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Conserved domains on  [gi|954580906|gb|ALP48317|]
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RNA polymerase II second largest subunit, partial [Dissoconium aciculare]

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;
1-388 3.04e-111

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: 351.18  E-value: 3.04e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTSGLRYCLATGNWGdqkkasSA 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GG 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   81 KAGVSQVLNRYTYASTLSHLQRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPTRPLV 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  161 HFLQSRYLEPLEDYDPAASPNATKIFLNGVWLGVTHGPNQLVDMLHEIRRKGVISFEVTI--IRDVREREIKIFTDVGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  239 CRPLFVVDNkpgspgrGGLVLKREHLKRLeqDQEMLSstdgmseedrqnyiygWKGLLEDGVVEYLDAEEEETAMIIMTP 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL--KKGELT----------------FDDLVKMGVIEYLDAEEEENAYVALDP 613

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 954580906  319 EDL-EEHrmlrsglprfeeskadphrrikqkpnkhvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQ 388
Cdd:PRK08565  614 EDLtPEH--------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQ 652
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-388 3.04e-111

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 351.18  E-value: 3.04e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTSGLRYCLATGNWGdqkkasSA 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GG 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   81 KAGVSQVLNRYTYASTLSHLQRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPTRPLV 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  161 HFLQSRYLEPLEDYDPAASPNATKIFLNGVWLGVTHGPNQLVDMLHEIRRKGVISFEVTI--IRDVREREIKIFTDVGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  239 CRPLFVVDNkpgspgrGGLVLKREHLKRLeqDQEMLSstdgmseedrqnyiygWKGLLEDGVVEYLDAEEEETAMIIMTP 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL--KKGELT----------------FDDLVKMGVIEYLDAEEEENAYVALDP 613

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 954580906  319 EDL-EEHrmlrsglprfeeskadphrrikqkpnkhvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQ 388
Cdd:PRK08565  614 EDLtPEH--------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQ 652
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-389 1.09e-69

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: 235.54  E-value: 1.09e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTSGLRYCLATGNWGDQKKASSa 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ- 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  81 KAGVSQVLNRYTYASTLSHLQRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtptrpl 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 160 vhflqsrylepledydpaaspnatkiflngvwlgvthgpnqlvdmlheirrkgvisfevtiirdvrereikiftdvGRVC 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 240 RPLFVVDNKpgspgrgglvlkrehlkrleqdqemlsstdgmseedrqnyiygwkglledgvveyldaeeeetamiimtpe 319
Cdd:cd00653  386 RPYRIVEKE----------------------------------------------------------------------- 394

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 320 dleehrmlrsglprfeeskadphrrikqkpnkhvrtWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQC 389
Cdd:cd00653  395 ------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-388 4.08e-37

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: 143.71  E-value: 4.08e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQveQNKEPNLALAIKTNILTSGLRYCLATGnwgdqkkassa 80
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQ--DVEAITPQSLINIRPVVAAIKEFFGSS----------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   81 kaGVSQVLNRYTYASTLSHLQRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTV 152
Cdd:COG0085   370 --QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  153 gtptrplvhflqsrylepledydpaaspnatkiflngvwlgvthgpnqlvdmlheirrkgvisfevtiirdvrereikif 232
Cdd:COG0085       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  233 tdVGRVCRPLFVVDNkpgspgrgGLVlkrehlkrleqdqemlssTDGmseedrqnyiygwkglledgvVEYLDAEEEETA 312
Cdd:COG0085   444 --YGFIETPYRKVEN--------GKV------------------TDE---------------------IEYLTADEEENY 474

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580906  313 MIIMTPEDLEEHRmlrsglpRFEESKADPHRR---IKQKPNKHvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQ 388
Cdd:COG0085   475 YIAQANAPLDEDG-------NFLEERVLVRYRgeeVLVPPEEV----DYMDVSPKQIVSVATSLIPFLEHDDANRALMG 542
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 4.59e-30

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: 110.69  E-value: 4.59e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580906   86 QVLNRYTYASTLSHLQRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 149
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-388 3.04e-111

