCCCC
Q ss_conf             9729904368999999999539-----------------99625537654045103057974489999577872133212
Q 002545           39 RQAKISYTGKLMADVEFQYLDA-----------------GSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAA  101 (910)
Q Consensus        39 R~r~~TYs~~l~v~i~~~~~~~-----------------~~~~~~~~v~iG~iPIMv~S~~C~L~~~s~~el~~~~E~~~  101 (910)
                      |+|++||+|+|+|++.+++...                 .......+|+||+|||||+|++|||++++++++++.||||+
T Consensus       101 R~r~lTYs~~l~v~i~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv~S~~C~L~~~~~~~l~~~gEc~~  180 (1207)
T d1twfb_         101 RLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPF  180 (1207)
T ss_dssp             HHTTCCCEEEEECCEECCCCC-------------------------CCEEEEEECCTTSTTSGGGTCCHHHHHHTTCCTT
T ss_pred             HHCCCCCCEEEEEEEEEEEEECCCCCCCCCCEEECCCCCCCCEEEEEEEEEECCEEECCCCCCCCCCCHHHHHHCCCCCC
T ss_conf             84099513179999999997403566541110002345555315620899778878088854489969899987289977


Q ss_pred             CCCCEEEECCCEEEEEEEEEECCCCCEEEEECCCCCCCCCCEEEEEEEEEEECCCCC--EEEEEEEE-ECCE--EEEEEE
Q ss_conf             589489993940099999840499408997125447898510238999966519982--39999998-2890--899999
Q 002545          102 EMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSS--VTLKLYYL-LNGS--VRLGFW  176 (910)
Q Consensus       102 D~GGYFIInG~EKVIr~~i~~~~N~~~~~~r~~~~~~~~~~t~~~v~ir~~~~~~~~--~~~~l~~~-~~g~--~~l~~~  176 (910)
                      |+||||||||+||||++|+...+|+++++.+     ++..++.+++.+||+.+++..  .+..+.+. .++.  ..+++.
T Consensus       181 D~GGYFIING~EKVIi~Q~r~~~n~~~v~~~-----~~~~~~~~~~~irS~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~  255 (1207)
T d1twfb_         181 DMGGYFIINGSEKVLIAQERSAGNIVQVFKK-----AAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKAT  255 (1207)
T ss_dssp             CCCCSEEETTEEEEECEEEEECSSCCEEEEC-----CTTSSEEEEEEEECCCSSSCCCCCEEEEEEESCSSCSSCCEEEE
T ss_pred             CCCCEEEECCEEEEEEEEEECCCCEEEEEEC-----CCCCCEEEEEEEEEEECCCCCEEEEEEEEEEECCCCCCEEEEEE
T ss_conf             8981799899999999997469976999974-----79993699999999927997343799999987188653699999


Q ss_pred             EECCCCCCCHHHHHHHCCCCCHHHHHHHHCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             60643331097799861479888999871012210010002788981167899999999984023129899999850346
Q 002545          177 LQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQ  256 (910)
Q Consensus       177 ~~k~~~~IPi~illkALg~~sD~eI~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~~i~t~~~al~yig~~f~  256 (910)
                      +.+...+||+++||||||..+|+||++.++.           +..+..+.+.+...++.  ...+.|+++|+.|||++++
T Consensus       256 ~~~~~~~IPl~illrALG~~sD~eI~~~i~~-----------~~~~~~~~~~l~~~~~~--~~~~~t~e~al~yig~~~~  322 (1207)
T d1twfb_         256 LPYIKQDIPIVIIFRALGIIPDGEILEHICY-----------DVNDWQMLEMLKPCVED--GFVIQDRETALDFIGRRGT  322 (1207)
T ss_dssp             CTTCSSCEEHHHHHHHTTCCSHHHHHHHHCC-----------CTTCHHHHHHHHHHHHH--TTTCCSHHHHHHHHHHTTS
T ss_pred             EEHHCCCCHHHHHHHHHCCCCHHHHHHHCCC-----------CCHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHCC
T ss_conf             5101045318888987388510434644046-----------73016789998888763--0104668899999876312


