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Conserved domains on  [gi|68131890|gb|AAY85223|]
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RNA polymerase II second largest subunit, partial [Nelumbo nucifera]

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;
2-865 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: 916.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     2 ARLRNLTYSAPLYVDVTKRVikkghDCEEvTETQEfakVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:PRK08565   76 ARLRNLTYAAPLYLTMIPVE-----NGIE-YEPEE---VKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIIN 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQnRPPSSMfVRMlsrtsaKGGSsgqyIRATLPYIRTEIPI 161
Cdd:PRK08565  147 GSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSRAGY-RAQVTV-ERR------KDGT----IYVSFPAVPGKIPF 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   162 IIVFRALGFVADKDILEHIcydFSDTQMMELLRPSLEEAFVIQN-QQVALDYIGKRgSTVGVTREKRIKYAKEILQKEML 240
Cdd:PRK08565  215 VILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASSIAAtVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLL 290

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   241 PHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKD 320
Cdd:PRK08565  291 PHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRK 370

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   321 VNLQFAIKAKTITSGLKYSLATGNWGqanaaGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMM 400
Cdd:PRK08565  371 LDLRAIVRPDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   401 CPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVGIHRNPELLVKTLRQ 480
Cdd:PRK08565  446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRE 525

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   481 LRRQVDVNTEVGV--IRDIRLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIRALQQRESSeeggWHDLVAKGFIEYVDT 558
Cdd:PRK08565  526 LRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELT----FDDLVKMGVIEYLDA 601

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   559 EEEETTMISmtindlvtarLNPEEAYSEtYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLR 638
Cdd:PRK08565  602 EEEENAYVA----------LDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIR 670

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   639 MDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 718
Cdd:PRK08565  671 TDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPG 750

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   719 LVKEDFGRPSrENTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAQDDSQGQSSRYTRRDHSTSLRHSESG 795
Cdd:PRK08565  751 GQEDKIEIPE-PNVRGYRgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQERRDTSVTVRHGEKG 829

                         810       820       830       840       850       860       870
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   796 MVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:PRK08565  830 IVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAI 899
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-865 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 916.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     2 ARLRNLTYSAPLYVDVTKRVikkghDCEEvTETQEfakVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:PRK08565   76 ARLRNLTYAAPLYLTMIPVE-----NGIE-YEPEE---VKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIIN 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQnRPPSSMfVRMlsrtsaKGGSsgqyIRATLPYIRTEIPI 161
Cdd:PRK08565  147 GSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSRAGY-RAQVTV-ERR------KDGT----IYVSFPAVPGKIPF 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   162 IIVFRALGFVADKDILEHIcydFSDTQMMELLRPSLEEAFVIQN-QQVALDYIGKRgSTVGVTREKRIKYAKEILQKEML 240
Cdd:PRK08565  215 VILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASSIAAtVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLL 290

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   241 PHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKD 320
Cdd:PRK08565  291 PHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRK 370

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   321 VNLQFAIKAKTITSGLKYSLATGNWGqanaaGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMM 400
Cdd:PRK08565  371 LDLRAIVRPDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   401 CPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVGIHRNPELLVKTLRQ 480
Cdd:PRK08565  446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRE 525

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   481 LRRQVDVNTEVGV--IRDIRLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIRALQQRESSeeggWHDLVAKGFIEYVDT 558
Cdd:PRK08565  526 LRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELT----FDDLVKMGVIEYLDA 601

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   559 EEEETTMISmtindlvtarLNPEEAYSEtYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLR 638
Cdd:PRK08565  602 EEEENAYVA----------LDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIR 670

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   639 MDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 718
Cdd:PRK08565  671 TDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPG 750

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   719 LVKEDFGRPSrENTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAQDDSQGQSSRYTRRDHSTSLRHSESG 795
Cdd:PRK08565  751 GQEDKIEIPE-PNVRGYRgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQERRDTSVTVRHGEKG 829

                         810       820       830       840       850       860       870
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   796 MVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:PRK08565  830 IVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAI 899
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-865 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: 801.01  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   2 ARLRNLTYSAPLYVDVTKRVIKKGHDCEEvtetqefaKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:cd00653  64 CRLRDLTYSAPLYVDIRLTVNDKGKIKEQ--------EVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIIN 135

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  82 GSEKVLIAQEKMSTNHVYVFkkrqPNKYAYVAEVRSMAESQNRPPSSMFVRMLSRTsakggssgQYIRATLPYIRteipi 161
Cdd:cd00653 136 GTEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK--------DRIYVRIDLKR----- 198

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 162 iivfralgfvadkdilehicydfsdtqmmellrpsleeafviqnQQVALDYIGKRGstvgvtrekrikyakeilqkemlp 241
Cdd:cd00653 199 --------------------------------------------QEEALKYIGKRF------------------------ 210

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 242 hvgvgeycetkkaYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDV 321
Cdd:cd00653 211 -------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL 277

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 322 NLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLHNSHWGMM 400
Cdd:cd00653 278 TPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRI 357

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 401 CPAETPEGQACGLVKNLALMVYITvgsaanpilefleewstenfeeispavipqatkifvngcwvgihrnpellvktlrq 480
Cdd:cd00653 358 CPIETPEGENCGLVKNLALMARIS-------------------------------------------------------- 381

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 481 lrrqvdvntevgvirdirlkelrlytdyGRCSRPLFIVEKQrllikkkdiralqqresseeggwhdlvakgfieyvdtee 560
Cdd:cd00653 382 ----------------------------GRIERPYRIVEKE--------------------------------------- 394

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 561 eettmismtindlvtarlnpeeaysetYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMD 640
Cdd:cd00653 395 ---------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMD 447

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 641 TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKmgtlV 720
Cdd:cd00653 448 TKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRK----T 523