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 351.18  E-value: 3.04e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTSGLRYCLATGNWGdqkkasSA 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GG 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   81 KAGVSQVLNRYTYASTLSHLQRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPTRPLV 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  161 HFLQSRYLEPLEDYDPAASPNATKIFLNGVWLGVTHGPNQLVDMLHEIRRKGVISFEVTI--IRDVREREIKIFTDVGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  239 CRPLFVVDNkpgspgrGGLVLKREHLKRLeqDQEMLSstdgmseedrqnyiygWKGLLEDGVVEYLDAEEEETAMIIMTP 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL--KKGELT----------------FDDLVKMGVIEYLDAEEEENAYVALDP 613

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 954580906  319 EDL-EEHrmlrsglprfeeskadphrrikqkpnkhvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQ 388
Cdd:PRK08565  614 EDLtPEH--------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQ 652
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-389 1.09e-69

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: 235.54  E-value: 1.09e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTSGLRYCLATGNWGDQKKASSa 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ- 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  81 KAGVSQVLNRYTYASTLSHLQRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtptrpl 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 160 vhflqsrylepledydpaaspnatkiflngvwlgvthgpnqlvdmlheirrkgvisfevtiirdvrereikiftdvGRVC 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 240 RPLFVVDNKpgspgrgglvlkrehlkrleqdqemlsstdgmseedrqnyiygwkglledgvveyldaeeeetamiimtpe 319
Cdd:cd00653  386 RPYRIVEKE----------------------------------------------------------------------- 394

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 320 dleehrmlrsglprfeeskadphrrikqkpnkhvrtWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQC 389
Cdd:cd00653  395 ------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-171 1.40e-50

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 177.45  E-value: 1.40e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTSGLRYCLATGNWgdqkkaSSA 80
Cdd:PRK09606 328 DDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGG 401

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  81 KAGVSQVLNRYTYASTLSHLQRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPTRPLV 160
Cdd:PRK09606 402 RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481

                        170
                 ....*....|.
gi 954580906 161 HFLQSRYLEPL 171
Cdd:PRK09606 482 EILKELGVEPE 492
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 183-388 2.37e-41

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 154.35  E-value: 2.37e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 183 TKIFLNGVWLGVTHGPNQLVDMLHEIRRKGVISFEVTIIRDVREREIKIFTDVGRVCRPLFVVDNkpGSPgrgglVLKRE 262
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN--GEP-----LLTEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906 263 HLKRLEQDQEmlsstdgmseedrqnyiyGWKGLLEDGVVEYLDAEEEETAMIIMTPEDL-EEHrmlrsglprfeeskadp 341
Cdd:PRK07225  78 HIEKLKNGEL------------------TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH----------------- 122

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 954580906 342 hrrikqkpnkhvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQ 388
Cdd:PRK07225 123 ---------------THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-388 4.08e-37

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: 143.71  E-value: 4.08e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQveQNKEPNLALAIKTNILTSGLRYCLATGnwgdqkkassa 80
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQ--DVEAITPQSLINIRPVVAAIKEFFGSS----------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   81 kaGVSQVLNRYTYASTLSHLQRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTV 152
Cdd:COG0085   370 --QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  153 gtptrplvhflqsrylepledydpaaspnatkiflngvwlgvthgpnqlvdmlheirrkgvisfevtiirdvrereikif 232
Cdd:COG0085       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906  233 tdVGRVCRPLFVVDNkpgspgrgGLVlkrehlkrleqdqemlssTDGmseedrqnyiygwkglledgvVEYLDAEEEETA 312
Cdd:COG0085   444 --YGFIETPYRKVEN--------GKV------------------TDE---------------------IEYLTADEEENY 474

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580906  313 MIIMTPEDLEEHRmlrsglpRFEESKADPHRR---IKQKPNKHvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQ 388
Cdd:COG0085   475 YIAQANAPLDEDG-------NFLEERVLVRYRgeeVLVPPEEV----DYMDVSPKQIVSVATSLIPFLEHDDANRALMG 542
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 4.59e-30

