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Conserved domains on  [gi|45545353|gb|AAS67524|]
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DNA-dependent RNA polymerase II second largest subunit, partial [Usnea cornuta]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 1000145)

DNA-directed RNA polymerase subunit B family protein similar to fungal DNA-directed RNA polymerase II subunit RPB2

CATH:  3.90.1110.10|3.90.1070.20
EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0000428|GO:0008270|GO:0003677|GO:0006351
PubMed:  11839495
SCOP:  4003708

Graphical summary

 Zoom to residue level

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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;
1-903 0e+00

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK08565:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1103  Bit Score: 889.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353     1 SEKVLIAQERSAANIVQVFK-KAQSNTPYVAEIRSAVeKGSRLISSMQMKlyekgegsKGGfgqTIKCTLPYIKTEIPIA 79
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKgEAGSSITHTAKVISSR-AGYRAQVTVERR--------KDG---TIYVSFPAVPGKIPFV 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    80 IVFRALGVVSDEDILNHICYDrkdTQMLEMLKPCIEEAF-VIQDREVALDFIGKRGnSQGVTRDKRIKYARDIMQKELLP 158
Cdd:PRK08565  216 ILMRALGLETDRDIVYAVSLD---PEIQQELLPSLEQASsIAATVEDALDYIGKRV-AIGQPREYRIERAEQILDKYLLP 291

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   159 HISQVEGSETRKAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEF 238
Cdd:PRK08565  292 HLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKL 371

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   239 NMTLAVKSTHLTNGLRYSLATGNWGDQKkaasvkAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLV 318
Cdd:PRK08565  372 DLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   319 CPAETPEGQACGLVKNLALMCYITVGTPSEPIVDfmIQRNMEV--LEEYEPLNSPNATKIFVNGVWVGVHRDPAHLVGTV 396
Cdd:PRK08565  446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   397 QNLRRRGLISHEVSlVRDIRDREFK---VFTDAGRVCRPLFVIDNdprssnrGNLVLTKDHVLKLEMDrenwattepdvr 473
Cdd:PRK08565  524 RELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLKKG------------ 583

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   474 eetDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDleisrqlqagyVMPEanpeelnkrvkapmnptaHTwtHCEIHPSM 553
Cdd:PRK08565  584 ---ELTFDDLVKMGVIEYLDAEEEENAYVALDPED-----------LTPE------------------HT--HLEIWPPA 629

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   554 ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 633
Cdd:PRK08565  630 ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAV 709

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   634 ACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPmrSDTLKLKHG--TYDKLDDDGLVAPGVRV 711
Cdd:PRK08565  710 LSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEV 787

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   712 SGEDIIIGKTAP--IAPDAEELGQRTKlhVKRDTSTPLRSTENGIVDQVLLSTNAEGLRFVKVRMRTTKIPQIGDKFASR 789
Cdd:PRK08565  788 KGGDVLIGKTSPprFLEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASR 865

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   790 HGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLREHG 869
Cdd:PRK08565  866 HGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLG 945

                         890       900       910
                  ....*....|....*....|....*....|....
gi 45545353   870 YQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:PRK08565  946 YKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-903 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 889.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353     1 SEKVLIAQERSAANIVQVFK-KAQSNTPYVAEIRSAVeKGSRLISSMQMKlyekgegsKGGfgqTIKCTLPYIKTEIPIA 79
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKgEAGSSITHTAKVISSR-AGYRAQVTVERR--------KDG---TIYVSFPAVPGKIPFV 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    80 IVFRALGVVSDEDILNHICYDrkdTQMLEMLKPCIEEAF-VIQDREVALDFIGKRGnSQGVTRDKRIKYARDIMQKELLP 158
Cdd:PRK08565  216 ILMRALGLETDRDIVYAVSLD---PEIQQELLPSLEQASsIAATVEDALDYIGKRV-AIGQPREYRIERAEQILDKYLLP 291

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   159 HISQVEGSETRKAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEF 238
Cdd:PRK08565  292 HLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKL 371

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   239 NMTLAVKSTHLTNGLRYSLATGNWGDQKkaasvkAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLV 318
Cdd:PRK08565  372 DLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   319 CPAETPEGQACGLVKNLALMCYITVGTPSEPIVDfmIQRNMEV--LEEYEPLNSPNATKIFVNGVWVGVHRDPAHLVGTV 396
Cdd:PRK08565  446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   397 QNLRRRGLISHEVSlVRDIRDREFK---VFTDAGRVCRPLFVIDNdprssnrGNLVLTKDHVLKLEMDrenwattepdvr 473
Cdd:PRK08565  524 RELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLKKG------------ 583

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   474 eetDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDleisrqlqagyVMPEanpeelnkrvkapmnptaHTwtHCEIHPSM 553
Cdd:PRK08565  584 ---ELTFDDLVKMGVIEYLDAEEEENAYVALDPED-----------LTPE------------------HT--HLEIWPPA 629

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   554 ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 633
Cdd:PRK08565  630 ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAV 709

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   634 ACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPmrSDTLKLKHG--TYDKLDDDGLVAPGVRV 711
Cdd:PRK08565  710 LSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEV 787

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   712 SGEDIIIGKTAP--IAPDAEELGQRTKlhVKRDTSTPLRSTENGIVDQVLLSTNAEGLRFVKVRMRTTKIPQIGDKFASR 789
Cdd:PRK08565  788 KGGDVLIGKTSPprFLEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASR 865

