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Conserved domains on  [gi|954580910|gb|ALP48319|]
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RNA polymerase II second largest subunit, partial [Dothidea sambuci]

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;
1-395 3.52e-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: 371.60  E-value: 3.52e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSSGLRYCLATGNWGdqkkaaSA 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GG 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   81 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPSEPII 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  161 EFMNQRNMELLEEYEPKNNPDATKVFVNGVWVGVHRDPAQLVKVVQSLRRSGTISFEISL--IRDVRDREFKIFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  239 MRPLFVVDNdstserrGHLVLARSNIERLqsdREMDLTglseeerdgsiygWKGLIGDGIIEYLDAEEEEAAMIIMSPED 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL---KKGELT-------------FDDLVKMGVIEYLDAEEEENAYVALDPED 615

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 954580910  319 L-DEHrqvragapayddvgldphrrfkakpnqsarmwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQAMG 395
Cdd:PRK08565  616 LtPEH--------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-395 3.52e-119

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 371.60  E-value: 3.52e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSSGLRYCLATGNWGdqkkaaSA 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GG 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   81 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPSEPII 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  161 EFMNQRNMELLEEYEPKNNPDATKVFVNGVWVGVHRDPAQLVKVVQSLRRSGTISFEISL--IRDVRDREFKIFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  239 MRPLFVVDNdstserrGHLVLARSNIERLqsdREMDLTglseeerdgsiygWKGLIGDGIIEYLDAEEEEAAMIIMSPED 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL---KKGELT-------------FDDLVKMGVIEYLDAEEEENAYVALDPED 615

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 954580910  319 L-DEHrqvragapayddvgldphrrfkakpnqsarmwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQAMG 395
Cdd:PRK08565  616 LtPEH--------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-395 2.03e-75

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: 250.56  E-value: 2.03e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSSGLRYCLATGNWGDQKKAASa 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ- 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  81 KAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgtpsepi 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910 160 iefmnqrnmelleeyepknnpdatkvfvngvwvgvhrdpaqlvkvvqslrrsgtisfeislirdvrdrefkiftdaGRVM 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910 240 RPLFVVDNDStserrghlvlarsnierlqsdremdltglseeerdgsiygwkgligdgiieyldaeeeeaamiimspedl 319
Cdd:cd00653  386 RPYRIVEKEV---------------------------------------------------------------------- 395

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 954580910 320 dehrqvragapayddvgldphrrfkakpnqsarmwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQAMG 395
Cdd:cd00653  396 -----------------------------------THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-395 2.78e-41

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: 155.65  E-value: 2.78e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRcvEGGKEFNLTLAVKANILSSGLRYCLATGnwgdqkkaasa 80
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS----------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   81 kaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSv 152
Cdd:COG0085   370 --QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  153 gtpsepiiefmnqrnmelleEYepknnpdatkvfvngvwvgvhrdpaqlvkvvqslrrsgtisfeislirdvrdrefkif 232
Cdd:COG0085   443 --------------------EY---------------------------------------------------------- 444

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  233 tdaGRVMRPLFVVDNdstserrghlvlarsnierlqsdremdltglseeerdgsiygwkGLIGDGiIEYLDAEEEEAAMI 312
Cdd:COG0085   445 ---GFIETPYRKVEN--------------------------------------------GKVTDE-IEYLTADEEENYYI 476

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  313 IMSPEDLDEHrqvraGAPAYDDVgldPHRRFKAKPNQSARMWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQ 392
Cdd:COG0085   477 AQANAPLDED-----GNFLEERV---LVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQ 548


                  ...
gi 954580910  393 AMG 395
Cdd:COG0085   549 AVP 551
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 8.76e-32

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: 114.93  E-value: 8.76e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580910   86 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 149
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-395 3.52e-119

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 371.60  E-value: 3.52e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSSGLRYCLATGNWGdqkkaaSA 80
Cdd:PRK08565  325 DDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GG 398

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   81 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPSEPII 160
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  161 EFMNQRNMELLEEYEPKNNPDATKVFVNGVWVGVHRDPAQLVKVVQSLRRSGTISFEISL--IRDVRDREFKIFTDAGRV 238
Cdd:PRK08565  479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  239 MRPLFVVDNdstserrGHLVLARSNIERLqsdREMDLTglseeerdgsiygWKGLIGDGIIEYLDAEEEEAAMIIMSPED 318
Cdd:PRK08565  559 RRPLIVVEN-------GKPKLTREHVEKL---KKGELT-------------FDDLVKMGVIEYLDAEEEENAYVALDPED 615

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 954580910  319 L-DEHrqvragapayddvgldphrrfkakpnqsarmwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQAMG 395
Cdd:PRK08565  616 LtPEH--------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-395 2.03e-75

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: 250.56  E-value: 2.03e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSSGLRYCLATGNWGDQKKAASa 80
Cdd:cd00653  231 DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ- 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  81 KAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgtpsepi 159
Cdd:cd00653  310 RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910 160 iefmnqrnmelleeyepknnpdatkvfvngvwvgvhrdpaqlvkvvqslrrsgtisfeislirdvrdrefkiftdaGRVM 239
Cdd:cd00653  382 ----------------------------------------------------------------------------GRIE 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910 240 RPLFVVDNDStserrghlvlarsnierlqsdremdltglseeerdgsiygwkgligdgiieyldaeeeeaamiimspedl 319
Cdd:cd00653  386 RPYRIVEKEV---------------------------------------------------------------------- 395

