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Conserved domains on  [gi|2264344774|gb|UTB60147|]
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ribosomal polymerase subunit beta, partial [Staphylococcus lugdunensis]

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;
1-287 0e+00

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: 588.61  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDidT 80
Cdd:PRK00405   440 NPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVV--D 517

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:PRK00405   518 GKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDA 597

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRlieENGKEYEGELDRYPLAK 240
Cdd:PRK00405   598 NRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV---EELDPGEDGVDIYNLIK 674

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:PRK00405   675 FQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLV 721
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-287 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 588.61  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDidT 80
Cdd:PRK00405   440 NPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVV--D 517

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:PRK00405   518 GKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDA 597

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRlieENGKEYEGELDRYPLAK 240
Cdd:PRK00405   598 NRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV---EELDPGEDGVDIYNLIK 674

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:PRK00405   675 FQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLV 721
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-287 2.33e-179

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: 522.69  E-value: 2.33e-179
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIDT 80
Cdd:TIGR02013  395 NPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGK 474

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:TIGR02013  475 VVVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDA 554

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRliEENGKEYEGELDRYPLAK 240
Cdd:TIGR02013  555 NRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY--DEDEEEPDGGIDIYRLLK 632

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:TIGR02013  633 YQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLV 679
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-287 2.29e-154

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: 456.11  E-value: 2.29e-154
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiDT 80
Cdd:COG0085    379 NPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKV--EN 456

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:COG0085    457 GKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDA 536

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPfvgtgmehvaardsgaaitakyrgrvehvesneilvrrlieengkeyegeLDRYPLAK 240
Cdd:COG0085    537 NRALMGANMQRQAVPLLRPEAP--------------------------------------------------LLHYPLQK 566

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:COG0085    567 FQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLV 613
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-268 3.15e-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: 207.81  E-value: 3.15e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   1 NPLAELTHKRRLSAlgpGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNefGFIETPYRKVDIDT 80
Cdd:cd00653   321 NPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEKEV 395

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  81 naitdqidyltadeedsyvvaqansrldengrflddevvcrfrgnntvmakekmDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:cd00653   396 ------------------------------------------------------THIEISPSQILSVAASLIPFPEHNQS 421

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774 161 NRALMGANMQRQAVP----------------LMNPEAPFVGTGMEHVAARD---SGA-AITAkyrgrvehVESNE----- 215
Cdd:cd00653   422 PRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFGelpLGQnAIVA--------VMSYSgynfe 493

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2264344774 216 ---ILVRRLIEEnG-------KEYEGELDRYPLAKFKRSNSGTCY---------NQRPIVSIGDVVEYNEIL 268
Cdd:cd00653   494 daiIINKSSVDR-GffrsihyKKYEIELRKTKNGPEEITRGDIPNvseeklknlDEDGIIRPGARVEPGDIL 564
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-62 1.98e-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: 114.16  E-value: 1.98e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2264344774   1 NPLAELTHKRRLSAlGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAR 62
Cdd:pfam04565   7 NYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-287 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 588.61  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDidT 80
Cdd:PRK00405   440 NPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVV--D 517

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:PRK00405   518 GKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDA 597

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRlieENGKEYEGELDRYPLAK 240
Cdd:PRK00405   598 NRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV---EELDPGEDGVDIYNLIK 674

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:PRK00405   675 FQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLV 721
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-287 2.33e-179

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: 522.69  E-value: 2.33e-179
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIDT 80
Cdd:TIGR02013  395 NPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGK 474

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:TIGR02013  475 VVVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDA 554

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRliEENGKEYEGELDRYPLAK 240
Cdd:TIGR02013  555 NRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY--DEDEEEPDGGIDIYRLLK 632

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:TIGR02013  633 YQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLV 679
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-287 2.29e-154

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: 456.11  E-value: 2.29e-154
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiDT 80
Cdd:COG0085    379 NPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKV--EN 456

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:COG0085    457 GKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDA 536

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPfvgtgmehvaardsgaaitakyrgrvehvesneilvrrlieengkeyegeLDRYPLAK 240
Cdd:COG0085    537 NRALMGANMQRQAVPLLRPEAP--------------------------------------------------LLHYPLQK 566

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:COG0085    567 FQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLV 613
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-287 2.15e-117

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 370.88  E-value: 2.15e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDidT 80
Cdd:PRK14844   540 NPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVV--N 617