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   790 HGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLREHG 869
Cdd:PRK08565  866 HGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLG 945

                         890       900       910
                  ....*....|....*....|....*....|....
gi 45545353   870 YQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:PRK08565  946 YKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-903 0e+00

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: 788.30  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   1 SEKVLIAQERSAANIVQVFKKAQSntpYVAEIRSAVEKGSRLISSMQMKLYEKGegskggfgQTIKCTLPYIKteipiai 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVEDSKGK---RIYTKTSIPSYSPYRGSWLEVKSDKKK--------DRIYVRIDLKR------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  81 vfralgvvsdedilnhicydrkdtqmlemlkpcieeafviqdREVALDFIGKRGNsqgvtrdkrikyardimqkellphi 160
Cdd:cd00653 199 ------------------------------------------QEEALKYIGKRFE------------------------- 211

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 161 sqvegsetrkafFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNM 240
Cdd:cd00653 212 ------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTP 279

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 241 TLAVKSTHLTNGLRYSLATGNWGDQKKAASvKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVC 319
Cdd:cd00653 280 QLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRIC 358

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 320 PAETPEGQACGLVKNLALMCYITvgtpsepivdfmiqrnmevleeyeplnspnatkifvngvwvgvhrdpahlvgtvqnl 399
Cdd:cd00653 359 PIETPEGENCGLVKNLALMARIS--------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 400 rrrglishevslvrdirdrefkvftdaGRVCRPLFVIDNDprssnrgnlvltkdhvlklemdrenwattepdvreetdmg 479
Cdd:cd00653 382 ---------------------------GRIERPYRIVEKE---------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 480 wqglvkegvveyvdaeeeetimivmtpedleisrqlqagyvmpeanpeelnkrvkapmnptahtWTHCEIHPSMILGICA 559
Cdd:cd00653 395 ----------------------------------------------------------------VTHIEISPSQILSVAA 410

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 560 SIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGY 639
Cdd:cd00653 411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 640 NQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGmsvvEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIG 719
Cdd:cd00653 491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVG 566

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 720 KTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLST---NAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTI 796
Cdd:cd00653 567 KITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVI 646

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 797 GITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLREHGYQSRGFE 876
Cdd:cd00653 647 SKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKE 726

                       890       900
                ....*....|....*....|....*..
gi 45545353 877 VMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKH 753
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 376-903 0e+00

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: 578.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   376 IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNdprssnrGNLVLTKDHV 455
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   456 LKLEmdrenwattepdvreETDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDLeisrqlqagyvmpeaNPEelnkrvka 535
Cdd:TIGR03670  74 EKLK---------------EGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL---------------TPE-------- 115

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   536 pmnptaHTwtHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSM 615
Cdd:TIGR03670 116 ------HT--HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   616 EFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPmrSDTLKLKHG- 694
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGe 265

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   695 -TYDKLDDDGLVAPGVRVSGEDIIIGKTAPiaP----DAEELGQRTKlhVKRDTSTPLRSTENGIVDQVLLSTNAEGLRF 769
Cdd:TIGR03670 266 eAYKHLDEDGIVYPEVEVKGGDVLIGKTSP--PrfleELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKL 341

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   770 VKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGD 849
Cdd:TIGR03670 342 VKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVD 421

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 45545353   850 ATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:TIGR03670 422 GTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 558-903 7.25e-158

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: 467.01  E-value: 7.25e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   558 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 637
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   638 GYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSvVEQFEKPMRSDTLKLKHgtydkLDDDGLVAPGVRVSGEDII 717
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPI-EEITRDIPNVSEEALKK-----LDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   718 IGKTAPIAPDAE---ELGQrtKLHVKRDTSTPLRSTENGIVDQVLL-STNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 793
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGE--KARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   794 GTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVT--VDSVSRLLREHGYQ 871
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYN 312

                         330       340       350
                  ....*....|....*....|....*....|..
gi 45545353   872 SRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-903 1.01e-147

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: 462.27  E-value: 1.01e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    1 SEKVLIAQERSAANIVQVFKKAQSNTP-YVAEIRSAveKGSRLIssmqmklYEKgegSKGGfgqTIKCTLPYiKTEIPIA 79
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDlYSAKVIPS--RGAWLE-------FET---DKDG---TIYVRIDR-KRKIPVT 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   80 IVFRALGVVSDEDILNHIcydrKDTQMLEMLKPCIEEAfVIQDREVALDFIGKR---GnsqgvtRDKRIKYARDIMQKEL 156
Cdd:COG0085  181 VLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpG------EPPTIERAEQLLDNLF 249

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  157 -------LPHI---------SQVEGSETR--KAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFN 218
Cdd:COG0085  250 fdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  219 KLTKDVyKYlQKCVENNKEFNMTLAVKSTHLTNGLRYSLATGnwgdqkkaasvkaGVSQVLNRYTFASTLSHLRRTNT-- 296
Cdd:COG0085  330 RMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlg 394

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  297 --PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITvgtpsepivdfmiqrnmevleEYeplns 370
Cdd:COG0085  395 pgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------------EY----- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  371 pnatkifvngvwvgvhrdpahlvgtvqnlrrrglishevslvrdirdrefkvftdaGRVCRPLFVIDNdprssnrgnlvl 450
Cdd:COG0085  445 --------------------------------------------------------GFIETPYRKVEN------------ 456

