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Conserved domains on  [gi|1277950818|gb|PIV48235|]
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MAG: DNA-directed RNA polymerase subunit beta, partial [Gallionellaceae bacterium CG02_land_8_20_14_3_00_60_115]

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;
1-556 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: 877.89  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:PRK00405   715 LGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA 794

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTReglqrdkraqqiiddelar 160
Cdd:PRK00405   795 EVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------- 855

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:PRK00405       --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkLTQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:PRK00405   856 -------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLG 922

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKiadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlragvpFATPV 400
Cdd:PRK00405   923 VPSRMNIGQILETHLGWAAKGLGIK--------------------------------------------------FATPV 952

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  401 FDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 480
Cdd:PRK00405   953 FDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFG 1032

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1277950818  481 GQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDLERH 556
Cdd:PRK00405  1033 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-556 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 877.89  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:PRK00405   715 LGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA 794

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTReglqrdkraqqiiddelar 160
Cdd:PRK00405   795 EVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------- 855

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:PRK00405       --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkLTQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:PRK00405   856 -------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLG 922

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKiadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlragvpFATPV 400
Cdd:PRK00405   923 VPSRMNIGQILETHLGWAAKGLGIK--------------------------------------------------FATPV 952

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  401 FDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 480
Cdd:PRK00405   953 FDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFG 1032

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1277950818  481 GQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDLERH 556
Cdd:PRK00405  1033 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-553 0e+00

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: 735.32  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:TIGR02013  673 LGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGA 752

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREglqrdkraqqiiddelar 160
Cdd:TIGR02013  753 EVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------ 814

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:TIGR02013      --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkltQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:TIGR02013  815 ---------------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLG 879

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKiadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlraGVPFATPV 400
Cdd:TIGR02013  880 VPSRMNIGQILETHLGWAGKRLGRK-----------------------------------------------GVPIATPV 912

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  401 FDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 480
Cdd:TIGR02013  913 FDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 992

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277950818  481 GQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDL 553
Cdd:TIGR02013  993 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-554 0e+00

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: 724.21  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:COG0085    607 LGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGA 686

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREglqrdkraqqiiddelar 160
Cdd:COG0085    687 EVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE------------------ 748

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:COG0085        --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkltQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:COG0085    749 ---------------EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLG 813

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKIAdmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlragvpfaTPV 400
Cdd:COG0085    814 VPSRMNVGQVLETHLGWAAALLGRRVA--------------------------------------------------TPV 843

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  401 FDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 480
Cdd:COG0085    844 FDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFG 923

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277950818  481 GQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDLE 554
Cdd:COG0085    924 GQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVL 997
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-554 2.73e-174

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: 514.81  E-value: 2.73e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITR-DIPNLSEAQMARLDECGIVHIG 79
Cdd:cd00653   476 LGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPG 555

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  80 AEVGIGDVLVGKVTPKGETQLTPeekllraIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREglqrdkraqqiiddela 159
Cdd:cd00653   556 ARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----------------- 611

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 160 rykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqk 239
Cdd:cd00653       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 240 rvefdaafelkkkkltqgdeLQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPL 319
Cdd:cd00653   612 --------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPH 671

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 320 GVPSRMNIGQVLEVHLGWAAKGLGKKIadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlragvpFATP 399
Cdd:cd00653   672 GFPSRMTIGQLLESLLGKAGALLGKFG-------------------------------------------------DATP 702

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 400 vFDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 479
Cdd:cd00653   703 -FDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRG 781

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 480 GGQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIV----------KGDHKIDAGMPESFNVLTKEIRSLAI 549
Cdd:cd00653   782 GGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNI 861


                  ....*
gi 1277950818 550 DIDLE 554
Cdd:cd00653   862 DPRLK 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-478 2.14e-151

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: 438.89  E-value: 2.14e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEEltVMARDTKLG-TEEITRDIPNLSEAQMARLDECGIVHIG 79
Cdd:pfam00562  68 LGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGpIEEITRDIPNVSEEALKKLDEDGIVRVG 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  80 AEVGIGDVLVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTreglqrdkraqqiiddela 159
Cdd:pfam00562 146 AEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------------------- 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 160 rykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqk 239
Cdd:pfam00562     --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 240 rvefdaafelkkkkltqgdeLQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPL 319
Cdd:pfam00562 201 --------------------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPH 260

