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Conserved domains on  [gi|45545331|gb|AAS67513|]
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DNA-dependent RNA polymerase II second largest subunit, partial [Hydnum repandum]

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;
1-887 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: 887.76  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331     1 SEKVLIAQERMAANHVYVFAKAQPSPISFLAEVRSAVeKGGKTistmqvkmfhrnpQKTVSLGN--VIRASLPYIRDDIP 78
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYRA-------------QVTVERRKdgTIYVSFPAVPGKIP 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    79 IWVVFRALGITSDRDILEHIcydTNDTQMVEMLKPCIDEGF-VIQEREVALDLIGKRgTTTGLSKDKRLRYAQEILQKEM 157
Cdd:PRK08565  214 FVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYL 289

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   158 LPHVSMGEGSESKKAFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHK 237
Cdd:PRK08565  290 LPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGR 369

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   238 DFNISIAVKSNTITNGLKYSLATGNWGDQKksmsskAGVSQVLNRYTFASTLSHLRRCNTPLGRDGKIAKPRQLHNTHWG 317
Cdd:PRK08565  370 KLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWG 443

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   318 MVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLQEWGLESLEE-NANAHGSATKVFVNGVWMGVHRDAPNLVKTL 396
Cdd:PRK08565  444 RICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEaREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   397 RRLRRKDDISSEVSI--VRDIREKELRLYTDAGRVCRPLFIVENQQLLLKKEHVnmlnDKSRTDPYKWTHLVKDGVIELL 474
Cdd:PRK08565  524 RELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHV----EKLKKGELTFDDLVKMGVIEYL 599

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   475 DAEEEETVMICMTPDDLensrtnqavaagyvsnagASDHdvaarvrstmtahtwTHCEIHPSMILGICASIIPFPDHNQS 554
Cdd:PRK08565  600 DAEEEENAYVALDPEDL------------------TPEH---------------THLEIWPPAILGITASIIPYPEHNQS 646

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   555 PRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYSGYNQEDSVIMNQS 634
Cdd:PRK08565  647 PRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKA 726

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   635 SIDRGLFRSMYYRSYTDAEKKVGVLPLEEFEKPtrDTTLRMKHG--TYEKLEDDGLIAPGTGVAGEDIIIGKTAPlPPDS 712
Cdd:PRK08565  727 SIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFL 803

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   713 EEL-GQRMRTHTRRDVSTPLKSTENGIVDQVLVTTNQDGLKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPF 791
Cdd:PRK08565  804 EELeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPF 883

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   792 TAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGYQSRGLEVMYHGHSGRKL 871
Cdd:PRK08565  884 TEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKI 963

                         890
                  ....*....|....*.
gi 45545331   872 QAQVYLGPTYYQRLKH 887
Cdd:PRK08565  964 KAPIFIGVVYYQKLHH 979
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-887 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 887.76  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331     1 SEKVLIAQERMAANHVYVFAKAQPSPISFLAEVRSAVeKGGKTistmqvkmfhrnpQKTVSLGN--VIRASLPYIRDDIP 78
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYRA-------------QVTVERRKdgTIYVSFPAVPGKIP 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    79 IWVVFRALGITSDRDILEHIcydTNDTQMVEMLKPCIDEGF-VIQEREVALDLIGKRgTTTGLSKDKRLRYAQEILQKEM 157
Cdd:PRK08565  214 FVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYL 289

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   158 LPHVSMGEGSESKKAFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHK 237
Cdd:PRK08565  290 LPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGR 369

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   238 DFNISIAVKSNTITNGLKYSLATGNWGDQKksmsskAGVSQVLNRYTFASTLSHLRRCNTPLGRDGKIAKPRQLHNTHWG 317
Cdd:PRK08565  370 KLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWG 443

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   318 MVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLQEWGLESLEE-NANAHGSATKVFVNGVWMGVHRDAPNLVKTL 396
Cdd:PRK08565  444 RICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEaREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   397 RRLRRKDDISSEVSI--VRDIREKELRLYTDAGRVCRPLFIVENQQLLLKKEHVnmlnDKSRTDPYKWTHLVKDGVIELL 474
Cdd:PRK08565  524 RELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHV----EKLKKGELTFDDLVKMGVIEYL 599

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   475 DAEEEETVMICMTPDDLensrtnqavaagyvsnagASDHdvaarvrstmtahtwTHCEIHPSMILGICASIIPFPDHNQS 554
Cdd:PRK08565  600 DAEEEENAYVALDPEDL------------------TPEH---------------THLEIWPPAILGITASIIPYPEHNQS 646

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   555 PRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYSGYNQEDSVIMNQS 634
Cdd:PRK08565  647 PRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKA 726

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   635 SIDRGLFRSMYYRSYTDAEKKVGVLPLEEFEKPtrDTTLRMKHG--TYEKLEDDGLIAPGTGVAGEDIIIGKTAPlPPDS 712
Cdd:PRK08565  727 SIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFL 803

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   713 EEL-GQRMRTHTRRDVSTPLKSTENGIVDQVLVTTNQDGLKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPF 791
Cdd:PRK08565  804 EELeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPF 883

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   792 TAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGYQSRGLEVMYHGHSGRKL 871
Cdd:PRK08565  884 TEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKI 963

