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Conserved domains on  [gi|954580878|gb|ALP48303|]
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RNA polymerase II second largest subunit, partial [Septoria protearum]

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;
1-396 2.30e-121

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: 377.37  E-value: 2.30e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKkasss 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR----- 399

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   81 kAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGSPLI 160
Cdd:PRK08565  400 -TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  161 DFMRQRGMDLLEEYDPVMNPRATKVMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTI--IRDVREREIRVFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  239 CRPLFVVDNdpkssnrGNLVLKQEQVERLQndqeilanlegvseeereKSIYGWKGLVDEGVVEYLDAEEEETAMITMTP 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKLK------------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDP 613

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580878  319 EDL-EEHknmragiqyddaredphrrikpkpnasvriwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:PRK08565  614 EDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-396 2.30e-121

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 377.37  E-value: 2.30e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKkasss 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR----- 399

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   81 kAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGSPLI 160
Cdd:PRK08565  400 -TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  161 DFMRQRGMDLLEEYDPVMNPRATKVMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTI--IRDVREREIRVFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  239 CRPLFVVDNdpkssnrGNLVLKQEQVERLQndqeilanlegvseeereKSIYGWKGLVDEGVVEYLDAEEEETAMITMTP 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKLK------------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDP 613

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580878  319 EDL-EEHknmragiqyddaredphrrikpkpnasvriwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:PRK08565  614 EDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-396 5.55e-80

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: 262.89  E-value: 5.55e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKKaSSS 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRF-LMQ 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  81 KAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpgspl 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 160 idfmrqrgmdlleeydpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereirvftdaGRVC 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 240 RPLFVVDNDpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkglvdegvveyldaeeeetamitmtpe 319
Cdd:cd00653  386 RPYRIVEKE----------------------------------------------------------------------- 394

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 320 dleehknmragiqyddaredphrrikpkpnasvriWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:cd00653  395 -----------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-396 1.55e-40

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: 153.34  E-value: 1.55e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLhrcvETGREFNITLA--VKTNIITSGLRYCLATGnwgdqkkas 78
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERM----TTQDVEAITPQslINIRPVVAAIKEFFGSS--------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   79 sskaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYV 150
Cdd:COG0085   370 ----QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV 441

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  151 TvgtpgsplidfmrqrgmdlleEYdpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereir 230
Cdd:COG0085   442 N---------------------EY-------------------------------------------------------- 444

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  231 vftdaGRVCRPLFVVDNdpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkGLVDEGvVEYLDAEEEE 310
Cdd:COG0085   445 -----GFIETPYRKVEN----------------------------------------------GKVTDE-IEYLTADEEE 472

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  311 TAMITMTPEDLEEHKNmragiqYDDAREDPHRRIKPKPNASVRIwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAM 390
Cdd:COG0085   473 NYYIAQANAPLDEDGN------FLEERVLVRYRGEEVLVPPEEV-DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANM 545


                  ....*.
gi 954580878  391 GKQAMG 396
Cdd:COG0085   546 QRQAVP 551
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 1.41e-31

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: 1.41e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878   86 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 149
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-396 2.30e-121

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 377.37  E-value: 2.30e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKkasss 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR----- 399

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   81 kAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGSPLI 160
Cdd:PRK08565  400 -TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  161 DFMRQRGMDLLEEYDPVMNPRATKVMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTI--IRDVREREIRVFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  239 CRPLFVVDNdpkssnrGNLVLKQEQVERLQndqeilanlegvseeereKSIYGWKGLVDEGVVEYLDAEEEETAMITMTP 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKLK------------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDP 613

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580878  319 EDL-EEHknmragiqyddaredphrrikpkpnasvriwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:PRK08565  614 EDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-396 5.55e-80

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: 262.89  E-value: 5.55e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQKKaSSS 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRF-LMQ 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  81 KAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpgspl 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 160 idfmrqrgmdlleeydpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereirvftdaGRVC 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 240 RPLFVVDNDpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkglvdegvveyldaeeeetamitmtpe 319
Cdd:cd00653  386 RPYRIVEKE----------------------------------------------------------------------- 394

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 320 dleehknmragiqyddaredphrrikpkpnasvriWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:cd00653  395 -----------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 181-396 9.66e-50

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 176.69  E-value: 9.66e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 181 RATKVMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVDNdpkssnrGNLVLK 260
Cdd:PRK07225   3 RKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878 261 QEQVERLQNDqEIlanlegvseeereksiyGWKGLVDEGVVEYLDAEEEETAMITMTPEDL-EEHknmragiqyddared 339
Cdd:PRK07225  76 EEHIEKLKNG-EL-----------------TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH--------------- 122

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878 340 phrrikpkpnasvriwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:PRK07225 123 ----------------THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLG 163
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-167 1.43e-48