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  451 tkdhvlklemdrenwattepdvreetdmgwqGLVKEGVvEYVDAEEEETIMIVMTPEDLEISRQLQAGYVMPEANPEELN 530
Cdd:COG0085  457 -------------------------------GKVTDEI-EYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVL 504

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  531 krvkapMNPTAHTwtHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQqrmdtmanILYYP----- 605
Cdd:COG0085  505 ------VPPEEVD--YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPlqkfq 568

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  606 ---------QKPLAttRSMEFLK------------FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRA 664
Cdd:COG0085  569 rsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEE 646

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  665 YTDQEKR--IGMSVVeQFEKPMRSDTLklkhgtYDKLDDDGLVAPGVRVSGEDIIIGKTAP---IAPDAEELGQR----T 735
Cdd:COG0085  647 YEIEARDtkLGPEEI-TRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEERLLRaifgE 719

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  736 KLHVKRDTSTPLRSTENGIVDQVLLSTNAEG-------LRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFT 808
Cdd:COG0085  720 KAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFL 799

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  809 SEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLV 888
Cdd:COG0085  800 EDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFD 879

                        970
                 ....*....|....*
gi 45545353  889 TQVFLGPTYYQRLRH 903
Cdd:COG0085  880 NPVTVGYMYYLKLHH 894
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-903 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 889.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353     1 SEKVLIAQERSAANIVQVFK-KAQSNTPYVAEIRSAVeKGSRLISSMQMKlyekgegsKGGfgqTIKCTLPYIKTEIPIA 79
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKgEAGSSITHTAKVISSR-AGYRAQVTVERR--------KDG---TIYVSFPAVPGKIPFV 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    80 IVFRALGVVSDEDILNHICYDrkdTQMLEMLKPCIEEAF-VIQDREVALDFIGKRGnSQGVTRDKRIKYARDIMQKELLP 158
Cdd:PRK08565  216 ILMRALGLETDRDIVYAVSLD---PEIQQELLPSLEQASsIAATVEDALDYIGKRV-AIGQPREYRIERAEQILDKYLLP 291

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   159 HISQVEGSETRKAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEF 238
Cdd:PRK08565  292 HLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKL 371

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   239 NMTLAVKSTHLTNGLRYSLATGNWGDQKkaasvkAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLV 318
Cdd:PRK08565  372 DLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   319 CPAETPEGQACGLVKNLALMCYITVGTPSEPIVDfmIQRNMEV--LEEYEPLNSPNATKIFVNGVWVGVHRDPAHLVGTV 396
Cdd:PRK08565  446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   397 QNLRRRGLISHEVSlVRDIRDREFK---VFTDAGRVCRPLFVIDNdprssnrGNLVLTKDHVLKLEMDrenwattepdvr 473
Cdd:PRK08565  524 RELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLKKG------------ 583

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   474 eetDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDleisrqlqagyVMPEanpeelnkrvkapmnptaHTwtHCEIHPSM 553
Cdd:PRK08565  584 ---ELTFDDLVKMGVIEYLDAEEEENAYVALDPED-----------LTPE------------------HT--HLEIWPPA 629

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   554 ILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAI 633
Cdd:PRK08565  630 ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAV 709

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   634 ACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPmrSDTLKLKHG--TYDKLDDDGLVAPGVRV 711
Cdd:PRK08565  710 LSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEV 787

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   712 SGEDIIIGKTAP--IAPDAEELGQRTKlhVKRDTSTPLRSTENGIVDQVLLSTNAEGLRFVKVRMRTTKIPQIGDKFASR 789
Cdd:PRK08565  788 KGGDVLIGKTSPprFLEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASR 865

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   790 HGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLREHG 869
Cdd:PRK08565  866 HGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLG 945

                         890       900       910
                  ....*....|....*....|....*....|....
gi 45545353   870 YQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:PRK08565  946 YKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-903 0e+00

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: 788.30  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   1 SEKVLIAQERSAANIVQVFKKAQSntpYVAEIRSAVEKGSRLISSMQMKLYEKGegskggfgQTIKCTLPYIKteipiai 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVEDSKGK---RIYTKTSIPSYSPYRGSWLEVKSDKKK--------DRIYVRIDLKR------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  81 vfralgvvsdedilnhicydrkdtqmlemlkpcieeafviqdREVALDFIGKRGNsqgvtrdkrikyardimqkellphi 160
Cdd:cd00653 199 ------------------------------------------QEEALKYIGKRFE------------------------- 211

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 161 sqvegsetrkafFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNM 240
Cdd:cd00653 212 ------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTP 279

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 241 TLAVKSTHLTNGLRYSLATGNWGDQKKAASvKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVC 319
Cdd:cd00653 280 QLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRIC 358

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 320 PAETPEGQACGLVKNLALMCYITvgtpsepivdfmiqrnmevleeyeplnspnatkifvngvwvgvhrdpahlvgtvqnl 399
Cdd:cd00653 359 PIETPEGENCGLVKNLALMARIS--------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 400 rrrglishevslvrdirdrefkvftdaGRVCRPLFVIDNDprssnrgnlvltkdhvlklemdrenwattepdvreetdmg 479
Cdd:cd00653 382 ---------------------------GRIERPYRIVEKE---------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 480 wqglvkegvveyvdaeeeetimivmtpedleisrqlqagyvmpeanpeelnkrvkapmnptahtWTHCEIHPSMILGICA 559
Cdd:cd00653 395 ----------------------------------------------------------------VTHIEISPSQILSVAA 410