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 320 GVPSRMNIGQVLEVHLGWAAKGLgkkiadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlraGVPFATP 399
Cdd:pfam00562 261 GVPSRMTIGQLLETHLGKAAALL--------------------------------------------------GVFVDAT 290

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 400 VFDGATE--EEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKA 477
Cdd:pfam00562 291 PFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRA 370


                  .
gi 1277950818 478 Q 478
Cdd:pfam00562 371 R 371
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-556 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 877.89  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:PRK00405   715 LGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA 794

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTReglqrdkraqqiiddelar 160
Cdd:PRK00405   795 EVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------- 855

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:PRK00405       --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkLTQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:PRK00405   856 -------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLG 922

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKiadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlragvpFATPV 400
Cdd:PRK00405   923 VPSRMNIGQILETHLGWAAKGLGIK--------------------------------------------------FATPV 952

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  401 FDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 480
Cdd:PRK00405   953 FDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFG 1032

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1277950818  481 GQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDLERH 556
Cdd:PRK00405  1033 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-553 0e+00

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: 735.32  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:TIGR02013  673 LGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGA 752

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREglqrdkraqqiiddelar 160
Cdd:TIGR02013  753 EVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------ 814

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:TIGR02013      --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkltQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:TIGR02013  815 ---------------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLG 879

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKiadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlraGVPFATPV 400
Cdd:TIGR02013  880 VPSRMNIGQILETHLGWAGKRLGRK-----------------------------------------------GVPIATPV 912

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  401 FDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 480
Cdd:TIGR02013  913 FDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 992

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277950818  481 GQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDL 553
Cdd:TIGR02013  993 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-554 0e+00

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: 724.21  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:COG0085    607 LGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGA 686

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREglqrdkraqqiiddelar 160
Cdd:COG0085    687 EVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE------------------ 748

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:COG0085        --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkltQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:COG0085    749 ---------------EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLG 813

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKIAdmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlragvpfaTPV 400
Cdd:COG0085    814 VPSRMNVGQVLETHLGWAAALLGRRVA--------------------------------------------------TPV 843

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  401 FDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 480
Cdd:COG0085    844 FDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFG 923

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277950818  481 GQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDLE 554
Cdd:COG0085    924 GQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVL 997
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-556 0e+00

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 610.47  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:PRK14844   816 LGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGT 895

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREGLQRDKRAQQIIDDELAR 160
Cdd:PRK14844   896 RVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEIND 975

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 YKKDLADQMRIVESDAFARLEKLLHNkianggpkklaKGSKlNNEYLHSVEHHQWFDIRVADDAVAVQMEQIKEALAQKR 240
Cdd:PRK14844   976 FEKERDYIINVTSEYFYDELKKLLIN-----------SGSQ-DREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKV 1043

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 VEFDAAFELKKKKLTQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:PRK14844  1044 SHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLG 1123

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKIADML-------------------------------------------------- 350
Cdd:PRK14844  1124 VPSRMNVGQILETHVGWACKKLGEKVGNILdeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlnt 1203

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  351 -------------------AVEAKVADLRKFLGKIYS-GEQ---AEEIAAFSDEEVVEMCGNLRAGVPFATPVFDGATEE 407
Cdd:PRK14844  1204 pnknalndelnelvenylnSCKSAYSNLRNFLIEVYScGSNvsiCNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDE 1283

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  408 EIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEM 487
Cdd:PRK14844  1284 QIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEM 1363

                          570       580       590       600       610       620
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1277950818  488 EVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDIDLERH 556
Cdd:PRK14844  1364 ECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLKQN 1432
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-553 0e+00

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 594.59  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:PRK09603   806 LGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGT 885

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREGLQRDKRAQQIIDDELAR 160
Cdd:PRK09603   886 YVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAK 965

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 YKKDLADQMRIVESDAFARL------EKLLHNKIANGgpKKLAKGSKLNNEYLHSVEHHQWFD-IRVADDAVAVQMEQIK 233
Cdd:PRK09603   966 LDMEHFDRLTMLNREELLRVssllsqAILEEPFSHNG--KDYKEGDQIPKEEIASINRFTLASlVKKYSKEVQNHYEITK 1043

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  234 EALAQKRVEFDAAFELKKKKLTQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVD 313
Cdd:PRK09603  1044 NNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVD 1123