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCC----CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCHHHHHHH
Q ss_conf             54468888617999999997674357999----84328999999999986107998889943112607745303069999
Q 002545          257 PVIDGLQSESYYAVAETVIRDYIFVHLND----NNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYL  332 (910)
Q Consensus       257 ~~~~~~~~~~~~~~g~~~L~~~ll~Hi~~----~~~K~~~L~~Mv~kLl~~~~g~~~~Dd~D~~~nkrv~l~G~Ll~~lf  332 (910)
                      ..  .....+..+.++++|++.+|||++.    +..|+.+|++|++||+.+..|.+.+||+|||+||||+++|+||+.+|
T Consensus       323 ~~--~~~~~~~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~~~f  400 (1207)
T d1twfb_         323 AL--GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF  400 (1207)
T ss_dssp             CT--TSCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHHHHH
T ss_pred             CC--CCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHHHH
T ss_conf             55--8874426899999987530123465432025678889999988777651446776345541004542789999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             99999999999999999886269841341068899987218972428999867414676644455444345418980430
Q 002545          333 KEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERL  412 (910)
Q Consensus       333 ~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~It~~l~~~lsTGnw~~~~~~~~~q~sGvsqvleRl  412 (910)
                      ++.|+++++.++..+.+.... .+.++      +   ....+++.||+++++|||||||..+.+ ++.|++|++|+|+|+
T Consensus       401 r~~~~~~~~~i~~~~~~~~~~-~~~~~------~---~~~~~~~~it~~i~~~~~TGn~~~~~~-~~~~~~G~sq~l~r~  469 (1207)
T d1twfb_         401 KTLFKKLTKDIFRYMQRTVEE-AHDFN------M---KLAINAKTITSGLKYALATGNWGEQKK-AMSSRAGVSQVLNRY  469 (1207)
T ss_dssp             HHHHHHHHHHHHHHHHSCCC------------------CCCCTHHHHHHHHHHHHHCCCC----------CCCEEECCCS
T ss_pred             HHHHHHHHHHHHHHHCCCCCC-CCCCC------H---HHHHCCCCHHHHHHHHHHCCCCCCCCC-CCCCCCCHHHHHHHC
T ss_conf             999999888887640011122-33567------3---453326707799999875076443445-544343022233304


Q ss_pred             CHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHHHH
Q ss_conf             25668553000136985566555666424777752101478999854454445661269920038988643320116889
Q 002545          413 NFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSI  492 (910)
Q Consensus       413 N~~~~lSh~Rrv~rg~~~~~~K~t~~R~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~Is~~~~~~~~~~~~~~~~~~i  492 (910)
                      ||++++||+||||+| +++++|+++||+||||||||+||+|||||++|||+||||++|+|+...+..           .+
T Consensus       470 n~l~~lSh~Rrv~~~-~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~-----------~~  537 (1207)
T d1twfb_         470 TYSSTLSHLRRTNTP-IGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPM-----------PI  537 (1207)
T ss_dssp             SHHHHHHHHTEEECC-C------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCH-----------HH
T ss_pred             CHHHHHHHHHCCCCC-CCCCCCCCHHHHCCHHHCCCEEEEECCCCCCCCCEECCCEEEEECCCCCCC-----------EE
T ss_conf             798998864414677-655555531533366445421002478987534321342146530366420-----------25


