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Conserved domains on  [gi|754297525|gb|AJI77506|]
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RNA polymerase beta, partial [Bradyrhizobium sp. Y2_3_nodule]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 1000195)

DNA-directed RNA polymerase subunit beta catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

CATH:  3.90.1110.10
EC:  2.7.7.6
Gene Ontology:  GO:0000428|GO:0003899|GO:0006351
PubMed:  6266829
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;
1-224 1.93e-172

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 503.09  E-value: 1.93e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQ 80
Cdd:PRK00405  460 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQ 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   81 ANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAP 160
Cdd:PRK00405  540 ANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAP 619

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754297525  161 FVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRAtEDLDPTKSGVDIYRLMKYQRSNQST 224
Cdd:PRK00405  620 LVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGEDGVDIYNLIKFQRSNQNT 682
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-224 1.93e-172

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 503.09  E-value: 1.93e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQ 80
Cdd:PRK00405  460 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQ 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   81 ANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAP 160
Cdd:PRK00405  540 ANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAP 619

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754297525  161 FVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRAtEDLDPTKSGVDIYRLMKYQRSNQST 224
Cdd:PRK00405  620 LVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGEDGVDIYNLIKFQRSNQNT 682
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-224 2.30e-143

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 426.39  E-value: 2.30e-143
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525     1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRV--TDEVVYLSAMEEGRYTV 78
Cdd:TIGR02013  415 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVI 494

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    79 AQANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAE 158
Cdd:TIGR02013  495 AQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSE 574

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 754297525   159 APFVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRATEDLDPTKSGVDIYRLMKYQRSNQST 224
Cdd:TIGR02013  575 APLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDIYRLLKYQRSNQDT 640
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-224 7.11e-117

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: 355.96  E-value: 7.11e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQ 80
Cdd:COG0085   399 SRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQ 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   81 ANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAP 160
Cdd:COG0085   479 ANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP 558

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754297525  161 FvgtgmegvvardsgaaiaarrsgvidqidatrvviratedldptksgvDIYRLMKYQRSNQST 224
Cdd:COG0085   559 L------------------------------------------------LHYPLQKFQRSNQGT 574
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-173 1.13e-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: 192.78  E-value: 1.13e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNkyGFVETPYRKVKdgrvtdevvylsameegrytvaq 80
Cdd:cd00653  338 FRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE----------------------- 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525  81 anvpldpkgrftedlvvcrhagevlpvtpDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVP------- 153
Cdd:cd00653  393 -----------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqq 443

                        170       180
                 ....*....|....*....|....*....
gi 754297525 154 ---------LVRAEAPFVGTGMEGVVARD 173
Cdd:cd00653  444 yrmdtklylLLYPQKPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 53-118 4.39e-38

RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.


Pssm-ID: 463067 [Multi-domain]  Cd Length: 66  Bit Score: 126.71  E-value: 4.39e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 754297525   53 YRKVKDGRVTDEVVYLSAMEEGRYTVAQANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVS 118
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-224 1.93e-172

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 503.09  E-value: 1.93e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQ 80
Cdd:PRK00405  460 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQ 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   81 ANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAP 160
Cdd:PRK00405  540 ANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAP 619

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754297525  161 FVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRAtEDLDPTKSGVDIYRLMKYQRSNQST 224
Cdd:PRK00405  620 LVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGEDGVDIYNLIKFQRSNQNT 682
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-224 2.30e-143

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 426.39  E-value: 2.30e-143
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525     1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRV--TDEVVYLSAMEEGRYTV 78
Cdd:TIGR02013  415 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVI 494

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    79 AQANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAE 158
Cdd:TIGR02013  495 AQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSE 574

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 754297525   159 APFVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRATEDLDPTKSGVDIYRLMKYQRSNQST 224
Cdd:TIGR02013  575 APLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDIYRLLKYQRSNQDT 640
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-224 7.11e-117

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: 355.96  E-value: 7.11e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQ 80
Cdd:COG0085   399 SRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQ 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   81 ANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAP 160
Cdd:COG0085   479 ANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP 558