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  314 IVLNPLGVPSRMNIGQVLEVHLGWAAKGLGKKIADMLAVEAK--VADLRKFLGKIYSGEQA------EEIAAFSDEEVVE 385
Cdd:PRK09603  1124 IVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKdfAKELRAKMLEIANAINEkdpltiHALENCSDEELLE 1203

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  386 MCGNLRAGVPFATPVFDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPY 465
Cdd:PRK09603  1204 YAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPY 1283

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  466 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIR 545
Cdd:PRK09603  1284 SLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQ 1363


                   ....*...
gi 1277950818  546 SLAIDIDL 553
Cdd:PRK09603  1364 SLALDINI 1371
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-554 2.73e-174

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: 514.81  E-value: 2.73e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITR-DIPNLSEAQMARLDECGIVHIG 79
Cdd:cd00653   476 LGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPG 555

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  80 AEVGIGDVLVGKVTPKGETQLTPeekllraIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREglqrdkraqqiiddela 159
Cdd:cd00653   556 ARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----------------- 611

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 160 rykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqk 239
Cdd:cd00653       --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 240 rvefdaafelkkkkltqgdeLQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPL 319
Cdd:cd00653   612 --------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPH 671

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 320 GVPSRMNIGQVLEVHLGWAAKGLGKKIadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlragvpFATP 399
Cdd:cd00653   672 GFPSRMTIGQLLESLLGKAGALLGKFG-------------------------------------------------DATP 702

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 400 vFDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 479
Cdd:cd00653   703 -FDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRG 781

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 480 GGQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIV----------KGDHKIDAGMPESFNVLTKEIRSLAI 549
Cdd:cd00653   782 GGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNI 861


                  ....*
gi 1277950818 550 DIDLE 554
Cdd:cd00653   862 DPRLK 866
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-551 2.48e-157

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 477.28  E-value: 2.48e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:CHL00207   646 LGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGS 725

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTREglqrdkraqqiiddelar 160
Cdd:CHL00207   726 KVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS------------------ 787

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  161 ykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqkr 240
Cdd:CHL00207       --------------------------------------------------------------------------------

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  241 vefdaafelkkkkltQGDELQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPLG 320
Cdd:CHL00207   788 ---------------KGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLG 852

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  321 VPSRMNIGQVLEVHLGWAAKGLGKKIA-----DMLAVEAKvadlrkflgKIYSGEQAEEIAAFSDEEVvemcgnlragvp 395
Cdd:CHL00207   853 VPSRMNVGQLFECLLGLAGDNLNKRFKilpfdEMYGSEYS---------RILINNKLNQASIKNNEYW------------ 911

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  396 fatpvfdgateeeikellaLADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGG 475
Cdd:CHL00207   912 -------------------LFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGG 972

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1277950818  476 KAQFGGQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGDHKIDAGMPESFNVLTKEIRSLAIDI 551
Cdd:CHL00207   973 KAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDI 1048
rpoB CHL00001
RNA polymerase beta subunit
 1-552 4.54e-156

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 473.62  E-value: 4.54e-156
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTEEITRDIPNLSEAQMARLDECGIVHIGA 80
Cdd:CHL00001   651 LGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGS 730

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   81 EVGIGDVLVGKVTPK--GETQLTPEEKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQvftreglqrdkraqqiiddel 158
Cdd:CHL00001   731 WVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR--------------------- 789

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  159 arykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqWfdirvaddavavqmeqikealaq 238
Cdd:CHL00001   790 --------------------------------------------------------W----------------------- 790

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  239 krvefdaafeLKKKKLTQGDElqagvqKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNP 318
Cdd:CHL00001   791 ----------IQKKGGSSYNP------ETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNP 854

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  319 LGVPSRMNIGQVLEVHLGWAAKGLGK--KIA---DMLAVEAKvadlRKFlgkiysgeqaeeiaAFSdeevvEMCgnlRAG 393
Cdd:CHL00001   855 LGVPSRMNVGQIFECLLGLAGDLLNRhyRIApfdERYEQEAS----RKL--------------VFS-----ELY---EAS 908

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  394 VPFATP-VFDgateeeikellalADLPvsGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQP 472
Cdd:CHL00001   909 KQTANPwVFE-------------PEYP--GKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQP 973

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  473 LGGKAQFGGQRFGEMEVWALEAYGAAYILQEMLTVKSDDVNGRTKVYENIVKGD--HKIDaGMPESFNVLTKEIRSLAID 550
Cdd:CHL00001   974 LRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGtiPKPE-DAPESFRLLVRELRSLALE 1052