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 560 SIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGY 639
Cdd:cd00653 411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 640 NQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGmsvvEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIG 719
Cdd:cd00653 491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVG 566

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 720 KTAPIAPDAEELGQRTKLHVKRDTSTPLRSTENGIVDQVLLST---NAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTI 796
Cdd:cd00653 567 KITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVI 646

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353 797 GITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLREHGYQSRGFE 876
Cdd:cd00653 647 SKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKE 726

                       890       900
                ....*....|....*....|....*..
gi 45545353 877 VMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKH 753
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 376-903 0e+00

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: 578.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   376 IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNdprssnrGNLVLTKDHV 455
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   456 LKLEmdrenwattepdvreETDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDLeisrqlqagyvmpeaNPEelnkrvka 535
Cdd:TIGR03670  74 EKLK---------------EGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL---------------TPE-------- 115

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   536 pmnptaHTwtHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSM 615
Cdd:TIGR03670 116 ------HT--HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   616 EFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPmrSDTLKLKHG- 694
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGe 265

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   695 -TYDKLDDDGLVAPGVRVSGEDIIIGKTAPiaP----DAEELGQRTKlhVKRDTSTPLRSTENGIVDQVLLSTNAEGLRF 769
Cdd:TIGR03670 266 eAYKHLDEDGIVYPEVEVKGGDVLIGKTSP--PrfleELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKL 341

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   770 VKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGD 849
Cdd:TIGR03670 342 VKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVD 421

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 45545353   850 ATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:TIGR03670 422 GTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 374-903 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 549.56  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  374 TKIFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVIDNdprssnrGNLVLTKD 453
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  454 HVLKLEmdrenwattepdvreETDMGWQGLVKEGVVEYVDAEEEETIMIVMTPEDLeisrqlqagyvmpeaNPEelnkrv 533
Cdd:PRK07225  78 HIEKLK---------------NGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL---------------TEE------ 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  534 kapmnptaHTwtHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTR 613
Cdd:PRK07225 122 --------HT--HLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQ 191

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  614 SMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSVVEQFEKPmrSDTLKLKH 693
Cdd:PRK07225 192 TQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIP--DKDVRGYR 269

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  694 G--TYDKLDDDGLVAPGVRVSGEDIIIGKTAPiaP----DAEELGQRTKlhVKRDTSTPLRSTENGIVDQVLLSTNAEGL 767
Cdd:PRK07225 270 GeeAYRHLDEDGLVNPETEVKEGDVLIGKTSP--PrfleEPDDFGISPE--KRRETSVTMRSGEEGIVDTVILTETEEGS 345

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  768 RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFE 847
Cdd:PRK07225 346 RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRR 425

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 45545353  848 GDATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:PRK07225 426 VDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHH 481
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 558-903 7.25e-158

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: 467.01  E-value: 7.25e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   558 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQQRMDTMANILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 637
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   638 GYNQEDSVIMNQSSIDRGLFRSLFYRAYTDQEKRIGMSvVEQFEKPMRSDTLKLKHgtydkLDDDGLVAPGVRVSGEDII 717
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPI-EEITRDIPNVSEEALKK-----LDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   718 IGKTAPIAPDAE---ELGQrtKLHVKRDTSTPLRSTENGIVDQVLL-STNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 793
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGE--KARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   794 GTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVT--VDSVSRLLREHGYQ 871
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYN 312

                         330       340       350
                  ....*....|....*....|....*....|..
gi 45545353   872 SRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-903 1.01e-147

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: 462.27  E-value: 1.01e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    1 SEKVLIAQERSAANIVQVFKKAQSNTP-YVAEIRSAveKGSRLIssmqmklYEKgegSKGGfgqTIKCTLPYiKTEIPIA 79
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDlYSAKVIPS--RGAWLE-------FET---DKDG---TIYVRIDR-KRKIPVT 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   80 IVFRALGVVSDEDILNHIcydrKDTQMLEMLKPCIEEAfVIQDREVALDFIGKR---GnsqgvtRDKRIKYARDIMQKEL 156
Cdd:COG0085  181 VLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpG------EPPTIERAEQLLDNLF 249

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  157 -------LPHI---------SQVEGSETR--KAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFN 218
Cdd:COG0085  250 fdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  219 KLTKDVyKYlQKCVENNKEFNMTLAVKSTHLTNGLRYSLATGnwgdqkkaasvkaGVSQVLNRYTFASTLSHLRRTNT-- 296
Cdd:COG0085  330 RMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlg 394

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  297 --PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITvgtpsepivdfmiqrnmevleEYeplns 370
Cdd:COG0085  395 pgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------------EY----- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  371 pnatkifvngvwvgvhrdpahlvgtvqnlrrrglishevslvrdirdrefkvftdaGRVCRPLFVIDNdprssnrgnlvl 450
Cdd:COG0085  445 --------------------------------------------------------GFIETPYRKVEN------------ 456

