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Conserved domains on  [gi|954580892|gb|ALP48310|]
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RNA polymerase II second largest subunit, partial [Houjia yanglingensis]

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;
1-399 4.66e-119

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: 371.21  E-value: 4.66e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLRYCLATGNWGDQkkaasv 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------ 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   81 RAGVSQVLNRFTYASTLSHLRRTNTPIGRDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTVGTPSVPLI 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  161 DFMRSRGMDLLEEFDVVHNSSATKVFLNGTWIGVHPNASFLTDQLLDVRRRGHISFEVTI--IRDVRERGIKVFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  239 CRPLFVVDNkpnsinrGRLVLKQEHIDKLladqtilthdEDGRMRseeeqmddvygWKGLVDDGVVEYLDAEEEETAMII 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL----------KKGELT-----------FDDLVKMGVIEYLDAEEEENAYVA 610

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  319 MTPEDLeehrqmregrTPEetrvdpHkrikpkpnpnvrlwTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 398
Cdd:PRK08565  611 LDPEDL----------TPE------H--------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSL 660


                  .
gi 954580892  399 G 399
Cdd:PRK08565  661 G 661
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-399 4.66e-119

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 371.21  E-value: 4.66e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLRYCLATGNWGDQkkaasv 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------ 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   81 RAGVSQVLNRFTYASTLSHLRRTNTPIGRDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTVGTPSVPLI 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  161 DFMRSRGMDLLEEFDVVHNSSATKVFLNGTWIGVHPNASFLTDQLLDVRRRGHISFEVTI--IRDVRERGIKVFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  239 CRPLFVVDNkpnsinrGRLVLKQEHIDKLladqtilthdEDGRMRseeeqmddvygWKGLVDDGVVEYLDAEEEETAMII 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL----------KKGELT-----------FDDLVKMGVIEYLDAEEEENAYVA 610

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  319 MTPEDLeehrqmregrTPEetrvdpHkrikpkpnpnvrlwTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 398
Cdd:PRK08565  611 LDPEDL----------TPE------H--------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSL 660


                  .
gi 954580892  399 G 399
Cdd:PRK08565  661 G 661
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-399 3.68e-78

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: 257.88  E-value: 3.68e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLRYCLATGNWGDQKKAASv 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ- 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  81 RAGVSQVLNRFTYASTLSHLRRTNT-PIGRDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTvgtpsvpl 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 160 idfmrsrgmdlleefdvvhnssatkvflngtwigvhpnasfltdqlldvrrrghisfevtiirdvrergikvftdaGRVC 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 240 RPLFVVDNKpnsinrgrlvlkqehidklladqtilthdedgrmrseeeqmddvygwkglvddgvveyldaeeeetamiim 319
Cdd:cd00653  386 RPYRIVEKE----------------------------------------------------------------------- 394

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 320 tpedleehrqmregrtpeetrvdphkrikpkpnpnvrlWTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 399
Cdd:cd00653  395 --------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-399 5.11e-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: 151.80  E-value: 5.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRcVDNgKEFNITLAIKSNILTTGLRYCLATGnwgdqkkaasv 80
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT-QDV-EAITPQSLINIRPVVAAIKEFFGSS----------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   81 raGVSQVLNRFTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTv 152
Cdd:COG0085   370 --QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  153 gtpsvplidfmrsrgmdlleEFdvvhnssatkvflngtwigvhpnasfltdqlldvrrrghisfevtiirdvrergikvf 232
Cdd:COG0085   443 --------------------EY---------------------------------------------------------- 444

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  233 tdaGRVCRPLFVVdnkpnsinrgrlvlkqehidklladqtilthdEDGRMRSEeeqmddvygwkglvddgvVEYLDAEEE 312
Cdd:COG0085   445 ---GFIETPYRKV--------------------------------ENGKVTDE------------------IEYLTADEE 471

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  313 ETAMIIMTPEDLEEHRQMREGRTPEETRVDPhkriKPKPNPNVrlwTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSA 392
Cdd:COG0085   472 ENYYIAQANAPLDEDGNFLEERVLVRYRGEE----VLVPPEEV---DYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544


                  ....*..
gi 954580892  393 MGKQAMG 399
Cdd:COG0085   545 MQRQAVP 551
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 8.37e-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: 109.54  E-value: 8.37e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580892   86 QVLNRFTYASTLSHLRRTNTPIG---RDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCF 149
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-399 4.66e-119

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 371.21  E-value: 4.66e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLRYCLATGNWGDQkkaasv 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------ 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   81 RAGVSQVLNRFTYASTLSHLRRTNTPIGRDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTVGTPSVPLI 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  161 DFMRSRGMDLLEEFDVVHNSSATKVFLNGTWIGVHPNASFLTDQLLDVRRRGHISFEVTI--IRDVRERGIKVFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  239 CRPLFVVDNkpnsinrGRLVLKQEHIDKLladqtilthdEDGRMRseeeqmddvygWKGLVDDGVVEYLDAEEEETAMII 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL----------KKGELT-----------FDDLVKMGVIEYLDAEEEENAYVA 610

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  319 MTPEDLeehrqmregrTPEetrvdpHkrikpkpnpnvrlwTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 398
Cdd:PRK08565  611 LDPEDL----------TPE------H--------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSL 660


                  .
gi 954580892  399 G 399
Cdd:PRK08565  661 G 661
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-399 3.68e-78

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: 257.88  E-value: 3.68e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLRYCLATGNWGDQKKAASv 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ- 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  81 RAGVSQVLNRFTYASTLSHLRRTNT-PIGRDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTvgtpsvpl 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 160 idfmrsrgmdlleefdvvhnssatkvflngtwigvhpnasfltdqlldvrrrghisfevtiirdvrergikvftdaGRVC 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 240 RPLFVVDNKpnsinrgrlvlkqehidklladqtilthdedgrmrseeeqmddvygwkglvddgvveyldaeeeetamiim 319
Cdd:cd00653  386 RPYRIVEKE----------------------------------------------------------------------- 394