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 721 KEDFGRPSRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDDS--QGQSSRYTRRDHSTSLRHSESGMVD 798
Cdd:cd00653 524 KNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETEStpIFGEKARDVRDTSLKYPGGEKGIVD 603

                       810       820       830       840       850       860       870
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 799 QVLLTT---NADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:cd00653 604 DVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 2-334 6.07e-166

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: 487.66  E-value: 6.07e-166
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     2 ARLRNLTYSAPLYVDVTKRVIkkghdceeVTETQEFAKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:pfam04563  73 CRLRNLTYSAPLYVDLELSVY--------NGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIIN 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSSMFVRMLSRTSakggssGQYIRATLPYIRTEIPI 161
Cdd:pfam04563 145 GSEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLEYLS------NGTIYFKFPYIKKEIPI 218

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   162 IIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVI--QNQQVALDYIGKRGSTV---GVTREKRIKYAKEILQ 236
Cdd:pfam04563 219 VIILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQ 298

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   237 KEMLPHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVD 316
Cdd:pfam04563 299 KEVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLG 378

                         330
                  ....*....|....*...
gi 68131890   317 NGKDVNLQFAIKAKTITS 334
Cdd:pfam04563 379 SPDDLMLQLLVNAKPITS 396
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-865 2.68e-159

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: 491.16  E-value: 2.68e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    2 ARLRNLTYSAPLYVDVtkRVIKKGhdCEEVtETQEfakVFIGKVPIMLRSsyctlyqnsekdltelgecpydqgGYFIIN 81
Cdd:COG0085   68 CKERDLTYAAPLYVKV--RLVNKE--TGEI-KEQE---VFMGDFPLMTDS------------------------GTFIIN 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSmaesqNRPPSSMFVRMlsrtsaKGGSsgqyIRATLPYIRTeIPI 161
Cdd:COG0085  116 GTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIP-----SRGAWLEFETD------KDGT----IYVRIDRKRK-IPV 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  162 IIVFRALGFVADKDILEHicydFSDTQMMELLRPSLEEAfVIQNQQVALDYIGKRgstVGVTREKRIKYAKEIL------ 235
Cdd:COG0085  180 TVLLRALGLETDEEILEA----FGDDPIQEYILATLEKD-NTKTQEEALLEIYRK---LRPGEPPTIERAEQLLdnlffd 251

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  236 -QKEMLPHVG-----------VGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKL 303
Cdd:COG0085  252 pKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM 331

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  304 TRDVR-----AYVQKcvdngkdVNLQFAIKAKTITSGLKYSLATGnwgqanaagtraGVSQVLNRLTYASTLSHLRRLN- 377
Cdd:COG0085  332 ERVVRermttQDVEA-------ITPQSLINIRPVVAAIKEFFGSS------------QLSQFMDQTNPLSELTHKRRLSa 392

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  378 ---SPIGREgklaKP----RQLHNSHWGMMCPAETPEGQACGLVKNLALMVYITVgsaanpilefleewstenfeeispa 450
Cdd:COG0085  393 lgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE------------------------- 443

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  451 vipqatkifvngcwvgihrnpellvktlrqlrrqvdvntevgvirdirlkelrlytdYGRCSRPLFIVEKQRLlikkkdi 530
Cdd:COG0085  444 ---------------------------------------------------------YGFIETPYRKVENGKV------- 459

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  531 ralqqresSEEggwhdlvakgfIEYVDTEEEETTMIS----------MTINDLVTARLNPEEAYSET--YTHCEIHPSLI 598
Cdd:COG0085  460 --------TDE-----------IEYLTADEEENYYIAqanapldedgNFLEERVLVRYRGEEVLVPPeeVDYMDVSPKQI 520

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  599 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLrmdtLAYVLY----------YPQKPLVttRAMEHLHFRQ-- 666
Cdd:COG0085  521 VSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----LHYPLQkfqrsnqgtcINQRPIV--RVGDRVEKGDvl 594

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  667 ----------LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGtlvKEDFGR----PSRE 730
Cdd:COG0085  595 adgpatdngeLALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARdtKLG---PEEITRdipnVSEE 671

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  731 ntmgmrhgSYDKLDDDGLAPPGTRVSGEDVIIGKTTP---------------IAqddsqGQSSRYtRRDHSTSLRHSESG 795
Cdd:COG0085  672 --------ALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteltpeerllraIF-----GEKARE-VRDTSLRVPHGEKG 737

                        890       900       910       920       930       940       950
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68131890  796 MVDQVLLTTNADG-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:COG0085  738 KVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGV 814
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 458-865 4.43e-159

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: 477.60  E-value: 4.43e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   458 IFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIRALQQRE 537
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   538 SSeeggWHDLVAKGFIEYVDTEEEETTMISMTINDLvtarlnpeeaySETYTHCEIHPSLILGVCASIIPFPDHNQSPRN 617
Cdd:TIGR03670  81 LT----WDDLVKQGVIEYLDAEEEENAYIALDPEEL-----------TPEHTHLEIDPSAILGIIASTIPYPEHNQSPRN 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   618 TYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 697
Cdd:TIGR03670 146 TMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   698 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPSREnTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAQDDSQ 774
Cdd:TIGR03670 226 RGLARSTFFRTYEAEERRYPGGQEDRFEIPEPD-VRGYRgEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprFLEELRE 304

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   775 GQSSRYTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGI 854
Cdd:TIGR03670 305 FGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGI 384

