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Conserved domains on  [gi|1928140166|gb|QOW94939|]
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RNA polymerase II second largest subunit, partial [Meira plantarum]

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;
4-352 6.24e-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: 304.96  E-value: 6.24e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166    4 LMTSLFRLTFRKLLKDVYRHLQKCVEDKKEFTLTSAVKSSTITNGLKYSLATGNWGDQKkmntkVGVSQVLNRYTYASTL 83
Cdd:PRK08565   341 LLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR-----TGVSQLLDRTNYLSTL 415

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   84 SHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSVGSPSGPIIEFLEEYGLDSLIDMQVA 163
Cdd:PRK08565   416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  164 D-PHATKVFVNGVWMGTADNATGLVDTLRELRRRDDISNEVSVTHDIREKELRVY--TDAGRVQRPLFIVEP----ETQN 236
Cdd:PRK08565   496 EyISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGEINEVYvnCDSGRVRRPLIVVENgkpkLTRE 575

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  237 LLVKQKHADWitdqvkpdgtqfGWSELLREGVIELLDAEEEETSMICMSPQDlanskiyranpdtyqsrsadpsarlvsv 316
Cdd:PRK08565   576 HVEKLKKGEL------------TFDDLVKMGVIEYLDAEEEENAYVALDPED---------------------------- 615

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1928140166  317 qtLLPDTfTHSEMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:PRK08565   616 --LTPEH-THLEIWPPAILGITASIIPYPEHNQSPR 648
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 4-352 6.24e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 304.96  E-value: 6.24e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166    4 LMTSLFRLTFRKLLKDVYRHLQKCVEDKKEFTLTSAVKSSTITNGLKYSLATGNWGDQKkmntkVGVSQVLNRYTYASTL 83
Cdd:PRK08565   341 LLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR-----TGVSQLLDRTNYLSTL 415

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   84 SHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSVGSPSGPIIEFLEEYGLDSLIDMQVA 163
Cdd:PRK08565   416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  164 D-PHATKVFVNGVWMGTADNATGLVDTLRELRRRDDISNEVSVTHDIREKELRVY--TDAGRVQRPLFIVEP----ETQN 236
Cdd:PRK08565   496 EyISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGEINEVYvnCDSGRVRRPLIVVENgkpkLTRE 575

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  237 LLVKQKHADWitdqvkpdgtqfGWSELLREGVIELLDAEEEETSMICMSPQDlanskiyranpdtyqsrsadpsarlvsv 316
Cdd:PRK08565   576 HVEKLKKGEL------------TFDDLVKMGVIEYLDAEEEENAYVALDPED---------------------------- 615

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1928140166  317 qtLLPDTfTHSEMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:PRK08565   616 --LTPEH-THLEIWPPAILGITASIIPYPEHNQSPR 648
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 3-352 7.79e-61

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: 209.35  E-value: 7.79e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   3 PLMTSLFRLTFRKLLKDVYRHLQKCVEDKKEFTLTSAVKSSTITNGLKYSLATGNWGDQKKMNTKVGVSQVLNRYTYAST 82
Cdd:cd00653   246 ELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSE 325

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  83 LSHLRRTNT-PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSvgspsgpiiefleeygldslidmq 161
Cdd:cd00653   326 LSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------ 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166 162 vadphatkvfvngvwmgtadnatglvdtlrelrrrddisnevsvthdirekelrvytdaGRVQRPLFIVEPETqnllvkq 241
Cdd:cd00653   382 -----------------------------------------------------------GRIERPYRIVEKEV------- 395

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166 242 khadwitdqvkpdgtqfgwsellregvielldaeeeetsmicmspqdlanskiyranpdtyqsrsadpsarlvsvqtllp 321
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340       350
                  ....*....|....*....|....*....|.
gi 1928140166 322 dtfTHSEMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:cd00653   396 ---THIEISPSQILSVAASLIPFPEHNQSPR 423
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 72-134 5.13e-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: 114.55  E-value: 5.13e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1928140166  72 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMA 134
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 4-352 3.69e-27

