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Conserved domains on  [gi|315259500|gb|ADT91949|]
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DNA-directed RNA polymerase beta subunit, partial [Enterococcus malodoratus]

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;
1-392 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: 881.75  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    1 KNEGVVEFVDAHEVRVRRDNGA-----LDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNV 75
Cdd:PRK00405  640 KRDGVVEYVDASRIVVRVEELDpgedgVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNV 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   76 VVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDG 155
Cdd:PRK00405  720 LVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPG 799

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  156 DLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTR-EAGDELSPGVNMLVRVYIVQKRK 234
Cdd:PRK00405  800 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRK 879

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  235 IHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDS 314
Cdd:PRK00405  880 IQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEE 959

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 315259500  315 DVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:PRK00405  960 EIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFG 1037
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-392 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 881.75  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    1 KNEGVVEFVDAHEVRVRRDNGA-----LDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNV 75
Cdd:PRK00405  640 KRDGVVEYVDASRIVVRVEELDpgedgVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNV 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   76 VVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDG 155
Cdd:PRK00405  720 LVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPG 799

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  156 DLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTR-EAGDELSPGVNMLVRVYIVQKRK 234
Cdd:PRK00405  800 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRK 879

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  235 IHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDS 314
Cdd:PRK00405  880 IQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEE 959

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 315259500  315 DVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:PRK00405  960 EIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFG 1037
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 23-392 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: 800.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   23 LDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNVVVAFMTWEGYNYEDAIIMSRRLVKDDV 102
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  103 YTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAEERLLHAIFG 182
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  183 EKAREVRDTSLRVPHGGGGIVHDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPF 262
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  263 LPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPF 342
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPF 878

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 315259500  343 DNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:COG0085   879 DNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFG 928
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-392 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: 761.51  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500     1 KNEGVVEFVDAHEVRVRRD------NGALDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQN 74
Cdd:TIGR02013  597 KRGGVVEYVDAKRIVIRYDedeeepDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRN 676

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    75 VVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHD 154
Cdd:TIGR02013  677 VLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKA 756

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   155 GDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGDELSPGVNMLVRVYIVQKRK 234
Cdd:TIGR02013  757 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRK 836

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   235 IHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLG---IHVATPVFDGA 311
Cdd:TIGR02013  837 IQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGA 916

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   312 QDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRF 391
Cdd:TIGR02013  917 SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 996


                   .
gi 315259500   392 G 392
Cdd:TIGR02013  997 G 997
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-385 0e+00

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: 532.49  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    1 KNEGVVEFVDAHEVRVRRDNG--ALDKYDITKFRRSNSGTS---YNQRPLVGLGeKVDVGDiladgpsmeNGELALGQNV 75
Cdd:pfam00562   3 SLIPFVDHNQSPRNTYQCAMGkqAMGIYTLNKFYRSDQNTYvlcYPQKPLVKTG-AVEAGG---------FGELPLGQNA 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   76 VVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYEseARDTKLGP-EEITREIPNVGEDALKNLDEMGIIRIGAEVHD 154
Cdd:pfam00562  73 IVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  155 GDLLVGKVTPKGVTelsaeeRLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTreagdeLSPGVNMLVRVYIVQKRK 234
Cdd:pfam00562 151 GDILVGKVGPTELT------KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQKRK 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  235 IHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQD- 313
Cdd:pfam00562 219 PEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTe 298

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 315259500  314 -SDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQ 385
Cdd:pfam00562 299 vEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 40-392 1.01e-170

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: 499.02  E-value: 1.01e-170
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  40 YNQRPLVGLGekvdvgdiladgpsMEN----GELALGQNVVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEA 115
Cdd:cd00653  455 YPQKPLVGTG--------------IEEyiafGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIEL 520

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 116 RDTKLGPEEITR-EIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAeerllhaIFGEKAREVRDTSLR 194
Cdd:cd00653  521 RKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLK 593

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 195 VPHGGGGIVHDVKIFTREagdeLSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLN 274
Cdd:cd00653  594 YPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILN 669