Q ss_pred             HHHHHHCCCEECCCCCCCCCCCCEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCE
Q ss_conf             99998469812587543589996069998989994544951899999999988816888899844799986789988805
Q 002545          493 LRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGL  572 (910)
Q Consensus       493 ~~~L~~lg~~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~~~lr~lk~~~~~~i~~~~ei~~v~~~~~~~~~~i  572 (910)
                      .++|..+|+..+. ........+.++||+||.|+|++  .++..+++.+|.+|+.|  .++.+.++.+.     ....++
T Consensus       538 ~~~l~~~g~~~~~-~~~~~~~~~~~~V~~nG~~~G~~--~~~~~l~~~lr~~R~~g--~i~~~~s~~~~-----~~~~~i  607 (1207)
T d1twfb_         538 ITFLSEWGMEPLE-DYVPHQSPDATRVFVNGVWHGVH--RNPARLMETLRTLRRKG--DINPEVSMIRD-----IREKEL  607 (1207)
T ss_dssp             HHHHHHTTCEEGG-GCCGGGCTTCEEEEETTEEEEEE--SCHHHHHHHHHHHHHHT--SSCTTCEEEEE-----TTTTEE
T ss_pred             EEEEECCCCCCCE-EEEECCCCCCCEEEEEEEEEEEE--CCHHEEEHHEEEEEECC--CCCCEEEEEEE-----CCCCCE
T ss_conf             6775135863202-44201056531033201278997--00101100035645416--76623444320-----345532


Q ss_pred             EEECCCCCEECEEEEECCCCC----------------------------------------CCCCEEEECCCCEEEEEEE
Q ss_conf             965499920000775058998----------------------------------------8875666475430534642
Q 002545          573 YLFTSPPKFVRPVRNISLPSE----------------------------------------ESQNIELIGPFEQVFMEIR  612 (910)
Q Consensus       573 ~I~td~gR~~RPv~~~~~~~~----------------------------------------~~g~iE~id~~Eq~~~~Ia  612 (910)
                      +|++|+||++|||+.+.++..                                        ..|.|||||+.||+++.||
T Consensus       608 ~i~td~Gr~~rPlfi~~nd~~~~~~~~~mqrq~v~~l~~~e~~~v~~~~e~~~~~~~~~~~~~g~ieyid~~E~~~~~Ia  687 (1207)
T d1twfb_         608 KIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIA  687 (1207)
T ss_dssp             EEECCSCCEEEEEEEEECCCTTSSCEESCCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTTCCEE
T ss_pred             EEEECCCCCCCCCEEECCHHHHCCCCEEEEHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCCCCCCEEEECCHHCCEEEEE
T ss_conf             89944765567734440522304544355676676541320112556631112125410045771355400004638999


Q ss_pred             CCCCCCCCCC-------------------CCCCCEECCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHCCCCCCCCCEEE
Q ss_conf             3899999987-------------------887730012478765320221254899998401111100001234431138
Q 002545          613 CPDGGDGGRR-------------------NAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQA  673 (910)
Q Consensus       613 ~~~~~~~~~~-------------------~~~~~th~Ei~p~~ils~~asliPF~~hNqspRn~yq~~M~KQaig~~~~n  673 (910)
                      ++++++....                   ....+||+||+|+++||++|++|||++|||||||+|||||+|||||++++|
T Consensus       688 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~th~Ei~p~~ilg~~as~iPf~~hNqSpRn~yq~qm~KQa~G~~~~~  767 (1207)
T d1twfb_         688 MQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTN  767 (1207)
T ss_dssp             SSGGGGCC---------CCCTTSCCCCCCCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHHHGGGBCBCSCTT
T ss_pred             ECCCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCCEEEEEECCEEEECCCCCCCCEEECCCCCCCCCCCCCCC
T ss_conf             62332442235544554455213201102455432222366127753120687312344564011034774567721134