                         410
                  ....*....|.
gi 68131890   855 TPDIIVNPHAI 865
Cdd:TIGR03670 385 VPDLIINPHAI 395
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-865 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 916.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     2 ARLRNLTYSAPLYVDVTKRVikkghDCEEvTETQEfakVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:PRK08565   76 ARLRNLTYAAPLYLTMIPVE-----NGIE-YEPEE---VKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIIN 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQnRPPSSMfVRMlsrtsaKGGSsgqyIRATLPYIRTEIPI 161
Cdd:PRK08565  147 GSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSRAGY-RAQVTV-ERR------KDGT----IYVSFPAVPGKIPF 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   162 IIVFRALGFVADKDILEHIcydFSDTQMMELLRPSLEEAFVIQN-QQVALDYIGKRgSTVGVTREKRIKYAKEILQKEML 240
Cdd:PRK08565  215 VILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASSIAAtVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLL 290

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   241 PHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKD 320
Cdd:PRK08565  291 PHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRK 370

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   321 VNLQFAIKAKTITSGLKYSLATGNWGqanaaGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSHWGMM 400
Cdd:PRK08565  371 LDLRAIVRPDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   401 CPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPAVIPQATKIFVNGCWVGIHRNPELLVKTLRQ 480
Cdd:PRK08565  446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRE 525

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   481 LRRQVDVNTEVGV--IRDIRLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIRALQQRESSeeggWHDLVAKGFIEYVDT 558
Cdd:PRK08565  526 LRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELT----FDDLVKMGVIEYLDA 601

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   559 EEEETTMISmtindlvtarLNPEEAYSEtYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLR 638
Cdd:PRK08565  602 EEEENAYVA----------LDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIR 670

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   639 MDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 718
Cdd:PRK08565  671 TDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPG 750

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   719 LVKEDFGRPSrENTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAQDDSQGQSSRYTRRDHSTSLRHSESG 795
Cdd:PRK08565  751 GQEDKIEIPE-PNVRGYRgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQERRDTSVTVRHGEKG 829

                         810       820       830       840       850       860       870
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   796 MVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:PRK08565  830 IVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAI 899
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-865 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: 801.01  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   2 ARLRNLTYSAPLYVDVTKRVIKKGHDCEEvtetqefaKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:cd00653  64 CRLRDLTYSAPLYVDIRLTVNDKGKIKEQ--------EVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIIN 135

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  82 GSEKVLIAQEKMSTNHVYVFkkrqPNKYAYVAEVRSMAESQNRPPSSMFVRMLSRTsakggssgQYIRATLPYIRteipi 161
Cdd:cd00653 136 GTEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK--------DRIYVRIDLKR----- 198

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 162 iivfralgfvadkdilehicydfsdtqmmellrpsleeafviqnQQVALDYIGKRGstvgvtrekrikyakeilqkemlp 241
Cdd:cd00653 199 --------------------------------------------QEEALKYIGKRF------------------------ 210

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 242 hvgvgeycetkkaYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDV 321
Cdd:cd00653 211 -------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL 277

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 322 NLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS-PIGREGKLAKPRQLHNSHWGMM 400
Cdd:cd00653 278 TPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRI 357

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 401 CPAETPEGQACGLVKNLALMVYITvgsaanpilefleewstenfeeispavipqatkifvngcwvgihrnpellvktlrq 480
Cdd:cd00653 358 CPIETPEGENCGLVKNLALMARIS-------------------------------------------------------- 381

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 481 lrrqvdvntevgvirdirlkelrlytdyGRCSRPLFIVEKQrllikkkdiralqqresseeggwhdlvakgfieyvdtee 560
Cdd:cd00653 382 ----------------------------GRIERPYRIVEKE--------------------------------------- 394

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 561 eettmismtindlvtarlnpeeaysetYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMD 640
Cdd:cd00653 395 ---------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMD 447

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 641 TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKmgtlV 720
Cdd:cd00653 448 TKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRK----T 523

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 721 KEDFGRPSRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDDS--QGQSSRYTRRDHSTSLRHSESGMVD 798
Cdd:cd00653 524 KNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETEStpIFGEKARDVRDTSLKYPGGEKGIVD 603

                       810       820       830       840       850       860       870
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890 799 QVLLTT---NADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:cd00653 604 DVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 2-334 6.07e-166

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: 487.66  E-value: 6.07e-166
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     2 ARLRNLTYSAPLYVDVTKRVIkkghdceeVTETQEFAKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:pfam04563  73 CRLRNLTYSAPLYVDLELSVY--------NGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIIN 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSSMFVRMLSRTSakggssGQYIRATLPYIRTEIPI 161
Cdd:pfam04563 145 GSEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLEYLS------NGTIYFKFPYIKKEIPI 218

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   162 IIVFRALGFVADKDILEHICYDFSDTQMMELLRPSLEEAFVI--QNQQVALDYIGKRGSTV---GVTREKRIKYAKEILQ 236
Cdd:pfam04563 219 VIILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQ 298

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   237 KEMLPHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVD 316
Cdd:pfam04563 299 KEVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLG 378

                         330
                  ....*....|....*...
gi 68131890   317 NGKDVNLQFAIKAKTITS 334
Cdd:pfam04563 379 SPDDLMLQLLVNAKPITS 396
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-865 2.68e-159

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: 491.16  E-value: 2.68e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    2 ARLRNLTYSAPLYVDVtkRVIKKGhdCEEVtETQEfakVFIGKVPIMLRSsyctlyqnsekdltelgecpydqgGYFIIN 81
Cdd:COG0085   68 CKERDLTYAAPLYVKV--RLVNKE--TGEI-KEQE---VFMGDFPLMTDS------------------------GTFIIN 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSmaesqNRPPSSMFVRMlsrtsaKGGSsgqyIRATLPYIRTeIPI 161
Cdd:COG0085  116 GTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIP-----SRGAWLEFETD------KDGT----IYVRIDRKRK-IPV 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  162 IIVFRALGFVADKDILEHicydFSDTQMMELLRPSLEEAfVIQNQQVALDYIGKRgstVGVTREKRIKYAKEIL------ 235
Cdd:COG0085  180 TVLLRALGLETDEEILEA----FGDDPIQEYILATLEKD-NTKTQEEALLEIYRK---LRPGEPPTIERAEQLLdnlffd 251