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  451 tkdhvlklemdrenwattepdvreetdmgwqGLVKEGVvEYVDAEEEETIMIVMTPEDLEISRQLQAGYVMPEANPEELN 530
Cdd:COG0085  457 -------------------------------GKVTDEI-EYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVL 504

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  531 krvkapMNPTAHTwtHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQqrmdtmanILYYP----- 605
Cdd:COG0085  505 ------VPPEEVD--YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPlqkfq 568

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  606 ---------QKPLAttRSMEFLK------------FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRA 664
Cdd:COG0085  569 rsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEE 646

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  665 YTDQEKR--IGMSVVeQFEKPMRSDTLklkhgtYDKLDDDGLVAPGVRVSGEDIIIGKTAP---IAPDAEELGQR----T 735
Cdd:COG0085  647 YEIEARDtkLGPEEI-TRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEERLLRaifgE 719

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  736 KLHVKRDTSTPLRSTENGIVDQVLLSTNAEG-------LRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFT 808
Cdd:COG0085  720 KAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFL 799

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  809 SEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGDATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLV 888
Cdd:COG0085  800 EDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFD 879

                        970
                 ....*....|....*
gi 45545353  889 TQVFLGPTYYQRLRH 903
Cdd:COG0085  880 NPVTVGYMYYLKLHH 894
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-251 1.82e-102

RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 324.33  E-value: 1.82e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353     1 SEKVLIAQERSAANIVQVFKKAQ-SNTPYVAEIRSAVEKGSRLISSMQMKLYEkgeGSKGGfgqTIKCTLPYIKTEIPIA 79
Cdd:pfam04563 146 SEKVIVAQEHRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVNVLE---YLSNG---TIYFKFPYIKKEIPIV 219

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    80 IVFRALGVVSDEDILNHICYDRKDTQMLEMLKPCIEEAFVI--QDREVALDFIGKRGNSQ---GVTRDKRIKYARDIMQK 154
Cdd:pfam04563 220 IILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQK 299

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   155 ELLPHISQVEGSETRKAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVEN 234
Cdd:pfam04563 300 EVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGS 379

                         250
                  ....*....|....*..
gi 45545353   235 NKEFNMTLAVKSTHLTN 251
Cdd:pfam04563 380 PDDLMLQLLVNAKPITS 396
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-366 1.53e-81

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 271.82  E-value: 1.53e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    1 SEKVLIAQERSAANIVQVFKKAQSNTP-YVAEIRSaVEKGSR-LISSmqmklyekgEGSKGGFgqtIKCTLPYIKTEIPI 78
Cdd:PRK09606 153 SERVLMTLEDLAPNKILVEKDERYGDRiEVAKVFS-QRRGYRaLVTV---------ERNRDGL---LEVSFPSVPGSIPF 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   79 AIVFRALGVVSDEDILNHICYDRK-DTQMLEMLkpciEEAfVIQDREVALDFIGKRGNSqGVTRDKRIKYARDIMQKELL 157
Cdd:PRK09606 220 VILMRALGLETDEEIVEAVSDDPEiVKFMLENL----EEA-EVDTQEEALEYIGKRVAP-GQTKEYRIKRAEYVIDRYLL 293

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  158 PHISQVEGSETRKAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVyKY-LQKCVENNK 236
Cdd:PRK09606 294 PHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDV-KYqLERANMRNR 372

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353  237 EFNMTLAVKSTHLTNGLRYSLATGNW--GdqkkaasvKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTH 314
Cdd:PRK09606 373 ELSIKTAVRSDVLTERLEHAMATGNWvgG--------RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 45545353  315 WGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIVDFMiqRNMEVLEEYE 366
Cdd:PRK09606 445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL--KELGVEPERG 494
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-203 8.30e-51

RNA polymerase Rpb2, domain 2; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).


Pssm-ID: 398318 [Multi-domain]  Cd Length: 185  Bit Score: 176.77  E-value: 8.30e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    12 AANIVQVFKKAQSNtpyvaEIRSAVEKGSRLISSMQMKLyEKGegskggfGQTIKCTLPYIKTEIPIAIVFRALGVVSDE 91
Cdd:pfam04561   1 RSNGIYVEKELDKN-----GIIATYTSSLISNRGSWLKL-EID-------GKTLIWSRPSKKRKIPIVIFLKALGLVSDR 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    92 DILNHICYDRKDTQMLEMLKPCIEEAFVIQDREVALDFIGKrGNSQGVTRDKRIKYARDIMQK-----ELLPHISQVEGS 166
Cdd:pfam04561  68 EILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEPF 146

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 45545353   167 ETR--KAFFLGYMVHRLLQCALGRREVDDRDHFGKKRLD 203
Cdd:pfam04561 147 ENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 73-903 6.76e-40

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: 159.83  E-value: 6.76e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353     73 KTEIPIAIVFRALGVVSDEDILNHIcyDRKDTQMLEMLK-PCI--EEAFVI----------QDREVA------LDFIGKR 133
Cdd:TIGR02013  193 KRKLPATVLLRALGYTIDTLILNRL--GSGEYIRNTLRKdPTNseEEALVEiyrklrpgepPTVEAArsllenLFFDPKR 270

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    134 GNSQGVTRDKrikyardiMQKELLPHISQVEGSETrKAFFLGYMVHrLLQCALGRREVDDRDHFGKKRLDLAGPLLASLF 213
Cdd:TIGR02013  271 YDLGRVGRYK--------LNKKLGLDVPESIGVLT-KEDIIATIKY-LIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQF 340