                   ..
gi 1277950818  551 ID 552
Cdd:CHL00001  1053 LN 1054
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-478 2.14e-151

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: 438.89  E-value: 2.14e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   1 LGQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEEltVMARDTKLG-TEEITRDIPNLSEAQMARLDECGIVHIG 79
Cdd:pfam00562  68 LGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGpIEEITRDIPNVSEEALKKLDEDGIVRVG 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  80 AEVGIGDVLVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDTSLRVKAGMSGTVIDVQVFTreglqrdkraqqiiddela 159
Cdd:pfam00562 146 AEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------------------- 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 160 rykkdladqmrivesdafarlekllhnkianggpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikealaqk 239
Cdd:pfam00562     --------------------------------------------------------------------------------

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 240 rvefdaafelkkkkltqgdeLQAGVQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVLNPL 319
Cdd:pfam00562 201 --------------------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPH 260

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 320 GVPSRMNIGQVLEVHLGWAAKGLgkkiadmlaveakvadlrkflgkiysgeqaeeiaafsdeevvemcgnlraGVPFATP 399
Cdd:pfam00562 261 GVPSRMTIGQLLETHLGKAAALL--------------------------------------------------GVFVDAT 290

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 400 VFDGATE--EEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGKA 477
Cdd:pfam00562 291 PFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRA 370


                  .
gi 1277950818 478 Q 478
Cdd:pfam00562 371 R 371
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 2-554 2.45e-53

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 191.01  E-value: 2.45e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   2 GQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTE-EITRDIPNL----SEAQMARLDECGIV 76
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIV 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  77 HIGAEVGIGDVLVGKVTPkgetqltP---EEkllRAIFGEKASDVKDTSLRVKAGMSGTVidvqvftreglqrdkraqqi 153
Cdd:TIGR03670 278 YPEVEVKGGDVLIGKTSP-------PrflEE---LREFGLVTERRRDTSVTVRHGEKGIV-------------------- 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 154 iddelarykkdlaDQMRIVESdafarlekllhnkianggpkklAKGSKLnneylhsvehhqwfdirvaddavavqmeqik 233
Cdd:TIGR03670 328 -------------DKVIITET----------------------EEGNKL------------------------------- 341

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 234 ealaqkrvefdaafelkkkkltqgdelqagvqkmVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVD 313
Cdd:TIGR03670 342 ----------------------------------VKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPD 387

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 314 IVLNPLGVPSRMNIGQVLEVhlgwaakgLGKKIAdmlAVEAKVADlrkflgkiysgeqaeeiaafsdeevvemcgnlrag 393
Cdd:TIGR03670 388 LIINPHAIPSRMTVGQLLEM--------IAGKVA---ALEGRRVD----------------------------------- 421

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 394 vpfATPvFDGATEEEI-KELLALADLPvSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQP 472
Cdd:TIGR03670 422 ---GTP-FEGEPEEELrKELLKLGFKP-DGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQP 496

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 473 LGGKAQFGGQRFGEMEVWALEAYGAAYILQEMLTVKSDDV--------------NGRTKVYENIVKGD----HKIDagMP 534
Cdd:TIGR03670 497 TEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYvvyvcencghiaweDKRKGTAYCPVCGEtgdiSPVE--MS 574

                         570       580
                  ....*....|....*....|
gi 1277950818 535 ESFNVLTKEIRSLAIDIDLE 554
Cdd:TIGR03670 575 YAFKLLLDELKSLGISPRLE 594
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-554 2.93e-52

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 192.48  E-value: 2.93e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818    2 GQNMMIAFMPWNGYNFEDSIMISERVVAEDRFTSIHIEELTVMARDTKLGTE-EITRDIPNLS----EAQMARLDECGIV 76
Cdd:PRK08565   702 GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVRgyrgEEYYRKLDEDGIV 781

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   77 HIGAEVGIGDVLVGKVTPKgetQLTPEEKLLRAIFGEKasdvKDTSLRVKAGMSGTVidvqvftreglqrdkraqqiidd 156
Cdd:PRK08565   782 SPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER----RDTSVTVRHGEKGIV----------------------- 831

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  157 elarykkdlaDQMRIVESdafarlekllhnkiaNGGpkklakgsklnneylhsvehhqwfdirvaddavavqmeqikeal 236
Cdd:PRK08565   832 ----------DTVLITES---------------PEG-------------------------------------------- 842

