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Conserved domains on  [gi|284799186|gb|ADB93949|]
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RNA polymerase II second largest subunit, partial [Neodevriesia strelitziae]

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

 Zoom to residue level

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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;
1-369 1.14e-90

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: 294.17  E-value: 1.14e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186    1 MAQIFRLKFNQLVRDMRLYLHRAIETGKQFNPTVAVKSNIMTMGLRYSLATGNWGDQKkaatakAGVSQVLNRYTYASTL 80
Cdd:PRK08565  342 LAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTL 415

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   81 SHLRRTNTPIGRDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSVGSIGEPLIEFMRQRGMELLEEYDPV 160
Cdd:PRK08565  416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  161 MYPNATKVFVNGTWVGIHMNPGHLTDHMKSLKRDGTINFETTI--IRHVREREIMFFTDAGRVCRPLFVIDNkhdspnrG 238
Cdd:PRK08565  496 EYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------G 568

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  239 NLVLKQDHLMRLRNDQLyladpenqdrseqeraedknyyGWDGLVREGVVEYLDAEEEETAMIIMTPEDLL-EHqaalrr 317
Cdd:PRK08565  569 KPKLTREHVEKLKKGEL----------------------TFDDLVKMGVIEYLDAEEEENAYVALDPEDLTpEH------ 620

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 284799186  318 eeelpdakddphrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:PRK08565  621 --------------------------THLEIWPPAILGITASIIPYPEHNQS 646
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-369 1.14e-90

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 294.17  E-value: 1.14e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186    1 MAQIFRLKFNQLVRDMRLYLHRAIETGKQFNPTVAVKSNIMTMGLRYSLATGNWGDQKkaatakAGVSQVLNRYTYASTL 80
Cdd:PRK08565  342 LAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTL 415

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   81 SHLRRTNTPIGRDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSVGSIGEPLIEFMRQRGMELLEEYDPV 160
Cdd:PRK08565  416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  161 MYPNATKVFVNGTWVGIHMNPGHLTDHMKSLKRDGTINFETTI--IRHVREREIMFFTDAGRVCRPLFVIDNkhdspnrG 238
Cdd:PRK08565  496 EYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------G 568

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  239 NLVLKQDHLMRLRNDQLyladpenqdrseqeraedknyyGWDGLVREGVVEYLDAEEEETAMIIMTPEDLL-EHqaalrr 317
Cdd:PRK08565  569 KPKLTREHVEKLKKGEL----------------------TFDDLVKMGVIEYLDAEEEENAYVALDPEDLTpEH------ 620

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 284799186  318 eeelpdakddphrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:PRK08565  621 --------------------------THLEIWPPAILGITASIIPYPEHNQS 646
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-369 9.37e-50

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: 178.92  E-value: 9.37e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   1 MAQIFRLKFNQLVRDMRLYLHRAIETGKQFNPTVAVKSNIMTMGLRYSLATGNWGDQKKAATaKAGVSQVLNRYTYASTL 80
Cdd:cd00653  248 LQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSEL 326

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  81 SHLRRTNT-PIGRDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSvgsigepliefmrqrgmelleeydp 159
Cdd:cd00653  327 SHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186 160 vmypnatkvfvngtwvgihmnpghltdhmkslkrdgtinfettiirhvrereimfftdaGRVCRPLFVIDNKHdspnrgn 239
Cdd:cd00653  382 -----------------------------------------------------------GRIERPYRIVEKEV------- 395

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186 240 lvlkqdhlmrlrndqlyladpenqdrseqeraedknyygwdglvregvveyldaeeeetamiimtpedllehqaalrree 319
Cdd:cd00653      --------------------------------------------------------------------------------

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|
gi 284799186 320 elpdakddphrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:cd00653  396 ------------------------THIEISPSQILSVAASLIPFPEHNQS 421
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 69-132 1.54e-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: 111.08  E-value: 1.54e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284799186   69 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCY 132
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-369 3.92e-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: 95.18  E-value: 3.92e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186    1 MAQIFRLKFNQLVRDMR----LYLHRAIetgkqfNPTVAVKSNIMTMGLRYSLATGnwgdqkkaatakaGVSQVLNRYTY 76
Cdd:COG0085   320 LQNQFRVGLSRMERVVRermtTQDVEAI------TPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNP 380

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   77 ASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSvgsigepliefmrq 148
Cdd:COG0085   381 LSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN-------------- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  149 rgmelleEYdpvmypnatkvfvngtwvgihmnpghltdhmkslkrdgtinfettiirhvrereimfftdaGRVCRPLFVI 228
Cdd:COG0085   443 -------EY-------------------------------------------------------------GFIETPYRKV 454

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  229 DNkhdspnrgnlvlkqdhlmrlrndqlyladpenqdrseqeraedknyygwdGLVREGvVEYLDAEEEETAMIIMTPEDL 308
Cdd:COG0085   455 EN--------------------------------------------------GKVTDE-IEYLTADEEENYYIAQANAPL 483

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284799186  309 ------LEHQAALRREEELPDAKDDPHrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:COG0085   484 dedgnfLEERVLVRYRGEEVLVPPEEV--------------DYMDVSPKQIVSVATSLIPFLEHDDA 536
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-369 1.14e-90

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 294.17  E-value: 1.14e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186    1 MAQIFRLKFNQLVRDMRLYLHRAIETGKQFNPTVAVKSNIMTMGLRYSLATGNWGDQKkaatakAGVSQVLNRYTYASTL 80
Cdd:PRK08565  342 LAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTL 415

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   81 SHLRRTNTPIGRDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSVGSIGEPLIEFMRQRGMELLEEYDPV 160
Cdd:PRK08565  416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  161 MYPNATKVFVNGTWVGIHMNPGHLTDHMKSLKRDGTINFETTI--IRHVREREIMFFTDAGRVCRPLFVIDNkhdspnrG 238
Cdd:PRK08565  496 EYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------G 568

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  239 NLVLKQDHLMRLRNDQLyladpenqdrseqeraedknyyGWDGLVREGVVEYLDAEEEETAMIIMTPEDLL-EHqaalrr 317
Cdd:PRK08565  569 KPKLTREHVEKLKKGEL----------------------TFDDLVKMGVIEYLDAEEEENAYVALDPEDLTpEH------ 620

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 284799186  318 eeelpdakddphrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:PRK08565  621 --------------------------THLEIWPPAILGITASIIPYPEHNQS 646
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-369 9.37e-50

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: 178.92  E-value: 9.37e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   1 MAQIFRLKFNQLVRDMRLYLHRAIETGKQFNPTVAVKSNIMTMGLRYSLATGNWGDQKKAATaKAGVSQVLNRYTYASTL 80
Cdd:cd00653  248 LQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSEL 326

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  81 SHLRRTNT-PIGRDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSvgsigepliefmrqrgmelleeydp 159
Cdd:cd00653  327 SHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186 160 vmypnatkvfvngtwvgihmnpghltdhmkslkrdgtinfettiirhvrereimfftdaGRVCRPLFVIDNKHdspnrgn 239
Cdd:cd00653  382 -----------------------------------------------------------GRIERPYRIVEKEV------- 395

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186 240 lvlkqdhlmrlrndqlyladpenqdrseqeraedknyygwdglvregvveyldaeeeetamiimtpedllehqaalrree 319
Cdd:cd00653      --------------------------------------------------------------------------------

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|
gi 284799186 320 elpdakddphrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:cd00653  396 ------------------------THIEISPSQILSVAASLIPFPEHNQS 421
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-156 2.76e-41

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 151.26  E-value: 2.76e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   1 MAQIFRLKFNQLVRDMRLYLHRAIETGKQFNPTVAVKSNIMTMGLRYSLATGNWgdqkkaATAKAGVSQVLNRYTYASTL 80
Cdd:PRK09606 345 MEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATL 418

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 284799186  81 SHLRRTNTPIGRDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSVGSIGEPLIEFMRQRGMELLEE 156
Cdd:PRK09606 419 SHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPERG 494
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 166-369 1.31e-35

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 137.01  E-value: 1.31e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186 166 TKVFVNGTWVGIHMNPGHLTDHMKSLKRDGTINFETTIIRHVREREIMFFTDAGRVCRPLFVIDNkhdspnrGNLVLKQD 245
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186 246 HLMRLRNDQLyladpenqdrseqeraedknyyGWDGLVREGVVEYLDAEEEETAMIIMTPEDLL-EHqaalrreeelpda 324
Cdd:PRK07225  78 HIEKLKNGEL----------------------TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTeEH------------- 122

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 284799186 325 kddphrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:PRK07225 123 -------------------THLEIDPSLILGIGAGMIPYPEHNAS 148
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 69-132 1.54e-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: 111.08  E-value: 1.54e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284799186   69 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCY 132
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 168-229 4.05e-25

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: 96.28  E-value: 4.05e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 284799186  168 VFVNGTWVGIHMNPGHLTDHMKSLKRDGTINFETTIIRHVREREIMFFTDAGRVCRPLFVID 229
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 279-350 1.26e-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: 1.26e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 284799186  279 WDGLVREGVVEYLDAEEEETAMIIMTPEDLlehqaalrrEEELPDAKDDPHRrikpkpntsiRTWTHCEIHP 350
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDL---------EESSREEREGPYA----------HTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-369 3.92e-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: 95.18  E-value: 3.92e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186    1 MAQIFRLKFNQLVRDMR----LYLHRAIetgkqfNPTVAVKSNIMTMGLRYSLATGnwgdqkkaatakaGVSQVLNRYTY 76
Cdd:COG0085   320 LQNQFRVGLSRMERVVRermtTQDVEAI------TPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNP 380

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   77 ASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVSvgsigepliefmrq 148
Cdd:COG0085   381 LSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN-------------- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  149 rgmelleEYdpvmypnatkvfvngtwvgihmnpghltdhmkslkrdgtinfettiirhvrereimfftdaGRVCRPLFVI 228
Cdd:COG0085   443 -------EY-------------------------------------------------------------GFIETPYRKV 454

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186  229 DNkhdspnrgnlvlkqdhlmrlrndqlyladpenqdrseqeraedknyygwdGLVREGvVEYLDAEEEETAMIIMTPEDL 308
Cdd:COG0085   455 EN--------------------------------------------------GKVTDE-IEYLTADEEENYYIAQANAPL 483

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 284799186  309 ------LEHQAALRREEELPDAKDDPHrrikpkpntsirtwTHCEIHPAMILGVCASIIPFPDHNQS 369
Cdd:COG0085   484 dedgnfLEERVLVRYRGEEVLVPPEEV--------------DYMDVSPKQIVSVATSLIPFLEHDDA 536
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
67-139 3.98e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 49.15  E-value: 3.98e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 284799186   67 VSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTYWGLVCPAETPEGQACGLVKNLSlmCYVSVGSIG 139
Cdd:PRK09603  525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS--TFTRVNDLG 599
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
67-141 7.78e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 48.08  E-value: 7.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   67 VSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTYWGLVCPAETPEGQACGLVKNLSLMCYVS-VGSIGEP 141
Cdd:PRK14844  532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkYGFIESP 611
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 67-128 8.51e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 44.70  E-value: 8.51e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 284799186   67 VSQVLNRYTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTYWGLVCPAETPEGQACGLVKNLS 128
Cdd:CHL00207  366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB CHL00001
RNA polymerase beta subunit
 68-144 8.07e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 41.43  E-value: 8.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 284799186   68 SQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTYWGLVCPAETPEGQACGLVKnlSLMCYVSV---GSIGE 140
Cdd:CHL00001  375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIghwGSLES 452


                  ....
gi 284799186  141 PLIE 144
Cdd:CHL00001  453 PFYE 456
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 100-128 5.42e-03

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 38.93  E-value: 5.42e-03
                          10        20
                  ....*....|....*....|....*....
gi 284799186  100 RQLHNTYWGLVCPAETPEGQACGLVKNLS 128
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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