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  236 -QKEMLPHVG-----------VGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKL 303
Cdd:COG0085  252 pKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRM 331

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  304 TRDVR-----AYVQKcvdngkdVNLQFAIKAKTITSGLKYSLATGnwgqanaagtraGVSQVLNRLTYASTLSHLRRLN- 377
Cdd:COG0085  332 ERVVRermttQDVEA-------ITPQSLINIRPVVAAIKEFFGSS------------QLSQFMDQTNPLSELTHKRRLSa 392

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  378 ---SPIGREgklaKP----RQLHNSHWGMMCPAETPEGQACGLVKNLALMVYITVgsaanpilefleewstenfeeispa 450
Cdd:COG0085  393 lgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE------------------------- 443

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  451 vipqatkifvngcwvgihrnpellvktlrqlrrqvdvntevgvirdirlkelrlytdYGRCSRPLFIVEKQRLlikkkdi 530
Cdd:COG0085  444 ---------------------------------------------------------YGFIETPYRKVENGKV------- 459

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  531 ralqqresSEEggwhdlvakgfIEYVDTEEEETTMIS----------MTINDLVTARLNPEEAYSET--YTHCEIHPSLI 598
Cdd:COG0085  460 --------TDE-----------IEYLTADEEENYYIAqanapldedgNFLEERVLVRYRGEEVLVPPeeVDYMDVSPKQI 520

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  599 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLrmdtLAYVLY----------YPQKPLVttRAMEHLHFRQ-- 666
Cdd:COG0085  521 VSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----LHYPLQkfqrsnqgtcINQRPIV--RVGDRVEKGDvl 594

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  667 ----------LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGtlvKEDFGR----PSRE 730
Cdd:COG0085  595 adgpatdngeLALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARdtKLG---PEEITRdipnVSEE 671

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  731 ntmgmrhgSYDKLDDDGLAPPGTRVSGEDVIIGKTTP---------------IAqddsqGQSSRYtRRDHSTSLRHSESG 795
Cdd:COG0085  672 --------ALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteltpeerllraIF-----GEKARE-VRDTSLRVPHGEKG 737

                        890       900       910       920       930       940       950
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68131890  796 MVDQVLLTTNADG-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:COG0085  738 KVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGV 814
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 458-865 4.43e-159

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: 477.60  E-value: 4.43e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   458 IFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIRALQQRE 537
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   538 SSeeggWHDLVAKGFIEYVDTEEEETTMISMTINDLvtarlnpeeaySETYTHCEIHPSLILGVCASIIPFPDHNQSPRN 617
Cdd:TIGR03670  81 LT----WDDLVKQGVIEYLDAEEEENAYIALDPEEL-----------TPEHTHLEIDPSAILGIIASTIPYPEHNQSPRN 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   618 TYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSID 697
Cdd:TIGR03670 146 TMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIE 225

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   698 RGFFRSLFFRSYRDEEKKMGTLVKEDFGRPSREnTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAQDDSQ 774
Cdd:TIGR03670 226 RGLARSTFFRTYEAEERRYPGGQEDRFEIPEPD-VRGYRgEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprFLEELRE 304

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   775 GQSSRYTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGI 854
Cdd:TIGR03670 305 FGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGI 384

                         410
                  ....*....|.
gi 68131890   855 TPDIIVNPHAI 865
Cdd:TIGR03670 385 VPDLIINPHAI 395
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 456-865 4.30e-156

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 470.21  E-value: 4.30e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  456 TKIFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELRLYTDYGRCSRPLFIVEKQRLLIKKKDIRALQQ 535
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  536 RESSeeggWHDLVAKGFIEYVDTEEEETTMISMTINDLvtarlNPEeaysetYTHCEIHPSLILGVCASIIPFPDHNQSP 615
Cdd:PRK07225  85 GELT----FDDLVKQGVIEYLDAEEEENAYIAVYEEDL-----TEE------HTHLEIDPSLILGIGAGMIPYPEHNASP 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  616 RNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSS 695
Cdd:PRK07225 150 RITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKAS 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  696 IDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPSRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP---IAQDD 772
Cdd:PRK07225 230 IERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfLEEPD 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  773 SQGQSSRyTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVE 852
Cdd:PRK07225 310 DFGISPE-KRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTES 388

                        410
                 ....*....|...
gi 68131890  853 GITPDIIVNPHAI 865
Cdd:PRK07225 389 GVVPDLIINPHAI 401
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 2-438 6.47e-121

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 375.06  E-value: 6.47e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    2 ARLRNLTYSAPLYVDVTkrVIKKGhdceevtETQEFAKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIIN 81
Cdd:PRK09606  81 ARLRNLTYSAPLYLEMS--PVEGG-------EEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVN 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   82 GSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVrsmaesqnrppssmfvrmlsrTSAKGG---------SSGQYIRATL 152
Cdd:PRK09606 152 GSERVLMTLEDLAPNKILVEKDERYGDRIEVAKV---------------------FSQRRGyralvtverNRDGLLEVSF 210

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  153 PYIRTEIPIIIVFRALGFVADKDILEHICydfSDTQMMELLRPSLEEAfVIQNQQVALDYIGKRGSTvGVTREKRIKYAK 232
Cdd:PRK09606 211 PSVPGSIPFVILMRALGLETDEEIVEAVS---DDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVAP-GQTKEYRIKRAE 285

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  233 EILQKEMLPHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQ 312
Cdd:PRK09606 286 YVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLE 365

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890  313 KCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWgqanaAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQL 392
Cdd:PRK09606 366 RANMRNRELSIKTAVRSDVLTERLEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDL 440

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*.
gi 68131890  393 HNSHWGMMCPAETPEGQACGLVKNLALMVYITVGSAANPILEFLEE 438
Cdd:PRK09606 441 HPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 602-865 1.01e-120

