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Conserved domains on  [gi|1710738101|gb|QDS03210|]
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RNA polymerase II subunit 2, partial [Atractospora aquatica]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 1000145)

DNA-directed RNA polymerase subunit B family protein similar to fungal DNA-directed RNA polymerase II subunit RPB2

CATH:  3.90.1110.10|3.90.1070.20
EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0000428|GO:0008270|GO:0003677|GO:0006351
PubMed:  11839495
SCOP:  4003708

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-355 8.10e-89

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK08565:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1103  Bit Score: 288.78  E-value: 8.10e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101    1 FRNIVRKMTSELMHYLKRcidgNRMFDIRMGMRHQTLTNALKYSLATGNWGDQKkamsstAGVSQVLNRYTFASTLSHLR 80
Cdd:PRK08565   350 FKQLVKDLKYQLEKSYAR----GRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLR 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   81 RTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPAEPIVDfmIARNMEV--LEEYEPLRY 158
Cdd:PRK08565   420 RVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEY 497

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  159 PNATKVFVNGTWVGVHQDPKHLVGLVQGLRRKGIIQSEVSL--IRDIRDREFKIFSDAGRVMRPLFAVEqednsesgveK 236
Cdd:PRK08565   498 ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE----------N 567

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  237 GALLLTKELVAKLEADEdlpsnhpdyFGWDGISRAGAIEYLDAEEEETAMICMTPEDLenyrlqkagfqipddmgdedln 316
Cdd:PRK08565   568 GKPKLTREHVEKLKKGE---------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------------------- 616

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1710738101  317 krlktklnptTHMYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:PRK08565   617 ----------TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-355 8.10e-89

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 288.78  E-value: 8.10e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101    1 FRNIVRKMTSELMHYLKRcidgNRMFDIRMGMRHQTLTNALKYSLATGNWGDQKkamsstAGVSQVLNRYTFASTLSHLR 80
Cdd:PRK08565   350 FKQLVKDLKYQLEKSYAR----GRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLR 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   81 RTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPAEPIVDfmIARNMEV--LEEYEPLRY 158
Cdd:PRK08565   420 RVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEY 497

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  159 PNATKVFVNGTWVGVHQDPKHLVGLVQGLRRKGIIQSEVSL--IRDIRDREFKIFSDAGRVMRPLFAVEqednsesgveK 236
Cdd:PRK08565   498 ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE----------N 567

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  237 GALLLTKELVAKLEADEdlpsnhpdyFGWDGISRAGAIEYLDAEEEETAMICMTPEDLenyrlqkagfqipddmgdedln 316
Cdd:PRK08565   568 GKPKLTREHVEKLKKGE---------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------------------- 616

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1710738101  317 krlktklnptTHMYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:PRK08565   617 ----------TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-355 5.15e-46

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 167.75  E-value: 5.15e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   1 FRNIVRKMTSELMHYLKRCIDGNRMFDIRMGMRHQTLTNALKYSLATGNWGDQKKAMSsTAGVSQVLNRYTFASTLSHLR 80
Cdd:cd00653   252 FRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKR 330

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  81 RTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgtpaepivdfmiarnmevleeyeplryp 159
Cdd:cd00653   331 RISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------------------- 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101 160 natkvfvngtwvgvhqdpkhlvglvqglrrkgiiqsevslirdirdrefkifsdaGRVMRPLFAVEQEdnsesgvekgal 239
Cdd:cd00653   382 -------------------------------------------------------GRIERPYRIVEKE------------ 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101 240 lltkelvakleadedlpsnhpdyfgwdgisragaieyldaeeeetamicmtpedlenyrlqkagfqipddmgdedlnkrl 319
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1710738101 320 ktklnptthmYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:cd00653   395 ----------VTHIEISPSQILSVAASLIPFPEHNQ 420
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 65-128 9.21e-32

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 114.16  E-value: 9.21e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1710738101  65 QVLNRYTFASTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 128
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 54-355 5.90e-21

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 94.41  E-value: 5.90e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   54 KKAMSSTaGVSQVLNRYTFASTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSL 125
Cdd:COG0085    363 KEFFGSS-QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLAL 437

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  126 MCYVSvgtpaepivdfmiarnmevleEYeplrypnatkvfvngtwvgvhqdpkhlvglvqglrrkgiiqsevslirdird 205
Cdd:COG0085    438 YARVN---------------------EY---------------------------------------------------- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  206 refkifsdaGRVMRPLFAveqednsesgVEKGalLLTKElvakleadedlpsnhpdyfgwdgisragaIEYLDAEEEETA 285
Cdd:COG0085    445 ---------GFIETPYRK----------VENG--KVTDE-----------------------------IEYLTADEEENY 474

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1710738101  286 MICMTPEDLenyrlqkagfqipDDMG---DEDLNKRLKTK-LNPTTHMYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:COG0085    475 YIAQANAPL-------------DEDGnflEERVLVRYRGEeVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDD 535
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-355 8.10e-89

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 288.78  E-value: 8.10e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101    1 FRNIVRKMTSELMHYLKRcidgNRMFDIRMGMRHQTLTNALKYSLATGNWGDQKkamsstAGVSQVLNRYTFASTLSHLR 80
Cdd:PRK08565   350 FKQLVKDLKYQLEKSYAR----GRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLR 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   81 RTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPAEPIVDfmIARNMEV--LEEYEPLRY 158
Cdd:PRK08565   420 RVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEY 497

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  159 PNATKVFVNGTWVGVHQDPKHLVGLVQGLRRKGIIQSEVSL--IRDIRDREFKIFSDAGRVMRPLFAVEqednsesgveK 236
Cdd:PRK08565   498 ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE----------N 567