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: 112.90  E-value: 3.69e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166    4 LMTSLFRLTFRKLLKDVYRHLQKcvEDKKEFTLTSAVKSSTITNGLKYSLATGnwgdqkkmntkvGVSQVLNRYTYASTL 83
Cdd:COG0085    319 LLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS------------QLSQFMDQTNPLSEL 384

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   84 SHLRRTNT----PIGRDgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSvgspsgpiiefleEYgld 155
Cdd:COG0085    385 THKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN-------------EY--- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  156 slidmqvadphatkvfvngvwmgtadnatglvdtlrelrrrddisnevsvthdirekelrvytdaGRVQRPLFIVEpetq 235
Cdd:COG0085    445 -----------------------------------------------------------------GFIETPYRKVE---- 455

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  236 NLLVkqkhadwiTDQvkpdgtqfgwsellregvIELLDAEEEETSMICMSPQDLanskiyraNPDTYQSRSADPSARLVS 315
Cdd:COG0085    456 NGKV--------TDE------------------IEYLTADEEENYYIAQANAPL--------DEDGNFLEERVLVRYRGE 501

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 1928140166  316 VQTLLPDTFTHSEMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:COG0085    502 EVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANR 538
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 4-352 6.24e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 304.96  E-value: 6.24e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166    4 LMTSLFRLTFRKLLKDVYRHLQKCVEDKKEFTLTSAVKSSTITNGLKYSLATGNWGDQKkmntkVGVSQVLNRYTYASTL 83
Cdd:PRK08565   341 LLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR-----TGVSQLLDRTNYLSTL 415

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   84 SHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSVGSPSGPIIEFLEEYGLDSLIDMQVA 163
Cdd:PRK08565   416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  164 D-PHATKVFVNGVWMGTADNATGLVDTLRELRRRDDISNEVSVTHDIREKELRVY--TDAGRVQRPLFIVEP----ETQN 236
Cdd:PRK08565   496 EyISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGEINEVYvnCDSGRVRRPLIVVENgkpkLTRE 575

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  237 LLVKQKHADWitdqvkpdgtqfGWSELLREGVIELLDAEEEETSMICMSPQDlanskiyranpdtyqsrsadpsarlvsv 316
Cdd:PRK08565   576 HVEKLKKGEL------------TFDDLVKMGVIEYLDAEEEENAYVALDPED---------------------------- 615

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1928140166  317 qtLLPDTfTHSEMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:PRK08565   616 --LTPEH-THLEIWPPAILGITASIIPYPEHNQSPR 648
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 3-352 7.79e-61

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: 209.35  E-value: 7.79e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   3 PLMTSLFRLTFRKLLKDVYRHLQKCVEDKKEFTLTSAVKSSTITNGLKYSLATGNWGDQKKMNTKVGVSQVLNRYTYAST 82
Cdd:cd00653   246 ELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSE 325

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  83 LSHLRRTNT-PIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSvgspsgpiiefleeygldslidmq 161
Cdd:cd00653   326 LSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------------------ 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166 162 vadphatkvfvngvwmgtadnatglvdtlrelrrrddisnevsvthdirekelrvytdaGRVQRPLFIVEPETqnllvkq 241
Cdd:cd00653   382 -----------------------------------------------------------GRIERPYRIVEKEV------- 395

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166 242 khadwitdqvkpdgtqfgwsellregvielldaeeeetsmicmspqdlanskiyranpdtyqsrsadpsarlvsvqtllp 321
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340       350
                  ....*....|....*....|....*....|.
gi 1928140166 322 dtfTHSEMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:cd00653   396 ---THIEISPSQILSVAASLIPFPEHNQSPR 423
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 4-154 3.30e-42

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 153.18  E-value: 3.30e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   4 LMTSLFRLTFRKLLKDVYRHLQKCVEDKKEFTLTSAVKSSTITNGLKYSLATGNWgdqkkMNTKVGVSQVLNRYTYASTL 83
Cdd:PRK09606  344 LMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW-----VGGRTGVSQLLDRTDYMATL 418

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1928140166  84 SHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSVGSPSGPIIEFLEEYGL 154
Cdd:PRK09606  419 SHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGV 489
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 168-352 7.70e-39