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: 369.94  E-value: 1.01e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   602 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYS 681
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   682 GYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTlVKEDFGRPSREntmgmRHGSYDKLDDDGLAPPGTRVSGEDVI 761
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-IEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   762 IGKTTPIAQ----DDSQGQSSRyTRRDHSTSLRHSESGMVDQVLL-TTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKG 836
Cdd:pfam00562 155 VGKVGPTELtkllRAIFGEKAR-DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKG 233

                         250       260
                  ....*....|....*....|....*....
gi 68131890   837 TVGMTYTQEDMPWTVEGITPDIIVNPHAI 865
Cdd:pfam00562 234 VVSRILPQEDMPFTEDGIPPDIILNPHGV 262
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 94-286 8.72e-60

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: 201.42  E-value: 8.72e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    94 STNHVYVFKKRQPNKYAYVaeVRSMAESQnrppSSMFVrmlsrtsaKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVAD 173
Cdd:pfam04561   1 RSNGIYVEKELDKNGIIAT--YTSSLISN----RGSWL--------KLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSD 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   174 KDILEHICYDFSDTQMMELLRPSLEEAFVIQNQQVALDYIGKrGSTVGVTREKRIKYAKEILQK-----EMLPHVGVGEY 248
Cdd:pfam04561  67 REILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEP 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 68131890   249 CETK--KAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLD 286
Cdd:pfam04561 146 FENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 5-862 2.00e-39

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: 158.29  E-value: 2.00e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890      5 RNLTYSAPLYVDVtkRVIKKGHDCEEVTETQEfakVFIGKVPIMlrssyctlyqnsekdlTELGEcpydqggyFIINGSE 84
Cdd:TIGR02013   85 RGLTYSAPLKVKL--RLINKEEDGTKEIKEQD---VYMGDIPLM----------------TDRGT--------FIINGAE 135

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     85 KVLIAQEKMSTNHVYVFKKRQPN--KYAYVAEV----RSMAESQNRPPSSMFVRmLSRtsakggssgqyiratlpyiRTE 158
Cdd:TIGR02013  136 RVVVSQLHRSPGVFFSSEKDTTKsgKVLFSARIipyrGSWLEFETDKKDVLYVR-IDR-------------------KRK 195

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    159 IPIIIVFRALGFVADKDILEHICydfSDTQMMELLRPSLEeafviQNQQVALDYIGKR---GSTVgvTREKrikyAKEIL 235
Cdd:TIGR02013  196 LPATVLLRALGYTIDTLILNRLG---SGEYIRNTLRKDPT-----NSEEEALVEIYRKlrpGEPP--TVEA----ARSLL 261

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    236 QK-----EMLPHVGVGEYCETKK-----AYYFGYIIHRLLLCAL--------GRRAEDDRDHYGNKRLDLAGPLLGGLFR 297
Cdd:TIGR02013  262 ENlffdpKRYDLGRVGRYKLNKKlgldvPESIGVLTKEDIIATIkyliklrnGKGEIDDIDHLGNRRIRSVGELLQNQFR 341

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    298 MLFRKLTRDVRAYVqkcvdNGKDVNL---QFAIKAKTITSGLKYSLATGNwgqanaagtragVSQVLNRLTYASTLSHLR 374
Cdd:TIGR02013  342 VGLARMERIVRERM-----STQDTDTltpQDLINAKPISAAIKEFFGSSQ------------LSQFMDQTNPLAELTHKR 404

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    375 RLNS--PIG--REGKLAKPRQLHNSHWGMMCPAETPEGQACGLVKNLAlmvyitvgsaanpilefleewsteNFEEISpa 450
Cdd:TIGR02013  405 RLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS------------------------TYARVN-- 458

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    451 vipqatkifvngcwvgihrnpellvktlrqlrrqvdvntevgvirdirlkelrlytDYGRCSRPLFIVEKQRllIKKKDI 530
Cdd:TIGR02013  459 --------------------------------------------------------EYGFIETPYRKVKDGK--VVVTDE 480

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    531 ralqqresseeggwhdlvakgfIEYVDTEEEETTMIS----------MTINDLVTARLNPE--EAYSETYTHCEIHPSLI 598
Cdd:TIGR02013  481 ----------------------IDYLTADEEDNYVIAqanapldengRFVEDLVVARYRGEitLVSPDQVDYMDVSPKQV 538

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    599 LGVCASIIPFPDHNQSPRNTYQSAMGKQAM----------------------------------------GIYVTNYQLR 638
Cdd:TIGR02013  539 VSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrggvveyvdakRIVIRYDEDE 618

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    639 MDTLAYVLYYP--------------QKPLVTT-------------RAMEHlhfRQLPAGINAIVAIACYSGYNQEDSVIM 691
Cdd:TIGR02013  619 EEPDGGIDIYRllkyqrsnqdtcinQRPIVSVgdrveagdvladgPSTDL---GELALGRNVLVAFMPWNGYNYEDAILI 695

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    692 NQSSIDRGFFRSLFFRSYRDE--EKKMGtlvKEDFGR--P--SRENTmgmrhgsyDKLDDDGLAPPGTRVSGEDVIIGKT 765
Cdd:TIGR02013  696 SERLVKDDVFTSIHIEEYEVEarDTKLG---PEEITRdiPnvSEEAL--------RNLDENGIVRIGAEVKAGDILVGKV 764

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    766 TPIAQDDSQ----------GQSSRYTRrdhSTSLR--HSESGMVDQVLLTTNADG-------LRFVKVRMRSVRIPQIGD 826
Cdd:TIGR02013  765 TPKGETELTpeekllraifGEKARDVR---DTSLRvpPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGD 841