                         890
                  ....*....|....*.
gi 45545331   872 QAQVYLGPTYYQRLKH 887
Cdd:PRK08565  964 KAPIFIGVVYYQKLHH 979
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-887 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: 806.79  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   1 SEKVLIAQERMAANHVYVFakaqPSPISFLAEVRSAVEKGGKTISTMQVKMFHRNpqktvslgNVIRASLPYIRddipiw 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK--------DRIYVRIDLKR------ 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  81 vvfralgitsdrdilehicydtndtqmvemlkpcidegfviqeREVALDLIGKRGtttglskdkrlryaqeilqkemlph 160
Cdd:cd00653 199 -------------------------------------------QEEALKYIGKRF------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 161 vsmgegseskkaFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHKDFN 240
Cdd:cd00653 211 ------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT 278

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 241 ISIAVKSNTITNGLKYSLATGNWGDQKKSMSsKAGVSQVLNRYTFASTLSHLRRCNT-PLGRDGKIAKPRQLHNTHWGMV 319
Cdd:cd00653 279 PQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRI 357

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 320 CPAETPEGQACGLVKNLSLMACISvgslsapvieflqewglesleenanahgsatkvfvngvwmgvhrdapnlvktlrrl 399
Cdd:cd00653 358 CPIETPEGENCGLVKNLALMARIS-------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 400 rrkddissevsivrdirekelrlytdaGRVCRPLFIVENQqlllkkehvnmlndksrtdpykwthlvkdgvielldaeee 479
Cdd:cd00653 382 ---------------------------GRIERPYRIVEKE---------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 480 etvmicmtpddlensrtnqavaagyvsnagasdhdvaarvrstmtahtWTHCEIHPSMILGICASIIPFPDHNQSPRNTY 559
Cdd:cd00653 395 ------------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLY 426

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 560 QSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRG 639
Cdd:cd00653 427 QSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRG 506

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 640 LFRSMYYRSYTDAEKKVGvlplEEFEKPTRDTTLRMKHGTYEKLEDDGLIAPGTGVAGEDIIIGKTAPLPPDSEELGQRM 719
Cdd:cd00653 507 FFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGE 582

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 720 RTHTRRDVSTPLKSTENGIVDQVLVTT---NQDGLKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPFTAEGI 796
Cdd:cd00653 583 KARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGI 662

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 797 TPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGYQSRGLEVMYHGHSGRKLQAQVY 876
Cdd:cd00653 663 PPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIF 742

                       890
                ....*....|.
gi 45545331 877 LGPTYYQRLKH 887
Cdd:cd00653 743 VGPVYYQRLKH 753
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 376-887 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: 582.37  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   376 VFVNGVWMGVHRDAPNLVKTLRRLRRKDDISSEVSIVRDIREKELRLYTDAGRVCRPLFIVENQQLLLKKEHVnmlnDKS 455
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHV----EKL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   456 RTDPYKWTHLVKDGVIELLDAEEEETVMICMTPDDLensrtnqavaagyvsnagASDHdvaarvrstmtahtwTHCEIHP 535
Cdd:TIGR03670  77 KEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL------------------TPEH---------------THLEIDP 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   536 SMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATV 615
Cdd:TIGR03670 124 SAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVV 203

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   616 AILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYTDAEKKVGVLPLEEFEKPTRDTTLRMKHGTYEKLEDDGLIAPGTGV 695
Cdd:TIGR03670 204 AVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEV 283

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   696 AGEDIIIGKTAPlPPDSEELGQRMR-THTRRDVSTPLKSTENGIVDQVLVTTNQDGLKFVKIRIRSTRIPQVGDKFASRH 774
Cdd:TIGR03670 284 KGGDVLIGKTSP-PRFLEELREFGLvTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRH 362

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   775 GQKGTVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGY 854
Cdd:TIGR03670 363 GQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGF 442

                         490       500       510
                  ....*....|....*....|....*....|...
gi 45545331   855 QSRGLEVMYHGHSGRKLQAQVYLGPTYYQRLKH 887
Cdd:TIGR03670 443 KPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 542-887 6.30e-162

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: 477.02  E-value: 6.30e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   542 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYS 621
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   622 GYNQEDSVIMNQSSIDRGLFRSMYYRSYTDAEKKVGvlpleEFEKPTRDTTlRMKHGTYEKLEDDGLIAPGTGVAGEDII 701
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-----PIEEITRDIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   702 IGKTAPLPPDSE---ELGQRMRthTRRDVSTPLKSTENGIVDQVLV-TTNQDGLKFVKIRIRSTRIPQVGDKFASRHGQK 777
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   778 GTVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTE--LTVESVSQLLRENGYQ 855
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGasTEVEDIGELLEKAGYN 312

                         330       340       350
                  ....*....|....*....|....*....|..
gi 45545331   856 SRGLEVMYHGHSGRKLQAQVYLGPTYYQRLKH 887
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-887 5.40e-154

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 478.06  E-value: 5.40e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    1 SEKVLIAQERMAANHVYVFAKAQPSPISFLAEVRSAveKGGKTIstmqvkmFHRNPQKTVSlgnvirASLPYIRDdIPIW 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE-------FETDKDGTIY------VRIDRKRK-IPVT 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   81 VVFRALGITSDRDILEHIcydtNDTQMVEMLKPCIDEGfVIQEREVALDLIGKR---GtttglsKDKRLRYAQEIL---- 153
Cdd:COG0085  181 VLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpG------EPPTIERAEQLLdnlf 249