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  237 GALLLTKELVAKLEADEdlpsnhpdyFGWDGISRAGAIEYLDAEEEETAMICMTPEDLenyrlqkagfqipddmgdedln 316
Cdd:PRK08565   568 GKPKLTREHVEKLKKGE---------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------------------- 616

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1710738101  317 krlktklnptTHMYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:PRK08565   617 ----------TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-355 5.15e-46

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 167.75  E-value: 5.15e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   1 FRNIVRKMTSELMHYLKRCIDGNRMFDIRMGMRHQTLTNALKYSLATGNWGDQKKAMSsTAGVSQVLNRYTFASTLSHLR 80
Cdd:cd00653   252 FRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKR 330

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  81 RTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgtpaepivdfmiarnmevleeyeplryp 159
Cdd:cd00653   331 RISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------------------- 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101 160 natkvfvngtwvgvhqdpkhlvglvqglrrkgiiqsevslirdirdrefkifsdaGRVMRPLFAVEQEdnsesgvekgal 239
Cdd:cd00653   382 -------------------------------------------------------GRIERPYRIVEKE------------ 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101 240 lltkelvakleadedlpsnhpdyfgwdgisragaieyldaeeeetamicmtpedlenyrlqkagfqipddmgdedlnkrl 319
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1710738101 320 ktklnptthmYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:cd00653   395 ----------VTHIEISPSQILSVAASLIPFPEHNQ 420
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 162-355 3.77e-36

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 138.17  E-value: 3.77e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101 162 TKVFVNGTWVGVHQDPKHLVGLVQGLRRKGIIQSEVSLIRDIRDREFKIFSDAGRVMRPLFAVEqednsesgveKGALLL 241
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVE----------NGEPLL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101 242 TKELVAKLEADEdlpsnhpdyFGWDGISRAGAIEYLDAEEEETAMICMTPEDLenyrlqkagfqipddmgdedlnkrlkt 321
Cdd:PRK07225   75 TEEHIEKLKNGE---------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL--------------------------- 118

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1710738101 322 klnptTHMYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:PRK07225  119 -----TEEHTHLEIDPSLILGIGAGMIPYPEHNA 147
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-154 4.10e-32

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 125.45  E-value: 4.10e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   1 FRNIVRKMTSELMHYLKRCIDGNRMFDIRMGMRHQTLTNALKYSLATGNWgdqkkaMSSTAGVSQVLNRYTFASTLSHLR 80
Cdd:PRK09606  349 FRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLR 422

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1710738101  81 RTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPAEPIVDFMiaRNMEVLEEYE 154
Cdd:PRK09606  423 RVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL--KELGVEPERG 494
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 65-128 9.21e-32

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 114.16  E-value: 9.21e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1710738101  65 QVLNRYTFASTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 128
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 164-225 7.83e-29

RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 105.91  E-value: 7.83e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1710738101 164 VFVNGTWVGVHQDPKHLVGLVQGLRRKGIIQSEVSLIRDIRDREFKIFSDAGRVMRPLFAVE 225
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 265-337 1.16e-22

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 89.52  E-value: 1.16e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1710738101 265 WDGISRAGAIEYLDAEEEETAMICMTPEDLENY-RLQKAGfqipddmgdedlnkrlktklnPTTHMYTHCEIHP 337
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREG---------------------PYAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 54-355 5.90e-21

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 94.41  E-value: 5.90e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   54 KKAMSSTaGVSQVLNRYTFASTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSL 125
Cdd:COG0085    363 KEFFGSS-QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLAL 437

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  126 MCYVSvgtpaepivdfmiarnmevleEYeplrypnatkvfvngtwvgvhqdpkhlvglvqglrrkgiiqsevslirdird 205
Cdd:COG0085    438 YARVN---------------------EY---------------------------------------------------- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101  206 refkifsdaGRVMRPLFAveqednsesgVEKGalLLTKElvakleadedlpsnhpdyfgwdgisragaIEYLDAEEEETA 285
Cdd:COG0085    445 ---------GFIETPYRK----------VENG--KVTDE-----------------------------IEYLTADEEENY 474

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1710738101  286 MICMTPEDLenyrlqkagfqipDDMG---DEDLNKRLKTK-LNPTTHMYTHCEIHPSMLLGICASIIPFPDHNQ 355
Cdd:COG0085    475 YIAQANAPL-------------DEDGnflEERVLVRYRGEeVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDD 535
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
59-150 1.89e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 53.09  E-value: 1.89e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710738101   59 STAGVSQVLNRYTFASTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS---- 130
Cdd:PRK14844   528 NSSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygf 607

                           90       100
                   ....*....|....*....|
gi 1710738101  131 VGTPAEPIVDFMIARNMEVL 150
Cdd:PRK14844   608 IESPYRKVVNRVVTDQIEYL 627
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
63-124 9.53e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.08  E-value: 9.53e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1710738101   63 VSQVLNRYTFASTLSHLRRTNTpIGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLS 124
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 63-124 2.21e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 46.24  E-value: 2.21e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1710738101   63 VSQVLNRYTFASTLSHLRRTNT--PIGRDgKLAKP---RQLHNTHWGLVCPAETPEGQACGLVKNLS 124
Cdd:CHL00207   366 LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 96-124 1.16e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 1.16e-04
                           10        20
                   ....*....|....*....|....*....
gi 1710738101   96 RQLHNTHWGLVCPAETPEGQACGLVKNLS 124
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 64-132 2.03e-03

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 40.27  E-value: 2.03e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1710738101   64 SQVLNRYTFASTLSHLRRTNT--PIGRDGKLA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVSVG 132
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIG 445
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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