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 145.49  E-value: 7.70e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166 168 TKVFVNGVWMGTADNATGLVDTLRELRRRDDISNEVSVTHDIREKELRVYTDAGRVQRPLFIVepETQNLLVKQKHadwi 247
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVV--ENGEPLLTEEH---- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166 248 TDQVKpDGtQFGWSELLREGVIELLDAEEEETSMICMSPQDLanskiyraNPDTyqsrsadpsarlvsvqtllpdtfTHS 327
Cdd:PRK07225   79 IEKLK-NG-ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL--------TEEH-----------------------THL 125

                         170       180
                  ....*....|....*....|....*
gi 1928140166 328 EMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:PRK07225  126 EIDPSLILGIGAGMIPYPEHNASPR 150
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 72-134 5.13e-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: 114.55  E-value: 5.13e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1928140166  72 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMA 134
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 170-231 2.69e-29

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: 107.07  E-value: 2.69e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1928140166 170 VFVNGVWMGTADNATGLVDTLRELRRRDDISNEVSVTHDIREKELRVYTDAGRVQRPLFIVE 231
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 4-352 3.69e-27

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: 112.90  E-value: 3.69e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166    4 LMTSLFRLTFRKLLKDVYRHLQKcvEDKKEFTLTSAVKSSTITNGLKYSLATGnwgdqkkmntkvGVSQVLNRYTYASTL 83
Cdd:COG0085    319 LLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS------------QLSQFMDQTNPLSEL 384

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   84 SHLRRTNT----PIGRDgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVSvgspsgpiiefleEYgld 155
Cdd:COG0085    385 THKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN-------------EY--- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  156 slidmqvadphatkvfvngvwmgtadnatglvdtlrelrrrddisnevsvthdirekelrvytdaGRVQRPLFIVEpetq 235
Cdd:COG0085    445 -----------------------------------------------------------------GFIETPYRKVE---- 455

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166  236 NLLVkqkhadwiTDQvkpdgtqfgwsellregvIELLDAEEEETSMICMSPQDLanskiyraNPDTYQSRSADPSARLVS 315
Cdd:COG0085    456 NGKV--------TDE------------------IEYLTADEEENYYIAQANAPL--------DEDGNFLEERVLVRYRGE 501

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 1928140166  316 VQTLLPDTFTHSEMHAAMILGVCASIVPFPDHNQSPR 352
Cdd:COG0085    502 EVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANR 538
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 260-330 7.23e-18

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: 76.43  E-value: 7.23e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1928140166 260 WSELLREGVIELLDAEEEETSMICMSPQDLANS-KIYRANPDTyqsrsadpsarlvsvqtllpDTFTHSEMH 330
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREGPYA--------------------HTYTHCEIH 52
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 3-47 1.45e-08

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: 55.85  E-value: 1.45e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1928140166   3 PLMTSLFRLTFRKLLKDVYRHLQKCVEDKKEFTLTSAVKSSTITN 47
Cdd:pfam04563 352 PLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
70-137 2.82e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 52.70  E-value: 2.82e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1928140166   70 VSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVVS 137
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
70-131 5.67e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.46  E-value: 5.67e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1928140166   70 VSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGMVCPAETPEGQACGLVKNLS 131
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 4-136 1.75e-06

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 49.70  E-value: 1.75e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166    4 LMTSLFRLTFRKLLKDVYRHLQKCVEDKKEftltsavKSSTITNGLKYSLATGNWGDQKkmntkvgVSQVLNRYTYASTL 83
Cdd:CHL00207   314 LLQNQFRIGLKRLERILRNRMTICDIDSLS-------KFNLINPKPLIALIREFFGSSQ-------LSQYMDQTNPLSEL 379

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1928140166   84 SHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVV 136
Cdd:CHL00207   380 THKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLATNARI 436
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 103-136 5.41e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 45.09  E-value: 5.41e-05
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1928140166  103 RQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVV 136
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLATYARV 502
rpoB CHL00001
RNA polymerase beta subunit
 71-151 9.83e-05

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 44.51  E-value: 9.83e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928140166   71 SQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAVV----SVGSPS 142
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIghwgSLESPF 454


                   ....*....
gi 1928140166  143 GPIIEFLEE 151
Cdd:CHL00001   455 YEISERSKE 463
 
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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