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 954580910 320 dehrqvragapayddvgldphrrfkakpnqsarmwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQAMG 395
Cdd:cd00653  396 -----------------------------------THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVG 436
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-175 4.18e-51

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 178.22  E-value: 4.18e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSSGLRYCLATGNWgdqkkaASA 80
Cdd:PRK09606 328 DDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGG 401

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  81 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGTPSEPII 160
Cdd:PRK09606 402 RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481

                        170
                 ....*....|....*
gi 954580910 161 EFMnqRNMELLEEYE 175
Cdd:PRK09606 482 EIL--KELGVEPERG 494
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 183-395 1.02e-45

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 165.90  E-value: 1.02e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910 183 TKVFVNGVWVGVHRDPAQLVKVVQSLRRSGTISFEISLIRDVRDREFKIFTDAGRVMRPLFVVDNdstserrGHLVLARS 262
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910 263 NIERLqsdremdltglseeeRDGSIyGWKGLIGDGIIEYLDAEEEEAAMIIMSPEDL-DEHrqvragapayddvgldphr 341
Cdd:PRK07225  78 HIEKL---------------KNGEL-TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH------------------- 122

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 954580910 342 rfkakpnqsarmwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQAMG 395
Cdd:PRK07225 123 -------------THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLG 163
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-395 2.78e-41

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: 155.65  E-value: 2.78e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRcvEGGKEFNLTLAVKANILSSGLRYCLATGnwgdqkkaasa 80
Cdd:COG0085   303 DDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS----------- 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   81 kaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSv 152
Cdd:COG0085   370 --QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  153 gtpsepiiefmnqrnmelleEYepknnpdatkvfvngvwvgvhrdpaqlvkvvqslrrsgtisfeislirdvrdrefkif 232
Cdd:COG0085   443 --------------------EY---------------------------------------------------------- 444

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  233 tdaGRVMRPLFVVDNdstserrghlvlarsnierlqsdremdltglseeerdgsiygwkGLIGDGiIEYLDAEEEEAAMI 312
Cdd:COG0085   445 ---GFIETPYRKVEN--------------------------------------------GKVTDE-IEYLTADEEENYYI 476

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910  313 IMSPEDLDEHrqvraGAPAYDDVgldPHRRFKAKPNQSARMWTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAVGKQ 392
Cdd:COG0085   477 AQANAPLDED-----GNFLEERV---LVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQ 548


                  ...
gi 954580910  393 AMG 395
Cdd:COG0085   549 AVP 551
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-149 8.76e-32

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: 114.93  E-value: 8.76e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 954580910   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 2.67e-30

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: 110.53  E-value: 2.67e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580910  185 VFVNGVWVGVHRDPAQLVKVVQSLRRSGTISFEISLIRDVRDREFKIFTDAGRVMRPLFVVD 246
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 290-361 1.53e-20

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: 84.13  E-value: 1.53e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 954580910  290 WKGLIGDGIIEYLDAEEEEAAMIIMSPEDLDEHrqvragapayddvgldpHRRFKAKPNqsARMWTHCEIHP 361
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEES-----------------SREEREGPY--AHTYTHCEIHP 53
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-60 5.55e-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: 5.55e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKEFNLTLAVKANILSS 60
Cdd:pfam04563 337 DDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 368-395 7.42e-11

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: 62.93  E-value: 7.42e-11
                          10        20
                  ....*....|....*....|....*...
gi 954580910  368 CASIIPFPDHNQSPRNTYQSAVGKQAMG 395
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMG 28
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-145 1.81e-10

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 63.02  E-value: 1.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFR---LKFTQLIRDTRVYLSRCVEGGKEFNLtlaVKANILSSGLRYCLATGNwgdqkka 77
Cdd:PRK09603  455 DDRDHLGNRRIRAVGELLANELHsglVKMQKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ------- 524

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 954580910   78 asakagVSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK09603  525 ------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-145 1.06e-08

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 57.41  E-value: 1.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFRLKFTQLIRDTRVYLSRCVEGGKE-FNL------TLAVKANILSSGLryclatgnwgd 73
Cdd:CHL00207  298 DDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSkFNLinpkplIALIREFFGSSQL----------- 366

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 954580910   74 qkkaasakagvSQVLNRYTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:CHL00207  367 -----------SQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-151 3.57e-08

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 55.78  E-value: 3.57e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910    1 DDRDHFGKKRLDLAGPLMAQVFR---LKFTQLIRDTRVYLSRCVEGGKEFnltlaVKANILSSGLRYCLATGNwgdqkka 77
Cdd:PRK14844  464 DDIDHLGNRRVRSVGEFIENQFRtglLKLERAVVDSMSTSSLDKVSPSDF-----INPKVLTNVLRDFFNSSQ------- 531

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 954580910   78 asakagVSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 151
Cdd:PRK14844  532 ------LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 117-145 1.57e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 1.57e-04
                          10        20
                  ....*....|....*....|....*....
gi 954580910  117 RQLHNTHWGLVCPAETPEGQACGLVKNLS 145
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 85-174 4.34e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.58  E-value: 4.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 954580910   85 SQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVSVG------T 154
Cdd:CHL00001  375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIGhwgsleS 452

                          90       100
                  ....*....|....*....|....
gi 954580910  155 PSEPIIEFMNQRNMELL----EEY 174
Cdd:CHL00001  453 PFYEISERSKEERMVYLspseDEY 476
 
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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