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  154 ---QKEMLPHV-----------SMGEGSESKKAFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFR 219
Cdd:COG0085  250 fdpKRYDLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  220 KLTKDV-YRhlqkcVETHKDFNISIA--VKSNTITNGLKYSLATGnwgdqkksmsskaGVSQVLNRYTFASTLSHLRRCN 296
Cdd:COG0085  330 RMERVVrER-----MTTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLS 391

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  297 T----PLGRDgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISvgslsapviEFlqewglesleenan 368
Cdd:COG0085  392 AlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY-------------- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  369 ahgsatkvfvngvwmgvhrdapnlvktlrrlrrkddissevsivrdirekelrlytdaGRVCRPLFIVENqqlllkkehv 448
Cdd:COG0085  445 ----------------------------------------------------------GFIETPYRKVEN---------- 456

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  449 NMLNDKsrtdpykwthlvkdgvIELLDAEEEETVMICM--TPDDLENSRTNQAVAA---GYVSNAGASDHDvaarvrstm 523
Cdd:COG0085  457 GKVTDE----------------IEYLTADEEENYYIAQanAPLDEDGNFLEERVLVryrGEEVLVPPEEVD--------- 511

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  524 tahtwtHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQvrmdtmanILYYP-------------- 589
Cdd:COG0085  512 ------YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPlqkfqrsnqgtcin 577

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  590 QKP-------------LATTRSMEYlrfRELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSY-TDAekk 655
Cdd:COG0085  578 QRPivrvgdrvekgdvLADGPATDN---GELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeIEA--- 651

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  656 vgvlpleefekptRDTTLRMKHGT----------YEKLEDDGLIAPGTGVAGEDIIIGKTAP-----LPPDsEEL----- 715
Cdd:COG0085  652 -------------RDTKLGPEEITrdipnvseeaLRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTPE-ERLlraif 717

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  716 GQRMRThtRRDVSTPLKSTENGIVDQVLVTTNQDG-------LKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHED 788
Cdd:COG0085  718 GEKARE--VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQED 795

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  789 MPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGYQSRGLEVMYHGHSG 868
Cdd:COG0085  796 MPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTG 875

                        970
                 ....*....|....*....
gi 45545331  869 RKLQAQVYLGPTYYQRLKH 887
Cdd:COG0085  876 EPFDNPVTVGYMYYLKLHH 894
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-887 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 887.76  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331     1 SEKVLIAQERMAANHVYVFAKAQPSPISFLAEVRSAVeKGGKTistmqvkmfhrnpQKTVSLGN--VIRASLPYIRDDIP 78
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYRA-------------QVTVERRKdgTIYVSFPAVPGKIP 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    79 IWVVFRALGITSDRDILEHIcydTNDTQMVEMLKPCIDEGF-VIQEREVALDLIGKRgTTTGLSKDKRLRYAQEILQKEM 157
Cdd:PRK08565  214 FVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYL 289

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   158 LPHVSMGEGSESKKAFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHK 237
Cdd:PRK08565  290 LPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGR 369

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   238 DFNISIAVKSNTITNGLKYSLATGNWGDQKksmsskAGVSQVLNRYTFASTLSHLRRCNTPLGRDGKIAKPRQLHNTHWG 317
Cdd:PRK08565  370 KLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWG 443

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   318 MVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLQEWGLESLEE-NANAHGSATKVFVNGVWMGVHRDAPNLVKTL 396
Cdd:PRK08565  444 RICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEaREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   397 RRLRRKDDISSEVSI--VRDIREKELRLYTDAGRVCRPLFIVENQQLLLKKEHVnmlnDKSRTDPYKWTHLVKDGVIELL 474
Cdd:PRK08565  524 RELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHV----EKLKKGELTFDDLVKMGVIEYL 599

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   475 DAEEEETVMICMTPDDLensrtnqavaagyvsnagASDHdvaarvrstmtahtwTHCEIHPSMILGICASIIPFPDHNQS 554
Cdd:PRK08565  600 DAEEEENAYVALDPEDL------------------TPEH---------------THLEIWPPAILGITASIIPYPEHNQS 646

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   555 PRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYSGYNQEDSVIMNQS 634
Cdd:PRK08565  647 PRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKA 726

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   635 SIDRGLFRSMYYRSYTDAEKKVGVLPLEEFEKPtrDTTLRMKHG--TYEKLEDDGLIAPGTGVAGEDIIIGKTAPlPPDS 712
Cdd:PRK08565  727 SIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFL 803

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   713 EEL-GQRMRTHTRRDVSTPLKSTENGIVDQVLVTTNQDGLKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPF 791
Cdd:PRK08565  804 EELeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPF 883

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   792 TAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGYQSRGLEVMYHGHSGRKL 871
Cdd:PRK08565  884 TEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKI 963

                         890
                  ....*....|....*.
gi 45545331   872 QAQVYLGPTYYQRLKH 887
Cdd:PRK08565  964 KAPIFIGVVYYQKLHH 979
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-887 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: 806.79  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   1 SEKVLIAQERMAANHVYVFakaqPSPISFLAEVRSAVEKGGKTISTMQVKMFHRNpqktvslgNVIRASLPYIRddipiw 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK--------DRIYVRIDLKR------ 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  81 vvfralgitsdrdilehicydtndtqmvemlkpcidegfviqeREVALDLIGKRGtttglskdkrlryaqeilqkemlph 160
Cdd:cd00653 199 -------------------------------------------QEEALKYIGKRF------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 161 vsmgegseskkaFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVETHKDFN 240
Cdd:cd00653 211 ------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT 278