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 275 PLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMI 354
Cdd:cd00653  670 PHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQ 749

                        330       340       350
                 ....*....|....*....|....*....|....*...
gi 315259500 355 KLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:cd00653  750 RLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFG 787
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-392 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 881.75  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    1 KNEGVVEFVDAHEVRVRRDNGA-----LDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNV 75
Cdd:PRK00405  640 KRDGVVEYVDASRIVVRVEELDpgedgVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNV 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   76 VVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDG 155
Cdd:PRK00405  720 LVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPG 799

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  156 DLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTR-EAGDELSPGVNMLVRVYIVQKRK 234
Cdd:PRK00405  800 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRK 879

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  235 IHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDS 314
Cdd:PRK00405  880 IQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEE 959

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 315259500  315 DVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:PRK00405  960 EIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFG 1037
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 23-392 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: 800.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   23 LDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNVVVAFMTWEGYNYEDAIIMSRRLVKDDV 102
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  103 YTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAEERLLHAIFG 182
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  183 EKAREVRDTSLRVPHGGGGIVHDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPF 262
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  263 LPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPF 342
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPF 878

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 315259500  343 DNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:COG0085   879 DNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFG 928
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-392 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: 761.51  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500     1 KNEGVVEFVDAHEVRVRRD------NGALDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQN 74
Cdd:TIGR02013  597 KRGGVVEYVDAKRIVIRYDedeeepDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRN 676

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    75 VVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHD 154
Cdd:TIGR02013  677 VLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKA 756

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   155 GDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGDELSPGVNMLVRVYIVQKRK 234
Cdd:TIGR02013  757 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRK 836

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   235 IHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLG---IHVATPVFDGA 311
Cdd:TIGR02013  837 IQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGA 916

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   312 QDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRF 391
Cdd:TIGR02013  917 SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 996


                   .
gi 315259500   392 G 392
Cdd:TIGR02013  997 G 997
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-385 0e+00

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: 532.49  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    1 KNEGVVEFVDAHEVRVRRDNG--ALDKYDITKFRRSNSGTS---YNQRPLVGLGeKVDVGDiladgpsmeNGELALGQNV 75
Cdd:pfam00562   3 SLIPFVDHNQSPRNTYQCAMGkqAMGIYTLNKFYRSDQNTYvlcYPQKPLVKTG-AVEAGG---------FGELPLGQNA 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   76 VVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYEseARDTKLGP-EEITREIPNVGEDALKNLDEMGIIRIGAEVHD 154
Cdd:pfam00562  73 IVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  155 GDLLVGKVTPKGVTelsaeeRLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTreagdeLSPGVNMLVRVYIVQKRK 234
Cdd:pfam00562 151 GDILVGKVGPTELT------KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQKRK 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  235 IHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQD- 313
Cdd:pfam00562 219 PEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTe 298

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 315259500  314 -SDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQ 385
Cdd:pfam00562 299 vEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 3-392 9.81e-180

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 528.51  E-value: 9.81e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    3 EGVVEFVDAHEVRVRRDNGALDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNVVVAFMTW 82
Cdd:CHL00207  578 EGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPW 657

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   83 EGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKV 162
Cdd:CHL00207  658 EGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKI 737

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  163 TPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGDELSPGVNMLVRVYIVQKRKIHEGDKMA 242
Cdd:CHL00207  738 TPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLA 817

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  243 GRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFD---GAQDSD--VW 317
Cdd:CHL00207  818 GRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDemyGSEYSRilIN 897

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  318 ETVREARMAAD----------AKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFG 387
Cdd:CHL00207  898 NKLNQASIKNNeywlfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHG 977


                  ....*
gi 315259500  388 GQRFG 392
Cdd:CHL00207  978 GQRFG 982
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 40-392 1.01e-170

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: 499.02  E-value: 1.01e-170
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  40 YNQRPLVGLGekvdvgdiladgpsMEN----GELALGQNVVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEA 115
Cdd:cd00653  455 YPQKPLVGTG--------------IEEyiafGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIEL 520