                          970       980       990
                   ....*....|....*....|....*....|....*.
gi 68131890    827 KFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 862
Cdd:TIGR02013  842 KMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNP 877
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 359-420 9.99e-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: 114.93  E-value: 9.99e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68131890   359 QVLNRLTYASTLSHLRRLNSPIG---REGKLAKPRQLHNSHWGMMCPAETPEGQACGLVKNLALM 420
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALY 65
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 458-519 6.19e-28

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: 106.68  E-value: 6.19e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 68131890   458 IFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGVIRDIRLKELRLYTDYGRCSRPLFIVE 519
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 67-862 1.82e-26

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 116.73  E-value: 1.82e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    67 LGECP-YDQGGYFIINGSEKVLIAQeKMSTNHVYvFKKRQPNKYayvaevRSMAESQNRPPSSMFVRMlsrtsakGGSSG 145
Cdd:CHL00207   96 IGNLPkMTQRGTFIINGLERVIVSQ-IIRSPGIY-FKKEIKKNS------NKIYSATLIPNRGSWIKF-------ELDKN 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   146 QYIRATLPYIRtEIPIIIVFRALGfVADKDILEHICYDFSdtqmMELLRPSLEEAFVIQNQQVALDYIGK--RGSTVGVT 223
Cdd:CHL00207  161 KEIWIRIDKNR-KKPLIIFLKALG-LTDQDIYSRLTKSEF----LKKLKPILLNSNSYTNEEILLEIYKNlsPIEPATVN 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   224 REKRIKYAKeILQKEMLPHVGVGEYCETKKAYY-------------FGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGP 290
Cdd:CHL00207  235 DANQNLFSR-FFDPKNYDLGKVGRYKINNKLNLnipervrnltyedILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGE 313

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   291 LLGGLFRMLFRKLTRDVRAYVQKCV-DNGKDVNLqfaIKAKTITSGLKYSLATGNwgqanaagtragVSQVLNRLTYAST 369
Cdd:CHL00207  314 LLQNQFRIGLKRLERILRNRMTICDiDSLSKFNL---INPKPLIALIREFFGSSQ------------LSQYMDQTNPLSE 378

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   370 LSHLRRLNSpIGREG--KLAKP---RQLHNSHWGMMCPAETPEGQACGLVKNLAlmvyitvgsaanpilefleewsteNF 444
Cdd:CHL00207  379 LTHKRRISI-LGPGGldKDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLA------------------------TN 433

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   445 EEISPAVIPQATKIFVNGCWVGIHRNPELLVKTLRQLRRQVdvntevgvIRDIRLKELRLYtdygrCSRPLFIVEKQRLL 524
Cdd:CHL00207  434 ARINKFGFIETPFYKVINGKVKKFGNPIYLTADSEDLYRIA--------PNDINLNKNNYF-----KKNIIPVRYKQEFK 500

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   525 IKKKDIralqqresseeggwHDLVAKGFIEyvdteeeettMISMTindlvtarlnpeeaysetythceihpslilgvcAS 604
Cdd:CHL00207  501 TVNPSK--------------VDFIAISPIQ----------VFSIA---------------------------------ES 523

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   605 IIPFPDHNQSPRNTYQSAMGKQAM-------------------------------GI--YVTNYQLRM--DTLAYVLYYP 649
Cdd:CHL00207  524 LIPFLEHNDANRALMGSNMQRQAVpllypekpivgtgyekqialdsgmtiislteGIvvSVSAYKIIIqdDNNRYIHYYL 603

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   650 QK-------------PLV-------------TTRAMEHlhfRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRS 703
Cdd:CHL00207  604 QKyqrsnqntcinyrPIVwvgekinigqilaDGSDIDN---SELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTS 680

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   704 LFFRSYrDEEKKMGTLVKEDFGRpsreNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAQDDSQGQSS----- 778
Cdd:CHL00207  681 IHIEKY-EIELRQTKLGSEEITR----NIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKllrai 755

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   779 -RYTRRD-HSTSLRHS--ESGMVDQVLLTTNADGLRF-------VKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDM 847
Cdd:CHL00207  756 fGEKAKDvKDTSLRMPngGYGRVIKVEIFSRSKGDELkfgyylkIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDM 835

                         890
                  ....*....|....*
gi 68131890   848 PWTVEGITPDIIVNP 862
Cdd:CHL00207  836 PYLPDGTPPDIILNP 850
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 544-595 7.04e-23

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: 92.22  E-value: 7.04e-23
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 68131890   544 WHDLVAKGFIEYVDTEEEETTMISMTINDLVTA-RLNPEEAYSETYTHCEIHP 595
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREGPYAHTYTHCEIHP 53
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 2-863 1.16e-18

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 91.70  E-value: 1.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     2 ARLRNLTYSAPLYVDVtkRVIKKghdceEVTETQEfAKVFIGKVPIMlrssyctlyqnsekdlTElgecpydqGGYFIIN 81
Cdd:PRK00405   86 CKERGLTYSAPLRVKL--RLINK-----ETGEIKE-QEVYMGDIPLM----------------TE--------NGTFIIN 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    82 GSEKVLIAQEKMSTNhVYvFK----KRQPNKYAYVAEV---R-SMAESQNRPPSSMFVRmLSRTsakggssgqyiratlp 153
Cdd:PRK00405  134 GTERVIVSQLHRSPG-VY-FDhdkdKTSSGKLLYSARIipyRgSWLEFEFDPKDILYVR-IDRR---------------- 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   154 yiRTeIPIIIVFRALGFvADKDILEHicydFSDTQMMELLRPSLEEAFViqNQQVALDYIGKRGSTV------GVTREKR 227
Cdd:PRK00405  195 --RK-LPVTVLLRALGY-SDEEILDL----FYEKEEFGKEIEVPVEYLL--GKVLAEDIVDEETGEVlaeandEITEELD 264