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 241 ISIAVKSNTITNGLKYSLATGNWGDQKKSMSsKAGVSQVLNRYTFASTLSHLRRCNT-PLGRDGKIAKPRQLHNTHWGMV 319
Cdd:cd00653 279 PQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRI 357

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 320 CPAETPEGQACGLVKNLSLMACISvgslsapvieflqewglesleenanahgsatkvfvngvwmgvhrdapnlvktlrrl 399
Cdd:cd00653 358 CPIETPEGENCGLVKNLALMARIS-------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 400 rrkddissevsivrdirekelrlytdaGRVCRPLFIVENQqlllkkehvnmlndksrtdpykwthlvkdgvielldaeee 479
Cdd:cd00653 382 ---------------------------GRIERPYRIVEKE---------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 480 etvmicmtpddlensrtnqavaagyvsnagasdhdvaarvrstmtahtWTHCEIHPSMILGICASIIPFPDHNQSPRNTY 559
Cdd:cd00653 395 ------------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLY 426

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 560 QSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRG 639
Cdd:cd00653 427 QSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRG 506

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 640 LFRSMYYRSYTDAEKKVGvlplEEFEKPTRDTTLRMKHGTYEKLEDDGLIAPGTGVAGEDIIIGKTAPLPPDSEELGQRM 719
Cdd:cd00653 507 FFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGE 582

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 720 RTHTRRDVSTPLKSTENGIVDQVLVTT---NQDGLKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPFTAEGI 796
Cdd:cd00653 583 KARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGI 662

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331 797 TPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGYQSRGLEVMYHGHSGRKLQAQVY 876
Cdd:cd00653 663 PPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIF 742

                       890
                ....*....|.
gi 45545331 877 LGPTYYQRLKH 887
Cdd:cd00653 743 VGPVYYQRLKH 753
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 376-887 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: 582.37  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   376 VFVNGVWMGVHRDAPNLVKTLRRLRRKDDISSEVSIVRDIREKELRLYTDAGRVCRPLFIVENQQLLLKKEHVnmlnDKS 455
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHV----EKL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   456 RTDPYKWTHLVKDGVIELLDAEEEETVMICMTPDDLensrtnqavaagyvsnagASDHdvaarvrstmtahtwTHCEIHP 535
Cdd:TIGR03670  77 KEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL------------------TPEH---------------THLEIDP 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   536 SMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATV 615
Cdd:TIGR03670 124 SAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVV 203

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   616 AILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYTDAEKKVGVLPLEEFEKPTRDTTLRMKHGTYEKLEDDGLIAPGTGV 695
Cdd:TIGR03670 204 AVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEV 283

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   696 AGEDIIIGKTAPlPPDSEELGQRMR-THTRRDVSTPLKSTENGIVDQVLVTTNQDGLKFVKIRIRSTRIPQVGDKFASRH 774
Cdd:TIGR03670 284 KGGDVLIGKTSP-PRFLEELREFGLvTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRH 362

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   775 GQKGTVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGY 854
Cdd:TIGR03670 363 GQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGF 442

                         490       500       510
                  ....*....|....*....|....*....|...
gi 45545331   855 QSRGLEVMYHGHSGRKLQAQVYLGPTYYQRLKH 887
Cdd:TIGR03670 443 KPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 374-887 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 550.72  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  374 TKVFVNGVWMGVHRDAPNLVKTLRRLRRKDDISSEVSIVRDIREKELRLYTDAGRVCRPLFIVENQQLLLKKEHVNMLND 453
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  454 KSRTdpykWTHLVKDGVIELLDAEEEETVMICMTPDDLEnsrtnqavaagyvsnagaSDHdvaarvrstmtahtwTHCEI 533
Cdd:PRK07225  85 GELT----FDDLVKQGVIEYLDAEEEENAYIAVYEEDLT------------------EEH---------------THLEI 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  534 HPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNA 613
Cdd:PRK07225 128 DPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNF 207

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  614 TVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYTDAEKKVGVLPLEEFEKPTRDttLRMKHG--TYEKLEDDGLIAP 691
Cdd:PRK07225 208 VVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKD--VRGYRGeeAYRHLDEDGLVNP 285

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  692 GTGVAGEDIIIGKTAPlP-----PDSEELGqrmrTHTRRDVSTPLKSTENGIVDQVLVTTNQDGLKFVKIRIRSTRIPQV 766
Cdd:PRK07225 286 ETEVKEGDVLIGKTSP-PrfleePDDFGIS----PEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPEL 360

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  767 GDKFASRHGQKGTVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVS 846
Cdd:PRK07225 361 GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLR 440

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|.
gi 45545331  847 QLLRENGYQSRGLEVMYHGHSGRKLQAQVYLGPTYYQRLKH 887
Cdd:PRK07225 441 EALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHH 481
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 542-887 6.30e-162

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: 477.02  E-value: 6.30e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   542 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQVRMDTMANILYYPQKPLATTRSMEYLRFRELPAGQNATVAILCYS 621
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   622 GYNQEDSVIMNQSSIDRGLFRSMYYRSYTDAEKKVGvlpleEFEKPTRDTTlRMKHGTYEKLEDDGLIAPGTGVAGEDII 701
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-----PIEEITRDIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   702 IGKTAPLPPDSE---ELGQRMRthTRRDVSTPLKSTENGIVDQVLV-TTNQDGLKFVKIRIRSTRIPQVGDKFASRHGQK 777
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   778 GTVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTE--LTVESVSQLLRENGYQ 855
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGasTEVEDIGELLEKAGYN 312