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 320 tpedleehrqmregrtpeetrvdphkrikpkpnpnvrlWTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 399
Cdd:cd00653  395 --------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-167 4.27e-51

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 178.61  E-value: 4.27e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLRYCLATGNW--Gdqkkaa 78
Cdd:PRK09606 328 DDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNWvgG------ 401

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  79 svRAGVSQVLNRFTYASTLSHLRRTNTPIGRDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTVGTPSVP 158
Cdd:PRK09606 402 --RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEE 479


                 ....*....
gi 954580892 159 LIDFMRSRG 167
Cdd:PRK09606 480 VKEILKELG 488
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 183-399 2.79e-47

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 170.14  E-value: 2.79e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 183 TKVFLNGTWIGVHPNASFLTDQLLDVRRRGHISFEVTIIRDVRERGIKVFTDAGRVCRPLFVVDNkpnsinrGRLVLKQE 262
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892 263 HIDKLladqtilthdEDGRMRseeeqmddvygWKGLVDDGVVEYLDAEEEETAMIIMTPEDL-EEHrqmregrtpeetrv 341
Cdd:PRK07225  78 HIEKL----------KNGELT-----------FDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH-------------- 122

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 954580892 342 dphkrikpkpnpnvrlwTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 399
Cdd:PRK07225 123 -----------------THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLG 163
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-399 5.11e-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: 151.80  E-value: 5.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRcVDNgKEFNITLAIKSNILTTGLRYCLATGnwgdqkkaasv 80
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT-QDV-EAITPQSLINIRPVVAAIKEFFGSS----------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   81 raGVSQVLNRFTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHDTHWGLVCPAETPEGQACGLVKNLSLMCFVTv 152
Cdd:COG0085   370 --QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  153 gtpsvplidfmrsrgmdlleEFdvvhnssatkvflngtwigvhpnasfltdqlldvrrrghisfevtiirdvrergikvf 232
Cdd:COG0085   443 --------------------EY---------------------------------------------------------- 444

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  233 tdaGRVCRPLFVVdnkpnsinrgrlvlkqehidklladqtilthdEDGRMRSEeeqmddvygwkglvddgvVEYLDAEEE 312
Cdd:COG0085   445 ---GFIETPYRKV--------------------------------ENGKVTDE------------------IEYLTADEE 471

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892  313 ETAMIIMTPEDLEEHRQMREGRTPEETRVDPhkriKPKPNPNVrlwTHCEIHPAMILGVCASIIPFPDHNQSPRNTYQSA 392
Cdd:COG0085   472 ENYYIAQANAPLDEDGNFLEERVLVRYRGEE----VLVPPEEV---DYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544


                  ....*..
gi 954580892  393 MGKQAMG 399
Cdd:COG0085   545 MQRQAVP 551
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 8.37e-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: 109.54  E-value: 8.37e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580892   86 QVLNRFTYASTLSHLRRTNTPIG---RDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSLMCF 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 5.53e-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: 102.06  E-value: 5.53e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580892  185 VFLNGTWIGVHPNASFLTDQLLDVRRRGHISFEVTIIRDVRERGIKVFTDAGRVCRPLFVVD 246
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 295-365 5.16e-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: 91.06  E-value: 5.16e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580892  295 WKGLVDDGVVEYLDAEEEETAMIIMTPEDLEEH-RQMREGrtpeetrvdphkrikpkpnPNVRLWTHCEIHP 365
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREG-------------------PYAHTYTHCEIHP 53
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-59 1.09e-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: 80.89  E-value: 1.09e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILT 59
Cdd:pfam04563 337 DDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPIT 395
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 372-399 3.66e-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: 3.66e-12
                          10        20
                  ....*....|....*....|....*...
gi 954580892  372 CASIIPFPDHNQSPRNTYQSAMGKQAMG 399
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMG 28
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-145 1.89e-10

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 63.02  E-value: 1.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLRYCLATGNwgdqkkaasv 80
Cdd:PRK09603  455 DDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQ---------- 524

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   81 ragVSQVLNRFTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHDTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK09603  525 ---LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-145 1.24e-08

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 57.02  E-value: 1.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVdngkefnITLAIKSNILTTGLRYCLATGNWGDQKkaasv 80
Cdd:CHL00207  298 DDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICD-------IDSLSKFNLINPKPLIALIREFFGSSQ----- 365

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 954580892   81 ragVSQVLNRFTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHDTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:CHL00207  366 ---LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-146 9.34e-08

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 54.63  E-value: 9.34e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLhrCVDNGKEFNITLAIKSNILTTGLRYCLATGNwgdqkkaasv 80
Cdd:PRK14844  464 DDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSM--STSSLDKVSPSDFINPKVLTNVLRDFFNSSQ---------- 531

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892   81 ragVSQVLNRFTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHDTHWGLVCPAETPEGQACGLVKNLSL 146
Cdd:PRK14844  532 ---LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI 598
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 117-145 4.40e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 42.40  E-value: 4.40e-04
                          10        20
                  ....*....|....*....|....*....
gi 954580892  117 RQLHDTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 1-145 8.09e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 41.81  E-value: 8.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580892    1 DDRDHFGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVDNGKEFNITLAIKSNILTTGLR-----YCLatgnwgdqk 75
Cdd:CHL00001  304 DDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYEsffgsHPL--------- 374

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 954580892   76 kaasvragvSQVLNRFTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHDTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:CHL00001  375 ---------SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
 
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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