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 116 RDTKLGPEEITR-EIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAeerllhaIFGEKAREVRDTSLR 194
Cdd:cd00653  521 RKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLK 593

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 195 VPHGGGGIVHDVKIFTREagdeLSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLN 274
Cdd:cd00653  594 YPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILN 669

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 275 PLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMI 354
Cdd:cd00653  670 PHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQ 749

                        330       340       350
                 ....*....|....*....|....*....|....*...
gi 315259500 355 KLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:cd00653  750 RLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFG 787
rpoB CHL00001
RNA polymerase beta subunit
 1-392 7.17e-170

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 502.90  E-value: 7.17e-170
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    1 KNEGVVEFVDAHEVrVRRDNGALDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNVVVAFM 80
Cdd:CHL00001  582 EHEGKIIYTDTDKI-ILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYM 660

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   81 TWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVG 160
Cdd:CHL00001  661 PWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVG 740

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  161 KVTPKGVTELS--AEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREAGDELSPGVnmlVRVYIVQKRKIHEG 238
Cdd:CHL00001  741 KLTPQEAEESSyaPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPET---IHVYILQKREIQVG 817

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  239 DKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFD---GAQDSD 315
Cdd:CHL00001  818 DKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDeryEQEASR 897

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  316 --VWETVREARMAAD----------AKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGK 383
Cdd:CHL00001  898 klVFSELYEASKQTAnpwvfepeypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGR 977


                  ....*....
gi 315259500  384 AQFGGQRFG 392
Cdd:CHL00001  978 SKQGGQRVG 986
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
4-392 1.15e-136

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 431.27  E-value: 1.15e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    4 GVVEFVDAHEVRV--RRDNGA-LDKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQNVVVAFM 80
Cdd:PRK09603  736 GVVEKIDSKNIYIlgEGKEEAyIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFM 815

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   81 TWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHDGDLLVG 160
Cdd:PRK09603  816 PWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVG 895

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  161 KVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTR----------------------------- 211
Cdd:PRK09603  896 KTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKkgyekdarvlsayeeekakldmehfdrlt 975

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500      --------------------------------------------------------------------------------
Cdd:PRK09603  976 mlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlaslvkkyskevqnhyeitknnfleqkkvlge 1055

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  212 ---------EAGDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRM 282
Cdd:PRK09603 1056 eheeklsilEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRM 1135

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  283 NIGQVLELHLGMAARQL----------------------------------------------------------GIHVA 304
Cdd:PRK09603 1136 NIGQILEMHLGLVGKEFgkqiasmledktkdfakelrakmleianainekdpltihalencsdeelleyakdwskGVKMA 1215

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  305 TPVFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKA 384
Cdd:PRK09603 1216 IPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKA 1295


                  ....*...
gi 315259500  385 QFGGQRFG 392
Cdd:PRK09603 1296 LFGGQRFG 1303
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-392 2.09e-120

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 384.36  E-value: 2.09e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500    1 KNEGVVEFVDAHEVRVRR-DNGAL-----DKYDITKFRRSNSGTSYNQRPLVGLGEKVDVGDILADGPSMENGELALGQN 74
Cdd:PRK14844  740 KRDGIVDSSDSNSIVIRAfDKERVnyldvDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQN 819

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   75 VVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTKLGPEEITREIPNVGEDALKNLDEMGIIRIGAEVHD 154
Cdd:PRK14844  820 LLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGP 899

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  155 GDLLVGKVTPKGVTELSAEERLLHAIFGEKAREVRDTSLRVPHGGGGIVHDVKIFTREA--------------------- 213
Cdd:PRK14844  900 GYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGveenerallikqkeindfeke 979

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500      --------------------------------------------------------------------------------
Cdd:PRK14844  980 rdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhe 1059

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  214 GDELSPGVNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIMLNPLGVPSRMNIGQVLELHLG 293
Cdd:PRK14844 1060 GYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVG 1139

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  294 MAARQL-------------------------------------------------------------------------- 299
Cdd:PRK14844 1140 WACKKLgekvgnildeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelven 1219