Q ss_pred             EEEECCCCEEECCCCCEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEECCCCCCCCCEEEEEEEEEEEEE
Q ss_conf             99841574255279981058346400138643689840168997336888553254420000147611249999999730
Q 002545          674 LKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLS  753 (910)
Q Consensus       674 ~~~R~d~~~y~L~~pQ~Plv~t~~~~~~~~~~~~~G~N~iVav~~y~Gyn~EDaiiink~s~~rG~~~~~~~~~~~~~~~  753 (910)
                      +..|.|++.|+|.|||+|||+|+.++.++++++|+|+||+||||||+|||||||||+||+|++||+||+++|+++.++..
T Consensus       768 ~~~r~D~~~~~l~~pQ~Plv~t~~~~~~~~~e~p~G~N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~  847 (1207)
T d1twfb_         768 YNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK  847 (1207)
T ss_dssp             TTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCC
T ss_pred             CCEECCCCCEEEECCCCCEEECCCHHHHHHHCCCCHHCEEEEEEECCCCCCCCCCCCCHHHHHHCCCCEEEEEEEEEEEC
T ss_conf             42330355406741787225002001112211520005289998045765554432356663203121223578998821


Q ss_pred             CCCCCCCCCCEEECCCC------CCHHHHCCCCCCCCCCCCCEECCCCCEEEEECCCC--------------CCEEEEEE
Q ss_conf             24787676501100598------87021102699998554706659994998321689--------------93434550
Q 002545          754 DDGNKVDRGQKLFRRNK------DAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTT--------------NSWRTNSR  813 (910)
Q Consensus       754 ~~~~~~~~~~~~f~~~~------~~~~~~~~ld~dG~~~~G~~v~~gdil~~~~~~~~--------------~~~~~~~~  813 (910)
                      ....   ...+.|..|.      .....+++||+||+|++|++|.+||+|++|..+..              .++.|+.+
T Consensus       848 ~~~~---~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~~~~~~~~~~s~~~  924 (1207)
T d1twfb_         848 KYGM---SITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPL  924 (1207)
T ss_dssp             CSCT---TCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC-------------CCBBCCEEC
T ss_pred             CCCC---CCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHCCCCCCCCCEEEEC
T ss_conf             3666---3221145654455433321112106521201332114689531345410478601210011122345256882


Q ss_pred             CCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEECCCCCCCEECCCCCCCEEEEEECCCCCCCCCCCCCCCCEEECCCCCC
Q ss_conf             69985699999997057999970899999224089766400024798237853204767684489999682973899866
Q 002545          814 KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFP  893 (910)
Q Consensus       814 ~~~e~g~v~~v~~~~~~~g~~~~~~~i~~r~~r~p~iGDKf~sRHGqKGv~s~~~~~~dmPf~~~~G~~pDiI~NPh~~P  893 (910)
                      +.+++|+||+|..+.+.++  .+.++|++|+.|+|+||||||||||||||||++||+|||||| +||++|||||||||||
T Consensus       925 ~~~~~g~V~~v~~~~~~~~--~~~~kv~i~~~R~p~iGDKfasRhGqKGv~s~i~p~eDMPf~-~dG~~pDiI~NP~g~P 1001 (1207)
T d1twfb_         925 RSTENGIVDQVLVTTNQDG--LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFT-AEGIVPDLIINPHAIP 1001 (1207)
T ss_dssp             CTTCCEEEEEEEEEECSSS--CEEEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTSCEE-TTSCCCSEEECGGGST
T ss_pred             CCCCCEEEEEEEEEECCCC--CCEEEEEEEEEECCCHHHHHHHCCCCCCEEEEEECHHHCCCC-CCCCCCCEEECCCCCC
T ss_conf             3799737899997202564--201249999873162155664225775134434136639948-8999861887898676


Q ss_pred             CCCCHHHHHHHHHCCC
Q ss_conf             5564889998730246
Q 002545          894 SRMTIAMLLESVAAKE  909 (910)
Q Consensus       894 SRMtiGql~E~~~gK~  909 (910)
                      ||||||||+|+++||+
T Consensus      1002 SRMtiGql~E~~~gk~ 1017 (1207)
T d1twfb_        1002 SRMTVAHLIECLLSKV 1017 (1207)
T ss_dssp             TTTCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH
T ss_conf             6671999999987788
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure