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Conserved domains on  [gi|114148517|gb|ABI51075|]
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RNA polymerase II second largest subunit, partial [Neonectria neomacrospora]

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;
1-370 2.83e-95

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: 306.50  E-value: 2.83e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517    1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNWGDQKkaasstAGVSQ 80
Cdd:PRK08565  331 ANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQ 404

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   81 VLNRYTFSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINR 160
Cdd:PRK08565  405 LLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYEL 484

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  161 GMEVVEEYEPLRYPHATKIFVNGTWVGVHQDPKHLVGQVLDTRRKSYLQYEVSlVRDIRDREFK---VFSDAGRVMRPVF 237
Cdd:PRK08565  485 GVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLI 563

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  238 TVQqeddhdtgiaKGQLVLTKDLVNKLAKeqsepsddpaSKIGWEGLIRAGAIEYLDAEEEETAMICMTPEDLdfyrlqk 317
Cdd:PRK08565  564 VVE----------NGKPKLTREHVEKLKK----------GELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------- 616

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 114148517  318 agiaveedigddpnrrlktktnptTHMYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:PRK08565  617 ------------------------TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-370 2.83e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 306.50  E-value: 2.83e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517    1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNWGDQKkaasstAGVSQ 80
Cdd:PRK08565  331 ANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQ 404

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   81 VLNRYTFSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINR 160
Cdd:PRK08565  405 LLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYEL 484

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  161 GMEVVEEYEPLRYPHATKIFVNGTWVGVHQDPKHLVGQVLDTRRKSYLQYEVSlVRDIRDREFK---VFSDAGRVMRPVF 237
Cdd:PRK08565  485 GVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLI 563

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  238 TVQqeddhdtgiaKGQLVLTKDLVNKLAKeqsepsddpaSKIGWEGLIRAGAIEYLDAEEEETAMICMTPEDLdfyrlqk 317
Cdd:PRK08565  564 VVE----------NGKPKLTREHVEKLKK----------GELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------- 616

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 114148517  318 agiaveedigddpnrrlktktnptTHMYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:PRK08565  617 ------------------------TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-370 8.69e-56

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: 195.87  E-value: 8.69e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNWGDQKKAaSSTAGVSQ 80
Cdd:cd00653  237 GNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFL-MQRSGLSQ 315

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  81 VLNRYTFSSTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsepliefmin 159
Cdd:cd00653  316 VLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517 160 rgmevveeyeplryphatkifvngtwvgvhqdpkhlvgqvldtrrksylqyevslvrdirdrefkvfsdaGRVMRPVFTV 239
Cdd:cd00653  382 ----------------------------------------------------------------------GRIERPYRIV 391

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517 240 QQEddhdtgiakgqlvltkdlvnklakeqsepsddpaskigwegliragaieyldaeeeetamicmtpedldfyrlqkag 319
Cdd:cd00653  392 EKE----------------------------------------------------------------------------- 394

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 114148517 320 iaveedigddpnrrlktktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:cd00653  395 -------------------------VTHIEISPSQILSVAASLIPFPEHNQ 420
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 80-143 1.06e-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: 1.06e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 114148517   80 QVLNRYTFSSTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 143
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-370 5.61e-25

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: 106.73  E-value: 5.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517    1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRcvEGNRHFNLAVGIKPGTLSNGLKYSLATGnwgdqkkaasstaGVSQ 80
Cdd:COG0085   309 GNRRVRLVGELLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQ 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   81 VLNRYTFSSTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsep 152
Cdd:COG0085   374 FMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  153 liefminrgmevveEYeplryphatkifvngtwvgvhqdpkhlvgqvldtrrksylqyevslvrdirdrefkvfsdaGRV 232
Cdd:COG0085   443 --------------EY-------------------------------------------------------------GFI 447

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  233 MRPVFTVQqeddhdtgiaKGqlVLTKDlvnklakeqsepsddpaskigwegliragaIEYLDAEEEETAMICMTPEDLDf 312
Cdd:COG0085   448 ETPYRKVE----------NG--KVTDE------------------------------IEYLTADEEENYYIAQANAPLD- 484

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 114148517  313 yrlqKAGIAVEEDIgddPNRRLKTKTNPTTHMYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:COG0085   485 ----EDGNFLEERV---LVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDD 535
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-370 2.83e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 306.50  E-value: 2.83e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517    1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNWGDQKkaasstAGVSQ 80
Cdd:PRK08565  331 ANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQ 404

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   81 VLNRYTFSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINR 160
Cdd:PRK08565  405 LLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYEL 484

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  161 GMEVVEEYEPLRYPHATKIFVNGTWVGVHQDPKHLVGQVLDTRRKSYLQYEVSlVRDIRDREFK---VFSDAGRVMRPVF 237
Cdd:PRK08565  485 GVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLI 563

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  238 TVQqeddhdtgiaKGQLVLTKDLVNKLAKeqsepsddpaSKIGWEGLIRAGAIEYLDAEEEETAMICMTPEDLdfyrlqk 317
Cdd:PRK08565  564 VVE----------NGKPKLTREHVEKLKK----------GELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------- 616

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 114148517  318 agiaveedigddpnrrlktktnptTHMYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:PRK08565  617 ------------------------TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-370 8.69e-56

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: 195.87  E-value: 8.69e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNWGDQKKAaSSTAGVSQ 80
Cdd:cd00653  237 GNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFL-MQRSGLSQ 315

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  81 VLNRYTFSSTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsepliefmin 159
Cdd:cd00653  316 VLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517 160 rgmevveeyeplryphatkifvngtwvgvhqdpkhlvgqvldtrrksylqyevslvrdirdrefkvfsdaGRVMRPVFTV 239
Cdd:cd00653  382 ----------------------------------------------------------------------GRIERPYRIV 391