                         330       340       350
                  ....*....|....*....|....*....|..
gi 45545331   856 SRGLEVMYHGHSGRKLQAQVYLGPTYYQRLKH 887
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-887 5.40e-154

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 478.06  E-value: 5.40e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    1 SEKVLIAQERMAANHVYVFAKAQPSPISFLAEVRSAveKGGKTIstmqvkmFHRNPQKTVSlgnvirASLPYIRDdIPIW 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE-------FETDKDGTIY------VRIDRKRK-IPVT 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   81 VVFRALGITSDRDILEHIcydtNDTQMVEMLKPCIDEGfVIQEREVALDLIGKR---GtttglsKDKRLRYAQEIL---- 153
Cdd:COG0085  181 VLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpG------EPPTIERAEQLLdnlf 249

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  154 ---QKEMLPHV-----------SMGEGSESKKAFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFR 219
Cdd:COG0085  250 fdpKRYDLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  220 KLTKDV-YRhlqkcVETHKDFNISIA--VKSNTITNGLKYSLATGnwgdqkksmsskaGVSQVLNRYTFASTLSHLRRCN 296
Cdd:COG0085  330 RMERVVrER-----MTTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLS 391

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  297 T----PLGRDgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISvgslsapviEFlqewglesleenan 368
Cdd:COG0085  392 AlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY-------------- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  369 ahgsatkvfvngvwmgvhrdapnlvktlrrlrrkddissevsivrdirekelrlytdaGRVCRPLFIVENqqlllkkehv 448
Cdd:COG0085  445 ----------------------------------------------------------GFIETPYRKVEN---------- 456

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  449 NMLNDKsrtdpykwthlvkdgvIELLDAEEEETVMICM--TPDDLENSRTNQAVAA---GYVSNAGASDHDvaarvrstm 523
Cdd:COG0085  457 GKVTDE----------------IEYLTADEEENYYIAQanAPLDEDGNFLEERVLVryrGEEVLVPPEEVD--------- 511

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  524 tahtwtHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQvrmdtmanILYYP-------------- 589
Cdd:COG0085  512 ------YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPlqkfqrsnqgtcin 577

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  590 QKP-------------LATTRSMEYlrfRELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSY-TDAekk 655
Cdd:COG0085  578 QRPivrvgdrvekgdvLADGPATDN---GELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeIEA--- 651

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  656 vgvlpleefekptRDTTLRMKHGT----------YEKLEDDGLIAPGTGVAGEDIIIGKTAP-----LPPDsEEL----- 715
Cdd:COG0085  652 -------------RDTKLGPEEITrdipnvseeaLRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTPE-ERLlraif 717

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  716 GQRMRThtRRDVSTPLKSTENGIVDQVLVTTNQDG-------LKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHED 788
Cdd:COG0085  718 GEKARE--VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQED 795

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  789 MPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVSQLLRENGYQSRGLEVMYHGHSG 868
Cdd:COG0085  796 MPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTG 875

                        970
                 ....*....|....*....
gi 45545331  869 RKLQAQVYLGPTYYQRLKH 887
Cdd:COG0085  876 EPFDNPVTVGYMYYLKLHH 894
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-252 4.80e-105

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: 330.50  E-value: 4.80e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331     1 SEKVLIAQERMAANHVYVFAKAQPSPISFLAEVRSAVEKGGKTISTMQVKMFHRNPqktvslGNVIRASLPYIRDDIPIW 80
Cdd:pfam04563 146 SEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLEYLS------NGTIYFKFPYIKKEIPIV 219

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    81 VVFRALGITSDRDILEHICYDTNDTQMVEMLKPCIDEGFVI--QEREVALDLIGKRGTT---TGLSKDKRLRYAQEILQK 155
Cdd:pfam04563 220 IILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQK 299

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   156 EMLPHVSMGEGSESKKAFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQKCVET 235
Cdd:pfam04563 300 EVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGS 379

                         250
                  ....*....|....*..
gi 45545331   236 HKDFNISIAVKSNTITN 252
Cdd:pfam04563 380 PDDLMLQLLVNAKPITS 396
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-361 3.04e-76

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 257.19  E-value: 3.04e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    1 SEKVLIAQERMAANHVYVfakaqpspisflaevrsavEKGGKTISTMQV-KMF------------HRNPqktvslGNVIR 67
Cdd:PRK09606 153 SERVLMTLEDLAPNKILV-------------------EKDERYGDRIEVaKVFsqrrgyralvtvERNR------DGLLE 207

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   68 ASLPYIRDDIPIWVVFRALGITSDRDILEHIcydTNDTQMVEMLKPCIDEGfVIQEREVALDLIGKRGTTtGLSKDKRLR 147
Cdd:PRK09606 208 VSFPSVPGSIPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVAP-GQTKEYRIK 282

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  148 YAQEILQKEMLPHVSMGEGSESKKAFFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYR 227
Cdd:PRK09606 283 RAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKY 362

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331  228 HLQKCVETHKDFNISIAVKSNTITNGLKYSLATGNWgdqkksMSSKAGVSQVLNRYTFASTLSHLRRCNTPLGRDGKIAK 307
Cdd:PRK09606 363 QLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFE 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 45545331  308 PRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSLSAPVIEFLQEWGLE 361
Cdd:PRK09606 437 ARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-204 1.02e-49