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    214 RGTFNKLTKDVYKYLqkcveNNKEFNmtlAVKSTHLTNGlryslatgnwgdQKKAASVK-----AGVSQVLNRYTFASTL 288
Cdd:TIGR02013  341 RVGLARMERIVRERM-----STQDTD---TLTPQDLINA------------KPISAAIKeffgsSQLSQFMDQTNPLAEL 400

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    289 SHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT----VGTPSEPIVDFMIQ---- 356
Cdd:TIGR02013  401 THKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNeygfIETPYRKVKDGKVVvtde 480

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    357 -RNMEVLEEYEPLNSPNATKIFVNGvwvgvhrdpaHLVGTVQNLRRRGlishEVSLVR----DIRDREFKVFTDAGRVCR 431
Cdd:TIGR02013  481 iDYLTADEEDNYVIAQANAPLDENG----------RFVEDLVVARYRG----EITLVSpdqvDYMDVSPKQVVSVAASLI 546

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    432 PLfvIDNDprSSNRGnlvltkdhVLKLEMDRENWATTEPDV---------REETDMGWQGLVKE-GVVEYVDAEEeetim 501
Cdd:TIGR02013  547 PF--LEHD--DANRA--------LMGSNMQRQAVPLLRSEAplvgtgmeaKVARDSGAVIVAKRgGVVEYVDAKR----- 609

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    502 IVMTPEDLeisrqlqagyvmpeanpeelnkrvkapmnptahtwthceihpsmilgicasiipfPDHNQSPRNTYQsamgk 581
Cdd:TIGR02013  610 IVIRYDED-------------------------------------------------------EEEPDGGIDIYR----- 629

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    582 qamgvfLTNYQQ-RMDTMANilyypQKP-------------LATTRSMEFlkfRELPAGQNAIVAIACYSGYNQEDSVIM 647
Cdd:TIGR02013  630 ------LLKYQRsNQDTCIN-----QRPivsvgdrveagdvLADGPSTDL---GELALGRNVLVAFMPWNGYNYEDAILI 695

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    648 NQSSIDRGLFRSLFyraytdqekrigmsvVEQFEKPMRsDTlklKHG----TYD----------KLDDDGLVAPGVRVSG 713
Cdd:TIGR02013  696 SERLVKDDVFTSIH---------------IEEYEVEAR-DT---KLGpeeiTRDipnvseealrNLDENGIVRIGAEVKA 756

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    714 EDIIIGKTAP---IAPDAEE------LGQRTKlHVkRDTSTPLRSTENGIVDQVLLSTNAEG-------LRFVKVRMRTT 777
Cdd:TIGR02013  757 GDILVGKVTPkgeTELTPEEkllraiFGEKAR-DV-RDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQK 834

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353    778 KIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKVSSLRGFEGD--ATP-FT 854
Cdd:TIGR02013  835 RKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFD 914

                          890       900       910       920
                   ....*....|....*....|....*....|....*....|....*....
gi 45545353    855 EVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:TIGR02013  915 GASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHH 963
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 277-340 8.68e-31

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 115.32  E-value: 8.68e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45545353   277 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 340
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 376-437 1.57e-30

RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 114.39  E-value: 1.57e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545353   376 IFVNGVWVGVHRDPAHLVGTVQNLRRRGLISHEVSLVRDIRDREFKVFTDAGRVCRPLFVID 437
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 181-903 4.14e-28

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 122.12  E-value: 4.14e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   181 LLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEfnmtlavKSTHLTNGLRYSLATG 260
Cdd:CHL00207  287 LINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLS-------KFNLINPKPLIALIRE 359

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   261 NWGDQKkaasvkagVSQVLNRYTFASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLA 336
Cdd:CHL00207  360 FFGSSQ--------LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   337 lmcyitvgtpsepivdfmiqrnmevleeyeplnspnaTKIFVNgvwvgvhrdpahlvgtvqnlrRRGLISHEVSLVRDIR 416
Cdd:CHL00207  432 -------------------------------------TNARIN---------------------KFGFIETPFYKVINGK 453

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   417 DREFKVFTdagrvcrplfvidndprssnrgnlvltkdhvlklemdrenwattepdvreetdmgwqglvkegvveYVDAEE 496
Cdd:CHL00207  454 VKKFGNPI------------------------------------------------------------------YLTADS 467

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   497 EETIMIvmTPEDLEISRQlqaGYVMPEANPEELNKRVKApMNPTAHTWTHceIHPSMILGICASIIPFPDHNQSPRNTYQ 576
Cdd:CHL00207  468 EDLYRI--APNDINLNKN---NYFKKNIIPVRYKQEFKT-VNPSKVDFIA--ISPIQVFSIAESLIPFLEHNDANRALMG 539

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   577 SAMGKQAMGVFL-------TNYQQRMDTMAN----------------------------ILYYPQK-------------P 608
Cdd:CHL00207  540 SNMQRQAVPLLYpekpivgTGYEKQIALDSGmtiisltegivvsvsaykiiiqddnnryIHYYLQKyqrsnqntcinyrP 619

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   609 -------------LATTRSMeflKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYtDQEKRIGMS 675
Cdd:CHL00207  620 ivwvgekinigqiLADGSDI---DNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-EIELRQTKL 695