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  300 -------------------------------------------------GIHVATPVFDGAQDSDVWETVREARMAADAK 330
Cdd:PRK14844 1220 ylnscksaysnlrnflievyscgsnvsicnnirdisdnnliefarklrdGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQ 1299

                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 315259500  331 TVLYDGRTGEPFDNRISVGVMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:PRK14844 1300 AVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFG 1361
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 40-392 3.58e-78

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: 252.26  E-value: 3.58e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   40 YNQRPLVglgeKVDVGDIladgpsMENGELALGQNVVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARDTK 119
Cdd:TIGR03670 176 YPQKPLV----KTRVLEL------IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYP 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  120 LGPE-EITREIPNV----GEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKgvtelsaeeRLL--HAIFGEKAREVRDTS 192
Cdd:TIGR03670 246 GGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTERRRDTS 316

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  193 LRVPHGGGGIVHDVKIFTREAGdelspgvNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVDIM 272
Cdd:TIGR03670 317 VTVRHGEKGIVDKVIITETEEG-------NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLI 389

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  273 LNPLGVPSRMNIGQVLELHLGMAARQLGIHV-ATPvFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVGVM 351
Cdd:TIGR03670 390 INPHAIPSRMTVGQLLEMIAGKVAALEGRRVdGTP-FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVI 468

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 315259500  352 YMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:TIGR03670 469 YYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFG 509
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 40-392 3.98e-75

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 244.48  E-value: 3.98e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  40 YNQRPLVglgeKVDVGDILA--DGPSmengelalGQNVVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARD 117
Cdd:PRK07225 182 YPQVPLV----KTQTQEIIGfdERPA--------GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERR 249

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 118 TKLGPEEiTREIPNV------GEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKgvtelsaeeRLL--HAIFGEKAREVR 189
Cdd:PRK07225 250 YPGGQED-RFEIPDKdvrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPP---------RFLeePDDFGISPEKRR 319

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 190 DTSLRVPHGGGGIVHDVKIFTREAGdelspgvNMLVRVYIVQKRKIHEGDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPV 269
Cdd:PRK07225 320 ETSVTMRSGEEGIVDTVILTETEEG-------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVP 392

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500 270 DIMLNPLGVPSRMNIGQVLELHLGMAARQLGIHVATPVFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVG 349
Cdd:PRK07225 393 DLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVG 472

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 315259500 350 VMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:PRK07225 473 VIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFG 515
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 40-392 3.12e-73

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 247.18  E-value: 3.12e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500   40 YNQRPLVglgeKVDVGDILA--DGPSmengelalGQNVVVAFMTWEGYNYEDAIIMSRRLVKDDVYTSIHIEEYESEARd 117
Cdd:PRK08565  680 YPQRPLV----QTRALEIIGynDRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEER- 746

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  118 TKLGPEEITREIP--NV----GEDALKNLDEMGIIRIGAEVHDGDLLVGKVTPKGVTELSAEERLlhaifGEKARevRDT 191
Cdd:PRK08565  747 KYPGGQEDKIEIPepNVrgyrGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSL-----GLQER--RDT 819

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  192 SLRVPHGGGGIVHDVKIFTreagdelSPGVNMLVRVYiVQKRKIHE-GDKMAGRHGNKGVVSRIMPEEDMPFLPDGTPVD 270
Cdd:PRK08565  820 SVTVRHGEKGIVDTVLITE-------SPEGNKLVKVR-VRDLRIPElGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPD 891

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315259500  271 IMLNPLGVPSRMNIGQVLELHLGMAARQLGIHV-ATPvFDGAQDSDVWETVREARMAADAKTVLYDGRTGEPFDNRISVG 349
Cdd:PRK08565  892 LIINPHAIPSRMTVGQLLESIAGKVAALEGRFVdATP-FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIG 970

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 315259500  350 VMYMIKLAHMVDDKLHARSIGPYSLVTQQPLGGKAQFGGQRFG 392
Cdd:PRK08565  971 VVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFG 1013
 
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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