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: 173.69  E-value: 1.02e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    12 AANHVYVFAKAQPSPISflAEVRSAVEKGGKTISTMQVKmfhrnpqktvslGNVIRASLPYIRDDIPIWVVFRALGITSD 91
Cdd:pfam04561   1 RSNGIYVEKELDKNGII--ATYTSSLISNRGSWLKLEID------------GKTLIWSRPSKKRKIPIVIFLKALGLVSD 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    92 RDILEHICYDTNDTQMVEMLKPCIDEGFVIQEREVALDLIGKrGTTTGLSKDKRLRYAQEILQK-----EMLPHVSMGEG 166
Cdd:pfam04561  67 REILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEP 145

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 45545331   167 SESK--KAFFFGYMIHRLLLAALERRELDDRDHFGKKRLD 204
Cdd:pfam04561 146 FENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 191-887 5.02e-47

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: 182.17  E-value: 5.02e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    191 ELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLqkcveTHKDFNiSIA----VKSNTITNGLKYSLATGNwgdq 266
Cdd:TIGR02013  317 EIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM-----STQDTD-TLTpqdlINAKPISAAIKEFFGSSQ---- 386

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    267 kksmsskagVSQVLNRYTFASTLSHLRRCNT--P--LGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACI 342
Cdd:TIGR02013  387 ---------LSQFMDQTNPLAELTHKRRLSAlgPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARV 457

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    343 SvgslsapvieflqEWGlesleenanahgsatkvfvngvwmgvhrdapnlvktlrrlrrkddissevsivrdirekelrl 422
Cdd:TIGR02013  458 N-------------EYG--------------------------------------------------------------- 461

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    423 ytdagrvcrplFIvenqqlllkkehvnmlndksrTDPYKwthLVKDGVIELldaeeeETVMICMTPDDLENSRTNQAVAA 502
Cdd:TIGR02013  462 -----------FI---------------------ETPYR---KVKDGKVVV------TDEIDYLTADEEDNYVIAQANAP 500

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    503 GYVSNAGASDHdVAARVR---STMTAHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAM----------- 568
Cdd:TIGR02013  501 LDENGRFVEDL-VVARYRgeiTLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvg 579

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    569 -----------------------------GIYLTNYQVRMDTMANILYYP--------------QKP------------- 592
Cdd:TIGR02013  580 tgmeakvardsgavivakrggvveyvdakRIVIRYDEDEEEPDGGIDIYRllkyqrsnqdtcinQRPivsvgdrveagdv 659

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    593 LATTRSMEylrFRELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYyrsytdaekkvgvlpLEEFEKPTRDTt 672
Cdd:TIGR02013  660 LADGPSTD---LGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIH---------------IEEYEVEARDT- 720

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    673 lrmKHGTYE--------------KLEDDGLIAPGTGVAGEDIIIGKTAP-----LPPDSEEL----GQRMRThtRRDVST 729
Cdd:TIGR02013  721 ---KLGPEEitrdipnvseealrNLDENGIVRIGAEVKAGDILVGKVTPkgeteLTPEEKLLraifGEKARD--VRDTSL 795

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    730 PLKSTENGIVDQVLVTTNQDG-------LKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPFTAEGITPDIII 802
Cdd:TIGR02013  796 RVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVL 875

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331    803 NPHAIPSRMTIGHLIECLLSKLATLIGNEGD--ATP-FTELTVESVSQLLRENGYQSRGLEVMYHGHSGRKLQAQVYLGP 879
Cdd:TIGR02013  876 NPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGY 955


                   ....*...
gi 45545331    880 TYYQRLKH 887
Cdd:TIGR02013  956 MYMLKLHH 963
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 179-887 1.11e-33

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 139.84  E-value: 1.11e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   179 IHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRM----LFRKLTKDvyrhlqkcvetHKDFNISIAVKSNTITNGL 254
Cdd:CHL00207  284 IDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIglkrLERILRNR-----------MTICDIDSLSKFNLINPKP 352

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   255 KYSLATGNWGdqkksmSSKagVSQVLNRYTFASTLSHLRRCNTpLGRDG----KIAKP-RQLHNTHWGMVCPAETPEGQA 329
Cdd:CHL00207  353 LIALIREFFG------SSQ--LSQYMDQTNPLSELTHKRRISI-LGPGGldkdRISFAvRDIHPSHYGRICPIETPEGPN 423

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   330 CGLVKnlSLMACISV---GSLSAP--------VIEFLQEWGLESLEENANahgsatkvfvngvwmgvhRDAPNLVKtlrr 398
Cdd:CHL00207  424 CGLIG--SLATNARInkfGFIETPfykvingkVKKFGNPIYLTADSEDLY------------------RIAPNDIN---- 479

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   399 LRRKDDISSEVSIVRdirekelrlytdagrvcrplfivENQQLLLKK-EHVNMLNdksrtdpykwthlvkdgvielldae 477
Cdd:CHL00207  480 LNKNNYFKKNIIPVR-----------------------YKQEFKTVNpSKVDFIA------------------------- 511

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   478 eeetvmicmtpddlensrtnqavaagyvsnagasdhdvaarvrstmtahtwthceIHPSMILGICASIIPFPDHNQSPRN 557
Cdd:CHL00207  512 -------------------------------------------------------ISPIQVFSIAESLIPFLEHNDANRA 536

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   558 TYQSAMGKQAM-------------------------------GI--YLTNYQVRMDTMAN--ILYYPQK----------- 591
Cdd:CHL00207  537 LMGSNMQRQAVpllypekpivgtgyekqialdsgmtiislteGIvvSVSAYKIIIQDDNNryIHYYLQKyqrsnqntcin 616