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:PRK14844   618 RVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDA 697

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRLiEENGKEYEGeLDRYPLAK 240
Cdd:PRK14844   698 NRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAF-DKERVNYLD-VDIYHLRK 775

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:PRK14844   776 FQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLV 822
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-287 2.10e-112

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 356.54  E-value: 2.10e-112
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDidT 80
Cdd:PRK09603   533 NPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVV--D 610

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:PRK09603   611 GKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDA 690

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVrrLIEENGKEYegeLDRYPLAK 240
Cdd:PRK09603   691 NRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI--LGEGKEEAY---IDAYSLQK 765

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:PRK09603   766 NLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRV 812
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-287 3.07e-109

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 340.14  E-value: 3.07e-109
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIDT 80
Cdd:CHL00207   374 NPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGK 453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:CHL00207   454 VKKFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDA 533

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  161 NRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRrliEENGKEYEgeldrYPLAK 240
Cdd:CHL00207   534 NRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ---DDNNRYIH-----YYLQK 605

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 2264344774  241 FKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:CHL00207   606 YQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLV 652
rpoB CHL00001
RNA polymerase beta subunit
 1-287 5.07e-107

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 334.18  E-value: 5.07e-107
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774    1 NPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKvdIDT 80
Cdd:CHL00001   382 NPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYE--ISE 459

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   81 NAITDQIDYLTADEEDSYVVAQANSrLDENGRFLDDEVV-CRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDD 159
Cdd:CHL00001   460 RSKEERMVYLSPSEDEYYMIAAGNS-LALNQGIQEEQVVpARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHND 538

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  160 SNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKYRGRVEHVESNEILVRRlieengkeyEGELDRYPLA 239
Cdd:CHL00001   539 ANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSG---------NGDTLSIPLV 609

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 2264344774  240 KFKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVV 287
Cdd:CHL00001   610 MYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLV 657
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-268 3.15e-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: 207.81  E-value: 3.15e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774   1 NPLAELTHKRRLSAlgpGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNefGFIETPYRKVDIDT 80
Cdd:cd00653   321 NPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEKEV 395

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774  81 naitdqidyltadeedsyvvaqansrldengrflddevvcrfrgnntvmakekmDYMDVSPKQVVSAATACIPFLENDDS 160
Cdd:cd00653   396 ------------------------------------------------------THIEISPSQILSVAASLIPFPEHNQS 421

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774 161 NRALMGANMQRQAVP----------------LMNPEAPFVGTGMEHVAARD---SGA-AITAkyrgrvehVESNE----- 215
Cdd:cd00653   422 PRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFGelpLGQnAIVA--------VMSYSgynfe 493

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2264344774 216 ---ILVRRLIEEnG-------KEYEGELDRYPLAKFKRSNSGTCY---------NQRPIVSIGDVVEYNEIL 268
Cdd:cd00653   494 daiIINKSSVDR-GffrsihyKKYEIELRKTKNGPEEITRGDIPNvseeklknlDEDGIIRPGARVEPGDIL 564
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-62 1.98e-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: 114.16  E-value: 1.98e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2264344774   1 NPLAELTHKRRLSAlGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAR 62
Cdd:pfam04565   7 NYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 73-140 3.89e-30

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: 108.22  E-value: 3.89e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2264344774  73 YRKVDIDTnaITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVS 140
Cdd:pfam10385   1 YRKVEDGK--VTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-63 9.46e-13

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 68.44  E-value: 9.46e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2264344774    1 NPLAELTHKRRLsaLGPggLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARV 63
Cdd:PRK08565   410 NYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI 468
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 3-65 1.25e-11

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 64.59  E-value: 1.25e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2264344774   3 LAELTHKRRLSAlgpgGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNE 65
Cdd:PRK09606  415 MATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIST 473
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 206-287 1.65e-08

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: 54.84  E-value: 1.65e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2264344774 206 GRVEHVESNEILVRRLIEEngkeyeGELDRYPLAKFKRSNSGT---CYNQRPIVSIGDvVEYneiladgpsMELGEMALG 282
Cdd:pfam00562   6 PFVDHNQSPRNTYQCAMGK------QAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEA---------GGFGELPLG 69


                  ....*
gi 2264344774 283 RNVVV 287
Cdd:pfam00562  70 QNAIV 74
 
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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