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 171.67  E-value: 1.43e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWgdqkkaSSS 80
Cdd:PRK09606 328 DDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGG 401

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  81 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGSPLI 160
Cdd:PRK09606 402 RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481


                 ....*..
gi 954580878 161 DFMRQRG 167
Cdd:PRK09606 482 EILKELG 488
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-396 1.55e-40

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: 153.34  E-value: 1.55e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLhrcvETGREFNITLA--VKTNIITSGLRYCLATGnwgdqkkas 78
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERM----TTQDVEAITPQslINIRPVVAAIKEFFGSS--------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   79 sskaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYV 150
Cdd:COG0085   370 ----QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV 441

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  151 TvgtpgsplidfmrqrgmdlleEYdpvmnpratkvmlngtwvgvhrnaghladtlrslrrkgllsfevtiirdvrereir 230
Cdd:COG0085   442 N---------------------EY-------------------------------------------------------- 444

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  231 vftdaGRVCRPLFVVDNdpkssnrgnlvlkqeqverlqndqeilanlegvseeereksiygwkGLVDEGvVEYLDAEEEE 310
Cdd:COG0085   445 -----GFIETPYRKVEN----------------------------------------------GKVTDE-IEYLTADEEE 472

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878  311 TAMITMTPEDLEEHKNmragiqYDDAREDPHRRIKPKPNASVRIwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAM 390
Cdd:COG0085   473 NYYIAQANAPLDEDGN------FLEERVLVRYRGEEVLVPPEEV-DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANM 545


                  ....*.
gi 954580878  391 GKQAMG 396
Cdd:COG0085   546 QRQAVP 551
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 1.41e-31

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: 1.41e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580878   86 QVLNRYTYASTLSHLRRTNTPIG---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 1.98e-31

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: 113.62  E-value: 1.98e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580878  185 VMLNGTWVGVHRNAGHLADTLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVD 246
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 292-362 4.54e-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: 88.37  E-value: 4.54e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 954580878  292 WKGLVDEGVVEYLDAEEEETAMITMTPEDLEEHKNMRAGIQYddaredphrrikpkpnasVRIWTHCEIHP 362
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREGPY------------------AHTYTHCEIHP 53
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-60 5.50e-16

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: 78.96  E-value: 5.50e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVETGREFNITLAVKTNIITS 60
Cdd:pfam04563 337 DDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 369-396 3.14e-12

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: 67.17  E-value: 3.14e-12
                          10        20
                  ....*....|....*....|....*...
gi 954580878  369 CASIIPFPDHNQSPRNTYQSAMGKQAMG 396
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMG 28
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-145 4.31e-11

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 64.94  E-value: 4.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFR---LKLQQLVKETKQYLHRCVETGREFNItlaVKTNIITSGLRYCLATGNwgdqkka 77
Cdd:PRK09603  455 DDRDHLGNRRIRAVGELLANELHsglVKMQKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ------- 524

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954580878   78 ssskagVSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK09603  525 ------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-145 7.35e-09

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 57.79  E-value: 7.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRLKLQQLVKETKQYLHRCVetgrefnITLAVKTNIITSGLRYCLATGNWGdqkkasSS 80
Cdd:CHL00207  298 DDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICD-------IDSLSKFNLINPKPLIALIREFFG------SS 364

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580878   81 KagVSQVLNRYTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:CHL00207  365 Q--LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-146 2.16e-08

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 56.55  E-value: 2.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFR---LKLQQLVKETKQYLHRCVETGREFnITLAVKTNIITSGLryclatgnwgdqkka 77
Cdd:PRK14844  464 DDIDHLGNRRVRSVGEFIENQFRtglLKLERAVVDSMSTSSLDKVSPSDF-INPKVLTNVLRDFF--------------- 527

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954580878   78 SSSKagVSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSL 146
Cdd:PRK14844  528 NSSQ--LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI 598
rpoB CHL00001
RNA polymerase beta subunit
 1-157 8.63e-05

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 44.89  E-value: 8.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878    1 DDRDHFGKKRLDLAGPLMAQVFRL---KLQQLVKETKQYLHRcvetgrefNITLAVKTNIITSGLrycLATgnwgdqkkA 77
Cdd:CHL00001  304 DDIDHLKNKRIRSVADLLQDQFGLalnRLENAVRGTICGAIR--------RKLIPTPQNLVTSTP---LTT--------T 364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580878   78 SSSKAG---VSQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYV 150
Cdd:CHL00001  365 YESFFGshpLSQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHA 442


                  ....*..
gi 954580878  151 TVGTPGS 157
Cdd:CHL00001  443 RIGHWGS 449
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 117-145 1.62e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 1.62e-04
                          10        20
                  ....*....|....*....|....*....
gi 954580878  117 RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
 
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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