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   228 IKYAKEILQKE---------------MLPhvG--------------------------VGEYCETKKAYYFGYIIHRLL- 265
Cdd:PRK00405  265 GPYIRNTLEKDptssreealveiyrrLRP--GepptveaarsllenlffdpkrydlskVGRYKLNKKLGLDEDEDVRVLt 342

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   266 ----------LCAL--GRRAEDDRDHYGNKRLDLAGPLLG-----GLFRMlfRKLTRDvRAYVQKcVDNGKDVNLqfaIK 328
Cdd:PRK00405  343 kediiatikyLINLrnGKGEVDDIDHLGNRRVRSVGELLQnqfriGLSRM--ERAVRE-RMSLQD-LDTLTPQDL---IN 415

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   329 AKTITSGLKYSLATgnwGQanaagtragVSQVL---NRLtyaSTLSHLRRLNS--PIG--REgklaKP----RQLHNSHW 397
Cdd:PRK00405  416 AKPVVAAIKEFFGS---SQ---------LSQFMdqtNPL---SELTHKRRLSAlgPGGltRE----RAgfevRDVHPTHY 476

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   398 GMMCPAETPEGQACGLVKNLAlmVYITVgsaaNPiLEFLEewstenfeeiSPavipqatkifvngcwvgihrnpellvkt 477
Cdd:PRK00405  477 GRICPIETPEGPNIGLINSLA--TYARV----NE-YGFIE----------TP---------------------------- 511

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   478 lrqLRRQVDvntevGVIRDirlkElrlytdygrcsrplfivekqrllikkkdiralqqresseeggwhdlvakgfIEYVD 557
Cdd:PRK00405  512 ---YRKVVD-----GKVTD----E---------------------------------------------------IVYLT 528

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   558 TEEEETTMIS----------MTINDLVTARLN--PEEAYSETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGK 625
Cdd:PRK00405  529 ADEEDNYVIAqanapldedgRFVDELVTARYKgeFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQR 608

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   626 QA--------------M-----------------GI--YVTN-------------------YQLR------MDTLayvly 647
Cdd:PRK00405  609 QAvpllrpeaplvgtgMerrvardsgavvvakrdGVveYVDAsrivvrveeldpgedgvdiYNLIkfqrsnQNTC----- 683

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   648 YPQKPLVttRAMEHLHFRQL----PA--------GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSY----RD 711
Cdd:PRK00405  684 INQRPIV--KVGDRVEKGDVladgPStdngelalGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYeieaRD 761

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   712 eeKKMGtlvKEDFGR--P--SRENTmgmRHgsydkLDDDGLAPPGTRVSGEDVIIGKTTPiaQDDSQ------------G 775
Cdd:PRK00405  762 --TKLG---PEEITRdiPnvSEEAL---RN-----LDESGIVRIGAEVKPGDILVGKVTP--KGETEltpeekllraifG 826

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   776 QSSRyTRRDhsTSLR--HSESGMV-DQVLLTTNADG-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQE 845
Cdd:PRK00405  827 EKAR-DVKD--TSLRvpHGEEGTViDVKVFTRIEQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVE 903

                        1050
                  ....*....|....*....
gi 68131890   846 DMPWTVEGiTP-DIIVNPH 863
Cdd:PRK00405  904 DMPYLEDG-TPvDIVLNPL 921
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
275-767 4.13e-15

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 80.35  E-value: 4.13e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   275 DDRDHYGNKRLDLAGPLLG-----GLFRMlfRKLTRDVRAYVQKCVDNGKDVNLqfaIKAKTITSGLkYSLATGnwGQan 349
Cdd:PRK09603  455 DDRDHLGNRRIRAVGELLAnelhsGLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTI-MEFFMG--GQ-- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   350 aagtragVSQVLNRLTYASTLSHLRRLnSPIGrEGKLAK------PRQLHNSHWGMMCPAETPEGQACGLVKNLAlmVYI 423
Cdd:PRK09603  525 -------LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS--TFT 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   424 TVGSaanpiLEFLEewstenfeeiSPavipqaTKIFVNGcwvgiHRNPELLVKTLRQlrrqvdvntEVGVIrdirlkelr 503
Cdd:PRK09603  594 RVND-----LGFIE----------AP------YKKVVDG-----KVVGETIYLTAIQ---------EDSHI--------- 629

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   504 lytdygrcsrplfivekqrllikkkdiralqqresseeggwhdlvakgfIEYVDTEEEETTMIsmtINDLVTARLNPEEA 583
Cdd:PRK09603  630 -------------------------------------------------IAPASTPIDEEGNI---LGDLIETRVEGEIV 657

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   584 YSET--YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTN--------------------------- 634
Cdd:PRK09603  658 LNEKskVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDapivgtgiekiiardswgaikanragv 737

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   635 ---------YQLRMDTL-AYVLYYP-QKPLvttRAMEHLHFRQLPA--------------------------GINAIVAI 677
Cdd:PRK09603  738 vekidskniYILGEGKEeAYIDAYSlQKNL---RTNQNTSFNQVPIvkvgdkveagqiiadgpsmdrgelalGKNVRVAF 814

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   678 ACYSGYNQEDSVIMNQSSIDRGFFRS--LFFRSYRDEEKKMGTlvkEDFGRpsreNTMGMRHGSYDKLDDDGLAPPGTRV 755
Cdd:PRK09603  815 MPWNGYNFEDAIVVSERITKDDIFTSthIYEKEVDARELKHGV---EEFTA----DIPDVKEEALAHLDESGIVKVGTYV 887

                         570
                  ....*....|..
gi 68131890   756 SGEDVIIGKTTP 767
Cdd:PRK09603  888 SAGMILVGKTSP 899
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
260-767 5.49e-13

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 73.50  E-value: 5.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   260 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRdvrAYVQKCVDNGKD-VNLQFAIKAKTITSGLKY 338
Cdd:PRK14844  449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLER---AVVDSMSTSSLDkVSPSDFINPKVLTNVLRD 525