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517 240 QQEddhdtgiakgqlvltkdlvnklakeqsepsddpaskigwegliragaieyldaeeeetamicmtpedldfyrlqkag 319
Cdd:cd00653  392 EKE----------------------------------------------------------------------------- 394

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 114148517 320 iaveedigddpnrrlktktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:cd00653  395 -------------------------VTHIEISPSQILSVAASLIPFPEHNQ 420
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 3-169 2.49e-36

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 137.77  E-value: 2.49e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   3 KRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGNRHFNLAVGIKPGTLSNGLKYSLATGNWgdqkkaASSTAGVSQVL 82
Cdd:PRK09606 336 KRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLL 409

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  83 NRYTFSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMinRGM 162
Cdd:PRK09606 410 DRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL--KEL 487


                 ....*..
gi 114148517 163 EVVEEYE 169
Cdd:PRK09606 488 GVEPERG 494
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 177-370 4.29e-35

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 135.47  E-value: 4.29e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517 177 TKIFVNGTWVGVHQDPKHLVGQVLDTRRKSYLQYEVSLVRDIRDREFKVFSDAGRVMRPVFTVQqeddhdtgiaKGQLVL 256
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVE----------NGEPLL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517 257 TKDLVNKLAKeqsepsddpaSKIGWEGLIRAGAIEYLDAEEEETAMICMTPEDLdfyrlqkagiaveedigddpnrrlkt 336
Cdd:PRK07225  75 TEEHIEKLKN----------GELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL-------------------------- 118

                        170       180       190
                 ....*....|....*....|....*....|....
gi 114148517 337 ktnptTHMYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:PRK07225 119 -----TEEHTHLEIDPSLILGIGAGMIPYPEHNA 147
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 80-143 1.06e-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: 1.06e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 114148517   80 QVLNRYTFSSTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 143
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 179-240 1.33e-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: 97.82  E-value: 1.33e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 114148517  179 IFVNGTWVGVHQDPKHLVGQVLDTRRKSYLQYEVSLVRDIRDREFKVFSDAGRVMRPVFTVQ 240
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 281-352 5.50e-25

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: 95.69  E-value: 5.50e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 114148517  281 WEGLIRAGAIEYLDAEEEETAMICMTPEDLD-FYRLQKAGiaveedigddpnrrlktktnPTTHMYTHCEIHP 352
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEeSSREEREG--------------------PYAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-370 5.61e-25

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: 106.73  E-value: 5.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517    1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRcvEGNRHFNLAVGIKPGTLSNGLKYSLATGnwgdqkkaasstaGVSQ 80
Cdd:COG0085   309 GNRRVRLVGELLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQ 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   81 VLNRYTFSSTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsep 152
Cdd:COG0085   374 FMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  153 liefminrgmevveEYeplryphatkifvngtwvgvhqdpkhlvgqvldtrrksylqyevslvrdirdrefkvfsdaGRV 232
Cdd:COG0085   443 --------------EY-------------------------------------------------------------GFI 447

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517  233 MRPVFTVQqeddhdtgiaKGqlVLTKDlvnklakeqsepsddpaskigwegliragaIEYLDAEEEETAMICMTPEDLDf 312
Cdd:COG0085   448 ETPYRKVE----------NG--KVTDE------------------------------IEYLTADEEENYYIAQANAPLD- 484

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 114148517  313 yrlqKAGIAVEEDIgddPNRRLKTKTNPTTHMYTHCEIHPSMILGICASIIPFPDHNQ 370
Cdd:COG0085   485 ----EDGNFLEERV---LVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDD 535
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-54 2.01e-07

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: 52.38  E-value: 2.01e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 114148517    1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGNRHFNLAVGIKPGTLSN 54
Cdd:pfam04563 343 GNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
78-203 5.44e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.85  E-value: 5.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   78 VSQVLNRYTFSSTLSHLRRTNTpIGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS----VG 147
Cdd:PRK09603  525 LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNdlgfIE 602

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114148517  148 SPSEPLIEFMINRgmEVV-----EEYEPLRYPHATKIFVNGtwvgvhqdpkHLVGQVLDTR 203
Cdd:PRK09603  603 APYKKVVDGKVVG--ETIyltaiQEDSHIIAPASTPIDEEG----------NILGDLIETR 651
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
74-163 1.46e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 50.39  E-value: 1.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517   74 STAGVSQVLNRYTFSSTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS---- 145
Cdd:PRK14844  528 NSSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygf 607

                          90
                  ....*....|....*...
gi 114148517  146 VGSPSEPLIEFMINRGME 163
Cdd:PRK14844  608 IESPYRKVVNRVVTDQIE 625
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-139 2.55e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 46.24  E-value: 2.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114148517    1 GKKRLDLAGPLLAKLFRGIMRRVNTELSNYLKRCVEGN-RHFNLavgIKPGTLSNGLKYSLAtgnwgdqkkaaSSTagVS 79
Cdd:CHL00207  304 KNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSlSKFNL---INPKPLIALIREFFG-----------SSQ--LS 367

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 114148517   80 QVLNRYTFSSTLSHLRRTNT--PIGRDgKLAKP---RQLHNTHWGLVCPAETPEGQACGLVKNLS 139
Cdd:CHL00207  368 QYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 111-139 1.31e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 1.31e-04
                          10        20
                  ....*....|....*....|....*....
gi 114148517  111 RQLHNTHWGLVCPAETPEGQACGLVKNLS 139
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 79-148 2.22e-03

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 40.27  E-value: 2.22e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 114148517   79 SQVLNRYTFSSTLSHLRRTNT--PIGRDGKLA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVSVGS 148
Cdd:CHL00001  375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIGH 446
 
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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