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   592 --P-------------LATTRSMEylrFRELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYYRSYtDAEKKV 656
Cdd:CHL00207  617 yrPivwvgekinigqiLADGSDID---NSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-EIELRQ 692

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   657 GVLPLEEFekpTRDTTlrmKHGTYE--KLEDDGLIAPGTGVAGEDIIIGKTAPLP----PDSEELGQRMRTHTRRDV-ST 729
Cdd:CHL00207  693 TKLGSEEI---TRNIP---NVSEYSlkNLDENGIISIGSKVLAGDILVGKITPKGesdqLPEGKLLRAIFGEKAKDVkDT 766

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   730 PLKSTENG---IVDQVLVTTNQ-DGLKF-----VKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPFTAEGITPDI 800
Cdd:CHL00207  767 SLRMPNGGygrVIKVEIFSRSKgDELKFgyylkIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDI 846

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   801 IINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTELTVESVS-----QLLRENGY----------QSRGLEVMYHG 865
Cdd:CHL00207  847 ILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSrilinNKLNQASIknneywlfnsYHPGKMVLRDG 926

                         810       820
                  ....*....|....*....|..
gi 45545331   866 HSGRKLQAQVYLGPTYYQRLKH 887
Cdd:CHL00207  927 RTGYKFKNPVTVGIAYMLKLIH 948
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 376-437 2.15e-32

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: 119.39  E-value: 2.15e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545331   376 VFVNGVWMGVHRDAPNLVKTLRRLRRKDDISSEVSIVRDIREKELRLYTDAGRVCRPLFIVE 437
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 606-887 3.74e-32

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 135.23  E-value: 3.74e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   606 ELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMYyrsytdaekkvgvlpLEEFEKPTRDTtlrmKHGTYE---- 681
Cdd:PRK00405  712 ELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIH---------------IEEYEIEARDT----KLGPEEitrd 772

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   682 ----------KLEDDGLIAPGTGVAGEDIIIGKTAP-----LPPdsEE------LGQRMRTHtrRDVSTPLKSTENGIVD 740
Cdd:PRK00405  773 ipnvseealrNLDESGIVRIGAEVKPGDILVGKVTPkgeteLTP--EEkllraiFGEKARDV--KDTSLRVPHGEEGTVI 848

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   741 QVLV-TTNQDG-------LKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPFTAEGiTP-DIIINPHAIPSRM 811
Cdd:PRK00405  849 DVKVfTRIEQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDG-TPvDIVLNPLGVPSRM 927

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45545331   812 TIGHLIECLLSKLATLIGNEGdATP-FTELTVESVSQLLRENGYQSRGLEVMYHGHSGRKLQAQVYLGPTYYQRLKH 887
Cdd:PRK00405  928 NIGQILETHLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHH 1003
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 278-340 3.07e-30

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: 113.78  E-value: 3.07e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45545331   278 QVLNRYTFASTLSHLRRCNTP---LGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMA 340
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPrggLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 462-535 8.16e-24

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: 94.91  E-value: 8.16e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45545331   462 WTHLVKDGVIELLDAEEEETVMICMTPDDLENSRTNQavaagyvsnagasdhdvaarvRSTMTAHTWTHCEIHP 535
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE---------------------REGPYAHTYTHCEIHP 53
rpoB CHL00001
RNA polymerase beta subunit
 478-839 4.66e-21

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 99.21  E-value: 4.66e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   478 EEETVMICMTPDDLENSRtnqaVAAGyvsNAGASDHD------VAARVRSTMTAHTWTHCE---IHPSMILGICASIIPF 548
Cdd:CHL00001  461 SKEERMVYLSPSEDEYYM----IAAG---NSLALNQGiqeeqvVPARYRQEFLTIAWEQIHlrsIFPFQYFSIGASLIPF 533

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   549 PDHNQSPRNTYQSAMGKQA---------------------------------------------------MGIYLTNYQv 577
Cdd:CHL00001  534 LEHNDANRALMGSNMQRQAvplsrsekcivgtglerqvaldsgvvaiaehegkiiytdtdkiilsgngdtLSIPLVMYQ- 612

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   578 R--MDTMANilyypQKPlaTTRSMEYLRFRELPA------------GQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRS 643
Cdd:CHL00001  613 RsnKNTCMH-----QKP--QVRRGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTS 685

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   644 MYYRSYtDAEKKVGVLPLEEFEK--PTRDTTLrMKHgtyekLEDDGLIAPGTGVAGEDIIIGKTAP-LPPDSEE------ 714
Cdd:CHL00001  686 FHIRKY-EIQTHVTSQGPERITKeiPHLEAHL-LRN-----LDKNGIVMLGSWVETGDILVGKLTPqEAEESSYapegrl 758

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   715 ----LGQRMRThTRrdvSTPLKSTENG---IVDQVLVT---TNQDGLKFVKIRIRSTRIPQVGDKFASRHGQKGTVGITY 784
Cdd:CHL00001  759 lraiFGIQVST-SK---ETCLKLPIGGrgrVIDVRWIQkkgGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKIL 834

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 45545331   785 RHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNEGDATPFTE 839
Cdd:CHL00001  835 PRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDE 889
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
191-831 5.98e-21