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   339 SLATGNwgqanaagtragVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSHWGMMCPAETPEGQACGLV 414
Cdd:PRK14844  526 FFNSSQ------------LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLI 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   415 KNLALMVYIT-VGSAANPILEFLEEWSTENFEEISPA------VIPQATKIFVNGCWVGihrnpELLVktLRQLRRQVDV 487
Cdd:PRK14844  594 NSLAIYARINkYGFIESPYRKVVNRVVTDQIEYLSAIdeglyyIADTSAKLDENNCFVD-----DMLY--CRYAGSFVMV 666

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   488 NTEVGVIRDIRLKE-------LRLYTDYGRCSRPLFIVEKQR----LLIKKKDIRALQQRESSEEGGWHDLVAK--GFIE 554
Cdd:PRK14844  667 SSDQVSYIDVSPKQvisvaasLIPFLENDDANRALMGSNMQRqavpLLKPTAPLVATGMESFVASGSGAVVLAKrdGIVD 746

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   555 YVDTEeeettmiSMTINDLVTARLNpeeaysetYTHCEIHpslilgvcasiipfpdH-NQSPRNTYQSAMGKQAMgIYVT 633
Cdd:PRK14844  747 SSDSN-------SIVIRAFDKERVN--------YLDVDIY----------------HlRKFQRSNHNTCINQKPL-VCVG 794

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   634 NYQLRMDTLAyvlyypQKPLVTTramehlhfRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRdee 713
Cdd:PRK14844  795 DYVKEGDVIA------DGPAINS--------GELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFE--- 857

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 68131890   714 kkmgtLVKEDFGRPSRENTM---GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 767
Cdd:PRK14844  858 -----CVVHDTPLGSEKITRaipGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTP 909
rpoB CHL00001
RNA polymerase beta subunit
 7-862 7.28e-13

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 72.63  E-value: 7.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890     7 LTYSAPLYVDVtkRVI-KKGHDCEEVTetqefakVFIGKVPIMlrssyctlyqNSEkdltelgecpydqgGYFIINGSEK 85
Cdd:CHL00001   74 LTYSSELYVPA--GLIwKKSRDMQEQT-------VFIGNIPLM----------NSL--------------GTFIINGIYR 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890    86 VLIAQekmstnhvyvfKKRQPNKYaYvaevRSMAESQNRPpssmfVRMLSRTSAKGGSSGQYI-RATLPYIRT----EIP 160
Cdd:CHL00001  121 VVINQ-----------ILRSPGIY-Y----RSELDHNGIS-----VYTGTIISDWGGRLELEIdRKARIWARVsrkqKIS 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   161 IIIVFRALGFvADKDILEHICYD--FSDTQMMELLRP--SLEEAFVIQNQQvaLDYIGKRGSTVGVTREKrikyakeiLQ 236
Cdd:CHL00001  180 ILVLLSAMGL-NLREILDNVCYPeiFLSFLNDKEKKKigSKENAILEFYQQ--FACVGGDPVFSESLCKE--------LQ 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   237 KEMLPHV----GVGEYCETKK------------------AyyfgyIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGG 294
Cdd:CHL00001  249 KKFFQQRcelgRIGRRNMNRKlnldipenntfllpqdvlA-----AADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQD 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   295 LFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLK-----YSLatgnwgqanaagtragvSQVLNRLTYAST 369
Cdd:CHL00001  324 QFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYEsffgsHPL-----------------SQFLDQTNPLTE 386

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   370 LSHLRRLNS--PIGREGKLA--KPRQLHNSHWGMMCPAETPEGQACGLVKNLAlmvyitvgsaanpilefleewstenfe 445
Cdd:CHL00001  387 IVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLA--------------------------- 439

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   446 eispavipqatkifvngcwvgIHRNpellvktlrqlrrqvdVNtevgvirdirlkelrlytDYGRCSRPLFIVEkqrlli 525
Cdd:CHL00001  440 ---------------------IHAR----------------IG------------------HWGSLESPFYEIS------ 458

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   526 kkkdiralqqrESSEEGGwhdlvakgfIEYVDTEEEETTMISmTINDLVTARLNPEEAYSETYTHCE------------- 592
Cdd:CHL00001  459 -----------ERSKEER---------MVYLSPSEDEYYMIA-AGNSLALNQGIQEEQVVPARYRQEfltiaweqihlrs 517

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   593 IHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQA----------MG-----------------------IYV------- 632
Cdd:CHL00001  518 IFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAvplsrsekciVGtglerqvaldsgvvaiaehegkiIYTdtdkiil 597

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   633 ------TNYQLRM------DTLAYvlyypQKPLVttRAMEHLHFRQLPA------------GINAIVAIACYSGYNQEDS 688
Cdd:CHL00001  598 sgngdtLSIPLVMyqrsnkNTCMH-----QKPQV--RRGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDA 670

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   689 VIMNQSSIDRGFFRSLFFRSYrDEEKKMGTLVKEDFGR--PSRENTMgMRHgsydkLDDDGLAPPGTRVSGEDVIIGKTT 766
Cdd:CHL00001  671 VLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERITKeiPHLEAHL-LRN-----LDKNGIVMLGSWVETGDILVGKLT 743

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131890   767 P-IAQDDSQGQSSR----------YTRRDhsTSLRhsesgmvdqvlLTTNADGlRFVKVRM-----------RSVRI--- 821
Cdd:CHL00001  744 PqEAEESSYAPEGRllraifgiqvSTSKE--TCLK-----------LPIGGRG-RVIDVRWiqkkggssynpETIHVyil 809

                         970       980       990      1000
                  ....*....|....*....|....*....|....*....|....*
gi 68131890   822 ----PQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNP 862
Cdd:CHL00001  810 qkreIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNP 854
 
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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