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  237 aqkrvefdaafelkkkkltqgdelqagvQKMVKVYVAVKRRLQPGDKMAGRHGNKGVVSRIVPVEDMPHMADGTPVDIVL 316
Cdd:PRK08565   843 ----------------------------NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLII 894

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  317 NPLGVPSRMNIGQVLEvhlgwaakglgkkiadmlAVEAKVADLRkflgkiysgeqaeeiAAFSDeevvemcgnlragvpf 396
Cdd:PRK08565   895 NPHAIPSRMTVGQLLE------------------SIAGKVAALE---------------GRFVD---------------- 925

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  397 ATPvFDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSLVTQQPLGGK 476
Cdd:PRK08565   926 ATP-FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGR 1004

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  477 AQFGGQRFGEMEVWALEAYGAAYILQEMLTVKSDDV--------------NGRTKVYENIVKGD----HKIDagMPESFN 538
Cdd:PRK08565  1005 AREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTtiyvcelcghiawyDRRKNKYVCPIHGDkgniSPVE--VSYAFK 1082

                          570
                   ....*....|....*.
gi 1277950818  539 VLTKEIRSLAIDIDLE 554
Cdd:PRK08565  1083 LLLQELMSMGISPRLK 1098
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 2-554 8.02e-48

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 175.92  E-value: 8.02e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818   2 GQNMMIAFMPWNGYNFEDSIMIS----ERVVAEDRF-TSIHIEEltvmaRDTKLGTEEiTRDIPNL------SEAQMARL 70
Cdd:PRK07225  204 GQNFVVAVMSYEGYNIEDALIMNkasiERGLGRSHFfRTYEGEE-----RRYPGGQED-RFEIPDKdvrgyrGEEAYRHL 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818  71 DECGIVHIGAEVGIGDVLVGKVTPkgetqltP---EEKllrAIFGEKASDVKDTSLRVKAGMSGTVidvqvftreglqrd 147
Cdd:PRK07225  278 DEDGLVNPETEVKEGDVLIGKTSP-------PrflEEP---DDFGISPEKRRETSVTMRSGEEGIV-------------- 333

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 148 kraqqiiddelarykkdlaDQMRIVESdafarlekllhnkiANGgpKKLAKgsklnneylhsvehhqwfdirvaddaVAV 227
Cdd:PRK07225  334 -------------------DTVILTET--------------EEG--SRLVK--------------------------VRV 352

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 228 QMEQIKEAlaqkrvefdaafelkkkkltqgdelqagvqkmvkvyvavkrrlqpGDKMAGRHGNKGVVSRIVPVEDMPHMA 307
Cdd:PRK07225  353 RDLRIPEL---------------------------------------------GDKFASRHGQKGVIGLIVPQEDMPFTE 387

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 308 DGTPVDIVLNPLGVPSRMNIGQVLEvhlgwaakglgkkiadMLAveAKVADLRkflGKIYSGeqaeeiaafsdeevvemc 387
Cdd:PRK07225  388 SGVVPDLIINPHAIPSRMTVGHVLE----------------MIG--GKVGSLE---GRRVDG------------------ 428

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 388 gnlragvpfaTPvFDGATEEEIKELLALADLPVSGQIQLYDGRTGEAFDRKTTVGYMHVLKLHHLVDDKMHARSTGPYSL 467
Cdd:PRK07225  429 ----------TA-FSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQV 497

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 468 VTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYILQEMLTVKSDDVN-------GRTKVYENI-------VKGD----HKI 529
Cdd:PRK07225  498 LTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEiyvcakcGMIAIYDKKrnrkycpICGEetdiYPV 577

                         570       580
                  ....*....|....*....|....*
gi 1277950818 530 DagMPESFNVLTKEIRSLAIDIDLE 554
Cdd:PRK07225  578 E--MSYAFKLLLDELKSLGIAPRLE 600
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 480-554 1.16e-31

RNA polymerase Rpb2, domain 7; 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.


Pssm-ID: 461355 [Multi-domain]  Cd Length: 87  Bit Score: 117.30  E-value: 1.16e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277950818 480 GGQRFGEMEVWALEAYGAAYILQEMLTVKSD----DVNGRTKVYEN-----IVKGDHKIDAG-MPESFNVLTKEIRSLAI 549
Cdd:pfam04560   1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80


                  ....*
gi 1277950818 550 DIDLE 554
Cdd:pfam04560  81 DPRLL 85
 
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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