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   676 VVEQFEKpmrsDTLKLKHGTYDKLDDDGLVAPGVRVSGEDIIIGKTAPiAPDAEELGQ---------RTKLHVKrDTSTP 746
Cdd:CHL00207  696 GSEEITR----NIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITP-KGESDQLPEgkllraifgEKAKDVK-DTSLR 769

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   747 LRSTENGIVDQVLLSTNAEGLR-----FVKVRMRTTKIP--QIGDKFASRHGQKGTIG-ITYRQeDMPFTSEGMVPDLII 818
Cdd:CHL00207  770 MPNGGYGRVIKVEIFSRSKGDElkfgyYLKIRVFIAQIRkiQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDGTPPDIIL 848

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   819 NPHAIPSRMTIAHLIECLLskvsslrGFEGD-------ATPFTEVTVDSVSRLLREHGYQSRGFE--------------- 876
Cdd:CHL00207  849 NPLGVPSRMNVGQLFECLL-------GLAGDnlnkrfkILPFDEMYGSEYSRILINNKLNQASIKnneywlfnsyhpgkm 921

                         810       820
                  ....*....|....*....|....*..
gi 45545353   877 VMYNGHTGRKLVTQVFLGPTYYQRLRH 903
Cdd:CHL00207  922 VLRDGRTGYKFKNPVTVGIAYMLKLIH 948
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 622-903 1.39e-26

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 117.12  E-value: 1.39e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   622 ELPAGQNAIVAIACYSGYNQEDSVIMNQSSI--DRglfrslfyraYTdqekrigmSV-VEQFEKPMRsDTlklKHG---- 694
Cdd:PRK00405  712 ELALGQNVLVAFMPWNGYNFEDAILISERLVkeDV----------FT--------SIhIEEYEIEAR-DT---KLGpeei 769

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   695 TYD----------KLDDDGLVAPGVRVSGEDIIIGKTAP---IAPDAEE------LGQRTKlHVKrDTStpLR--STENG 753
Cdd:PRK00405  770 TRDipnvseealrNLDESGIVRIGAEVKPGDILVGKVTPkgeTELTPEEkllraiFGEKAR-DVK-DTS--LRvpHGEEG 845

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   754 IV-DQVLLSTNAEG-------LRFVKV-----RmrttKIpQIGDKFASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINP 820
Cdd:PRK00405  846 TViDVKVFTRIEQGdelppgvNKLVKVyiaqkR----KI-QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNP 920

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   821 HAIPSRMTIAHLIECLLSKVSSLRG--FegdATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVTQVFLGPTY 897
Cdd:PRK00405  921 LGVPSRMNIGQILETHLGWAAKGLGikF---ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMY 997


                  ....*.
gi 45545353   898 YQRLRH 903
Cdd:PRK00405  998 MLKLHH 1003
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 480-551 3.87e-25

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 98.77  E-value: 3.87e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545353   480 WQGLVKEGVVEYVDAEEEETIMIVMTPEDLEISRQLQAGYvmpeanpeelnkrvkapmnPTAHTWTHCEIHP 551
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG-------------------PYAHTYTHCEIHP 53
rpoB CHL00001
RNA polymerase beta subunit
 622-888 4.35e-20

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 96.12  E-value: 4.35e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   622 ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYtdqekRIGMSVVEQ-FEKPMRS----DTLKLKHgty 696
Cdd:CHL00001  648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-----EIQTHVTSQgPERITKEiphlEAHLLRN--- 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   697 dkLDDDGLVAPGVRVSGEDIIIGKTAPiaPDAEELGQ-------RTKLHVKRDTS--TPLRSTENG---------IVDQV 758
Cdd:CHL00001  720 --LDKNGIVMLGSWVETGDILVGKLTP--QEAEESSYapegrllRAIFGIQVSTSkeTCLKLPIGGrgrvidvrwIQKKG 795

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   759 LLSTNAEGLRFVKVRMRttKIpQIGDKFASRHGQKGTIG-ITYRQeDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLL 837
Cdd:CHL00001  796 GSSYNPETIHVYILQKR--EI-QVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 45545353   838 skvsslrGFEGDatpftevtvdsvsrLLREHgYQSRGFEVMYNGHTGRKLV 888
Cdd:CHL00001  872 -------GLAGD--------------LLNRH-YRIAPFDERYEQEASRKLV 900
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
178-840 1.57e-14

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 78.43  E-value: 1.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   178 VHRLLQCALGRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQKCVENNKEFNMTLAVKSTHLTNGLRYSL 257
Cdd:PRK09603  441 VKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFF 520

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   258 ATGNwgdqkkaasvkagVSQVLNRYTFASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLV 332
Cdd:PRK09603  521 MGGQ-------------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLI 586

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   333 KNLALMCYIT----VGTPSEPIVDFMIQRNMEVL---EEYEPLNSPNATKIFVNGvwvgvhrdpaHLVGTVQNLRRRG-L 404
Cdd:PRK09603  587 NTLSTFTRVNdlgfIEAPYKKVVDGKVVGETIYLtaiQEDSHIIAPASTPIDEEG----------NILGDLIETRVEGeI 656

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   405 ISHEVSLVrDIRDREFKVFTDAGRVCRPLFVIDNDPRSSNRGNLVLTKDHVLKLE-----------MDRENWATTEPDvr 473
Cdd:PRK09603  657 VLNEKSKV-TLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDapivgtgiekiIARDSWGAIKAN-- 733