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: 110.69  E-value: 4.59e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580906   86 QVLNRYTYASTLSHLQRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 149
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 185-246 1.14e-27

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: 103.99  E-value: 1.14e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580906  185 IFLNGVWLGVTHGPNQLVDMLHEIRRKGVISFEVTIIRDVREREIKIFTDVGRVCRPLFVVD 246
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 292-363 1.09e-23

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: 92.99  E-value: 1.09e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580906  292 WKGLLEDGVVEYLDAEEEETAMIIMTPEDLEEHrmlrsglprfeeskadpHRRIKQKPNKHvrTWTHCEIHP 363
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEES-----------------SREEREGPYAH--TYTHCEIHP 53
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-60 2.13e-15

RNA polymerase beta subunit; 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). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 77.42  E-value: 2.13e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTS 60
Cdd:pfam04563 337 DDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-175 4.38e-10

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 61.95  E-value: 4.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFR---LKFAQLVKDTKQylTRQVEQNKEPNLalaIKTNILTSGLRyclatgnwgDQKKA 77
Cdd:PRK14844  464 DDIDHLGNRRVRSVGEFIENQFRtglLKLERAVVDSMS--TSSLDKVSPSDF---INPKVLTNVLR---------DFFNS 529

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   78 SSakagVSQVLNRYTYASTLSHLQRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMC----Y 149
Cdd:PRK14844  530 SQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYArinkY 605

                         170       180
                  ....*....|....*....|....*.
gi 954580906  150 VTVGTPTRPLVHFLQSRYLEPLEDYD 175
Cdd:PRK14844  606 GFIESPYRKVVNRVVTDQIEYLSAID 631
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-189 4.61e-10

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 61.86  E-value: 4.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTrqveqnkEPNLAL-------AIKTNILTSGLRYCLATGNwgd 73
Cdd:PRK09603  455 DDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLT-------TMSGAFdslmphdLVNSKMITSTIMEFFMGGQ--- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   74 qkkassakagVSQVLNRYTYASTLSHLQRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMC 148
Cdd:PRK09603  525 ----------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 954580906  149 YVT----VGTPTRPLVHFLQSR---YLEPLEDYDPAASPNATKIFLNG 189
Cdd:PRK09603  594 RVNdlgfIEAPYKKVVDGKVVGetiYLTAIQEDSHIIAPASTPIDEEG 641
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-145 2.40e-07

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 53.17  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLV-KDTKQYLTRQVEQ-------NKEPNLALaIKTNILTSGLryclatgnwg 72
Cdd:CHL00207  298 DDIDHLKNRRVRSVGELLQNQFRIGLKRLErILRNRMTICDIDSlskfnliNPKPLIAL-IREFFGSSQL---------- 366

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580906   73 dqkkassakagvSQVLNRYTYASTLSHLQRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:CHL00207  367 ------------SQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 370-389 5.08e-07

RNA polymerase Rpb2, domain 6; 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). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 51.38  E-value: 5.08e-07
                          10        20
                  ....*....|....*....|
gi 954580906  370 CASIIPFPDHNQSPRNTYQC 389
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQC 20
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 117-145 1.52e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.32  E-value: 1.52e-04
                          10        20
                  ....*....|....*....|....*....
gi 954580906  117 RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 1-169 4.82e-03

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 39.50  E-value: 4.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906    1 DDRDHFGKKRLDLAGPLMAQVFRLKFAQLVKDTKQYLTRQVEQNKEPNLALAIKTNILTSGLR-----YCLatgnwgdqk 75
Cdd:CHL00001  304 DDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYEsffgsHPL--------- 374

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580906   76 kassakagvSQVLNRYTYASTLSHLQRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVT 151
Cdd:CHL00001  375 ---------SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHAR 443

                         170
                  ....*....|....*...
gi 954580906  152 VGTptrplVHFLQSRYLE 169
Cdd:CHL00001  444 IGH-----WGSLESPFYE 456
 
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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