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754297525  161 FvgtgmegvvardsgaaiaarrsgvidqidatrvviratedldptksgvDIYRLMKYQRSNQST 224
Cdd:COG0085   559 L------------------------------------------------LHYPLQKFQRSNQGT 574
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-224 7.59e-102

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 323.50  E-value: 7.59e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQ 80
Cdd:PRK14844  560 TRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIAD 639

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   81 ANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAP 160
Cdd:PRK14844  640 TSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAP 719

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754297525  161 FVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRATEDLDPTKSGVDIYRLMKYQRSNQST 224
Cdd:PRK14844  720 LVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNT 783
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
2-224 3.55e-93

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 298.38  E-value: 3.55e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    2 RERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQA 81
Cdd:PRK09603  554 KDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPA 633

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   82 NVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPF 161
Cdd:PRK09603  634 STPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPI 713

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 754297525  162 VGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRATEDldpTKSGVDIYRLMKYQRSNQST 224
Cdd:PRK09603  714 VGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGK---EEAYIDAYSLQKNLRTNQNT 773
rpoB CHL00001
RNA polymerase beta subunit
 1-224 1.47e-87

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 279.09  E-value: 1.47e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRVTDEVVYLSAMEEGRYTVAQ 80
Cdd:CHL00001  402 TGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAA 481

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   81 AN-VPLDPKGRfTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEA 159
Cdd:CHL00001  482 GNsLALNQGIQ-EEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEK 560

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 754297525  160 PFVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRatedldpTKSGVDIYRLMKYQRSNQST 224
Cdd:CHL00001  561 CIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILS-------GNGDTLSIPLVMYQRSNKNT 618
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-224 3.01e-83

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 267.73  E-value: 3.01e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFVETPYRKVKDGRV--TDEVVYLSAMEEGRYTV 78
Cdd:CHL00207  394 DKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRI 473

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   79 AQANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAE 158
Cdd:CHL00207  474 APNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPE 553

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 754297525  159 APFVGTGMEGVVARDSGAAIAARRSGVIDQIDATRVVIRatedldpTKSGVDI-YRLMKYQRSNQST 224
Cdd:CHL00207  554 KPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ-------DDNNRYIhYYLQKYQRSNQNT 613
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-173 1.13e-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: 192.78  E-value: 1.13e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNkyGFVETPYRKVKdgrvtdevvylsameegrytvaq 80
Cdd:cd00653  338 FRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE----------------------- 392

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525  81 anvpldpkgrftedlvvcrhagevlpvtpDKVDYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVP------- 153
Cdd:cd00653  393 -----------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqq 443

                        170       180
                 ....*....|....*....|....*....
gi 754297525 154 ---------LVRAEAPFVGTGMEGVVARD 173
Cdd:cd00653  444 yrmdtklylLLYPQKPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 53-118 4.39e-38

RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.


Pssm-ID: 463067 [Multi-domain]  Cd Length: 66  Bit Score: 126.71  E-value: 4.39e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 754297525   53 YRKVKDGRVTDEVVYLSAMEEGRYTVAQANVPLDPKGRFTEDLVVCRHAGEVLPVTPDKVDYMDVS 118
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-42 8.48e-25

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: 92.59  E-value: 8.48e-25
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFAR 42
Cdd:pfam04565  26 FREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-154 4.89e-16

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 76.53  E-value: 4.89e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525    1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARV--------------------------NKY-------- 46
Cdd:PRK08565  426 SRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQIsvgvdeeeveeilyelgvvpveeareEEYiswsrvyl 505

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   47 -----GFVETP---YRKVKD----GRVTDEV------------VY-----------LSAMEEGRYTVAQANVPLDPKGRF 91
Cdd:PRK08565  506 ngrliGYHPDGeelAEKIRElrrsGKISDEVnvayietgeineVYvncdsgrvrrpLIVVENGKPKLTREHVEKLKKGEL 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754297525   92 T-EDLVvcrHAGEV------------LPVTPDKV----DYMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPL 154
Cdd:PRK08565  586 TfDDLV---KMGVIeyldaeeeenayVALDPEDLtpehTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGL 662
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-45 2.28e-14

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 71.13  E-value: 2.28e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 754297525   1 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNK 45
Cdd:PRK09606 429 SRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIST 473
 
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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