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   474 eetdmgwqglvKEGVVEYVDAEEeetimIVMTPEDLEisrqlqAGYVmpeaNPEELNKRVKAPMN------PTAHTWTHC 547
Cdd:PRK09603  734 -----------RAGVVEKIDSKN-----IYILGEGKE------EAYI----DAYSLQKNLRTNQNtsfnqvPIVKVGDKV 787

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   548 EIH------PSMILG-------ICASIIPFPDHNqsprntYQSAmgkqamgVFLTNYQQRMDTMANILYYPQKPLA---- 610
Cdd:PRK09603  788 EAGqiiadgPSMDRGelalgknVRVAFMPWNGYN------FEDA-------IVVSERITKDDIFTSTHIYEKEVDArelk 854

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   611 -----TTRSMEFLKFRELP-AGQNAIVAIACY--SG-------------------------YNQEDSVIMNQS------- 650
Cdd:PRK09603  855 hgveeFTADIPDVKEEALAhLDESGIVKVGTYvsAGmilvgktspkgeikstpeerllraiFGDKAGHVVNKSlycppsl 934

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   651 ---SIDRGLFRSLFYR-------AYTDQEKRIGMsvvEQFEKPM---RSDTLKLKHG-TYDKLDDDGLVAPGVRVSGEDI 716
Cdd:PRK09603  935 egtVIDVKVFTKKGYEkdarvlsAYEEEKAKLDM---EHFDRLTmlnREELLRVSSLlSQAILEEPFSHNGKDYKEGDQI 1011

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   717 IIGKTAPIAPDAeeLGQRTKlHVKRDTSTPLRSTENGIVDQ--VLLSTNAEGL--------------RFVKVRMRTTKIP 780
Cdd:PRK09603 1012 PKEEIASINRFT--LASLVK-KYSKEVQNHYEITKNNFLEQkkVLGEEHEEKLsilekddilpngviKKVKLYIATKRKL 1088

                         730       740       750       760       770       780
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   781 QIGDKFASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHLIECLLSKV 840
Cdd:PRK09603 1089 KVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLV 1148
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
187-834 2.27e-14

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 78.13  E-value: 2.27e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   187 GRREVDDRDHFGKKRLDLAGPLLASLFRGTFNKLTKDVYKYLQkcVENNKEFNMTLAVKSTHLTNGLRYSLATGNwgdqk 266
Cdd:PRK14844  459 GQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMS--TSSLDKVSPSDFINPKVLTNVLRDFFNSSQ----- 531

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   267 kaasvkagVSQVLNRYTFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT 342
Cdd:PRK14844  532 --------LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   343 ----VGTPSEPIVDFMIQRNMEVLEEYEPlnspnatkifvngvwvGVHrdpaHLVGTVQNLRrrglishevslvrdirdr 418
Cdd:PRK14844  604 kygfIESPYRKVVNRVVTDQIEYLSAIDE----------------GLY----YIADTSAKLD------------------ 645

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   419 EFKVFTDAGRVCRplfvidndprssNRGNLVLtkdhvlklemdrenwattepdvreetdmgwqglVKEGVVEYVDAEEEE 498
Cdd:PRK14844  646 ENNCFVDDMLYCR------------YAGSFVM---------------------------------VSSDQVSYIDVSPKQ 680

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   499 TIMIV--MTP--EDLEISRQLQAGYVMPEANPEelnKRVKAPMNPTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNT 574
Cdd:PRK14844  681 VISVAasLIPflENDDANRALMGSNMQRQAVPL---LKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRA 757

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   575 YQSAmGKQAMGV---FLTNYQQ-RMDTMANilyypQKPLatTRSMEFLK------------FRELPAGQNAIVAIACYSG 638
Cdd:PRK14844  758 FDKE-RVNYLDVdiyHLRKFQRsNHNTCIN-----QKPL--VCVGDYVKegdviadgpainSGELALGQNLLVAFMSWQG 829

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   639 YNQEDSVIMNQSSIDRGLFRSLFyraytdqekrigmsvVEQFE-----KPMRSDTLK-----LKHGTYDKLDDDGLVAPG 708
Cdd:PRK14844  830 YNFEDSIIISSEVVKKDLFTSIH---------------IEEFEcvvhdTPLGSEKITraipgVNEENLYHLDDSGIVKIG 894

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   709 VRVSGEDIIIGKTAP------------------------------IAPDAE--------------ELGQRTKLhVKRDTS 744
Cdd:PRK14844  895 TRVGPGYILVGKVTPkpslslppetkllmtifgeksfdcadsslyTSPDVEgtvidvqvftrrgvEENERALL-IKQKEI 973

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   745 TPLRSTENGIVD-----------QVLLSTNAE----------------GLR----------------------------- 768
Cdd:PRK14844  974 NDFEKERDYIINvtseyfydelkKLLINSGSQdrekfdsiereqwwgiGLKnqsiseqvkslkkdfdekvshaiaqfkrk 1053

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545353   769 ----------------FVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGMVPDLIINPHAIPSRMTIAHL 832
Cdd:PRK14844 1054 veklhegydlpqgvsmSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQI 1133


                  ..
gi 45545353   833 IE 834
Cdd:PRK14844 1134 LE 1135
 
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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