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Conserved domains on  [gi|490434234|gb|AGL12681|]
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RNA polymerase beta subunit, partial [Lelliottia amnigena]

Protein Classification

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;
1-212 1.60e-180

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: 523.51  E-value: 1.60e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:PRK00405  398 ERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 477

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTC 160
Cdd:PRK00405  478 RICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTA 557

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490434234  161 RSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:PRK00405  558 RYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQ 609
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-212 1.60e-180

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 523.51  E-value: 1.60e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:PRK00405  398 ERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 477

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTC 160
Cdd:PRK00405  478 RICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTA 557

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490434234  161 RSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:PRK00405  558 RYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQ 609
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-212 2.73e-157

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: 462.21  E-value: 2.73e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234     1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:TIGR02013  353 ERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 432

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLV 158
Cdd:TIGR02013  433 RICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLV 512

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 490434234   159 TCRSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:TIGR02013  513 VARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQ 566
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-212 1.63e-151

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: 445.32  E-value: 1.63e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:COG0085   337 ERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYG 416

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTC 160
Cdd:COG0085   417 RMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLV 496

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490434234  161 RSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:COG0085   497 RYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQ 548
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 9-212 2.99e-72

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: 234.77  E-value: 2.99e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   9 DTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgpGGLTRERAGFEVRDVHP 76
Cdd:cd00653  275 KDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHP 351

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234  77 THYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVTdgvvtdeihylsaieegnyviaqantnldeegrfvdd 156
Cdd:cd00653  352 SHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------------------------------- 392

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490434234 157 lvtcrskgesslfsnDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:cd00653  393 ---------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQ 433
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 37-104 4.04e-40

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: 131.49  E-value: 4.04e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490434234   37 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 104
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-212 1.60e-180

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 523.51  E-value: 1.60e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:PRK00405  398 ERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 477

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTC 160
Cdd:PRK00405  478 RICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTA 557

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490434234  161 RSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:PRK00405  558 RYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQ 609
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-212 2.73e-157

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: 462.21  E-value: 2.73e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234     1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:TIGR02013  353 ERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 432

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLV 158
Cdd:TIGR02013  433 RICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLV 512

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 490434234   159 TCRSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:TIGR02013  513 VARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQ 566
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-212 1.63e-151

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: 445.32  E-value: 1.63e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:COG0085   337 ERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYG 416

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTC 160
Cdd:COG0085   417 RMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLV 496

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490434234  161 RSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:COG0085   497 RYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQ 548
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-212 1.34e-104

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 330.43  E-value: 1.34e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:PRK14844  498 DSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 577

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTC 160
Cdd:PRK14844  578 RICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYC 657

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 490434234  161 RSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:PRK14844  658 RYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQ 709
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
6-212 3.36e-102

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 323.80  E-value: 3.36e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    6 GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPI 85
Cdd:PRK09603  496 GAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPI 575

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   86 ETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTCRSKGE 165
Cdd:PRK09603  576 ETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGE 655

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 490434234  166 SSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:PRK09603  656 IVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQ 702
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-212 2.80e-91

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 288.91  E-value: 2.80e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234    1 ERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYG 80
Cdd:CHL00207  332 NRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYG 411

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   81 RVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLV 158
Cdd:CHL00207  412 RICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNII 491

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 490434234  159 TCRSKGESSLFSNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:CHL00207  492 PVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQ 545
rpoB CHL00001
RNA polymerase beta subunit
 13-212 6.21e-88

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 279.48  E-value: 6.21e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   13 PQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPN 92
Cdd:CHL00001  352 PQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGIN 431

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   93 IGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSND 172
Cdd:CHL00001  432 AGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWE 511

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 490434234  173 QVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:CHL00001  512 QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQ 551
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 9-212 2.99e-72

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: 234.77  E-value: 2.99e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234   9 DTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgpGGLTRERAGFEVRDVHP 76
Cdd:cd00653  275 KDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHP 351

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234  77 THYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVTdgvvtdeihylsaieegnyviaqantnldeegrfvdd 156
Cdd:cd00653  352 SHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------------------------------- 392

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490434234 157 lvtcrskgesslfsnDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMGANMQRQ 212
Cdd:cd00653  393 ---------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQ 433
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 37-104 4.04e-40

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: 131.49  E-value: 4.04e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490434234   37 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 104
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 115-180 3.02e-39

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: 129.02  E-value: 3.02e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490434234  115 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLDEEGRFVDDLVTCRSKGESSLFSNDQVDYMDVS 180
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 36-104 1.67e-20

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 88.86  E-value: 1.67e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490434234   36 SQFMDQNNPLSEITHKRRIsaLGPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 104
Cdd:PRK08565  403 SQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 31-104 8.85e-19

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 83.85  E-value: 8.85e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490434234  31 GSSQLSQFMDQNNPLSEITHKRRISAlgPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 104
Cdd:PRK09606 401 GRTGVSQLLDRTDYMATLSHLRRVVS--P--LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 127-212 1.10e-04

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 42.26  E-value: 1.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490434234 127 IHYLSAIEEGNYVIAqantnLDEEgrfvdDLvtcrskgesslfsNDQVDYMDVSTQQIVSVGASLIPFLEHDDANRALMG 206
Cdd:PRK07225  98 IEYLDAEEEENAYIA-----VYEE-----DL-------------TEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMG 154


                 ....*.
gi 490434234 207 ANMQRQ 212
Cdd:PRK07225 155 AGMIKQ 160
 
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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