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 99.61  E-value: 5.98e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   191 ELDDRDHFGKKRLDLAGPLLAS-----LFRMlfRKLTKDVYRHLQKCVETHKDFNIsiaVKSNTITNGLKYSLATGNwgd 265
Cdd:PRK09603  453 KIDDRDHLGNRRIRAVGELLANelhsgLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ--- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   266 qkksmsskagVSQVLNRYTFASTLSHLRRCNTpLGRDGKIA-----KPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMA 340
Cdd:PRK09603  525 ----------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   341 CIS-VGSLSAPvieflqewglesLEENANAHGSATKVFVNGVWMGVHRDAPNLVKtlrrlrrkddISSEVSIVRDIREKe 419
Cdd:PRK09603  594 RVNdLGFIEAP------------YKKVVDGKVVGETIYLTAIQEDSHIIAPASTP----------IDEEGNILGDLIET- 650

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   420 lrlytdagrvcrplfivenqqlllKKEHVNMLNDKSRtdpykwthlvkdgvIELLDaeeeetvmicmtpddlensrtnqa 499
Cdd:PRK09603  651 ------------------------RVEGEIVLNEKSK--------------VTLMD------------------------ 668

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   500 vaagyvsnagasdhdvaarvrstmtahtwthceIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGIYLTNYQV-- 577
Cdd:PRK09603  669 ---------------------------------LSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIvg 715

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   578 ------------------------RMDTM-----------ANILYYP-QKPLATTRSMEY-------------------- 601
Cdd:PRK09603  716 tgiekiiardswgaikanragvveKIDSKniyilgegkeeAYIDAYSlQKNLRTNQNTSFnqvpivkvgdkveagqiiad 795

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   602 ---LRFRELPAGQNATVAILCYSGYNQEDSVIMNQSSIDRGLFRSMY-YRSYTDA-EKKVGVlplEEFekpTRDTTlRMK 676
Cdd:PRK09603  796 gpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHiYEKEVDArELKHGV---EEF---TADIP-DVK 868

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   677 HGTYEKLEDDGLIAPGTGVAGEDIIIGKTAP------------------------------LPPDSE------------- 713
Cdd:PRK09603  869 EEALAHLDESGIVKVGTYVSAGMILVGKTSPkgeikstpeerllraifgdkaghvvnkslyCPPSLEgtvidvkvftkkg 948

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   714 -ELGQRMRT-------------HTR------------------------------------------------------- 724
Cdd:PRK09603  949 yEKDARVLSayeeekakldmehFDRltmlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlaslv 1028

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   725 ----RDVSTPLKSTENGIVDQ--VLVTTNQDGL--------------KFVKIRIRSTRIPQVGDKFASRHGQKGTVGITY 784
Cdd:PRK09603 1029 kkysKEVQNHYEITKNNFLEQkkVLGEEHEEKLsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIV 1108

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|....*..
gi 45545331   785 RHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLSKLATLIGNE 831
Cdd:PRK09603 1109 PVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQ 1155
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
178-830 5.16e-18

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 90.07  E-value: 5.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   178 MIHRLLLAALERRELDDRDHFGKKRLDLAGPLLASLFRMLFRKLTKDVYRHLQkcVETHKDFNISIAVKSNTITNGLKys 257
Cdd:PRK14844  449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMS--TSSLDKVSPSDFINPKVLTNVLR-- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   258 latgnwgdqkkSMSSKAGVSQVLNRYTFASTLSHLRRCNT----PLGRDGKIAKPRQLHNTHWGMVCPAETPEGQACGLV 333
Cdd:PRK14844  525 -----------DFFNSSQLSQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLI 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   334 KNLSLMACIS-VGSLSAPVIEFLQEWGLESLEenanahgsatkvFVNGVWMGVHRDAPNLVKTLRRLRRKDDI------- 405
Cdd:PRK14844  594 NSLAIYARINkYGFIESPYRKVVNRVVTDQIE------------YLSAIDEGLYYIADTSAKLDENNCFVDDMlycryag 661

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   406 ------SSEVSIVrDIREKELrLYTDAGRVcrPLFIVE--NQQLL---LKKEHVNMLNDksrTDPykwthLVKDGvIELL 474
Cdd:PRK14844  662 sfvmvsSDQVSYI-DVSPKQV-ISVAASLI--PFLENDdaNRALMgsnMQRQAVPLLKP---TAP-----LVATG-MESF 728

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   475 DAEEEETVMICMTPDDLENSRTNQAVAAGY----VSNAGASDHDVAARVRSTmtahtwthceiHPSMIlgicasiipfpd 550
Cdd:PRK14844  729 VASGSGAVVLAKRDGIVDSSDSNSIVIRAFdkerVNYLDVDIYHLRKFQRSN-----------HNTCI------------ 785

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   551 hNQSPRntyqsamgkqamgIYLTNYQVRMDTMANilyypqKPLATTRsmeylrfrELPAGQNATVAILCYSGYNQEDSVI 630
Cdd:PRK14844  786 -NQKPL-------------VCVGDYVKEGDVIAD------GPAINSG--------ELALGQNLLVAFMSWQGYNFEDSII 837

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   631 MNQSSIDRGLFRSMYyrsytdaekkvgvlpLEEFEKPTRDTTL------RMKHGTYEK----LEDDGLIAPGTGVAGEDI 700
Cdd:PRK14844  838 ISSEVVKKDLFTSIH---------------IEEFECVVHDTPLgsekitRAIPGVNEEnlyhLDDSGIVKIGTRVGPGYI 902

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   701 IIGKTAP-----LPPDSEEL----GQR---------------------MRTHTRRDVS-------------TPLKSTENG 737
Cdd:PRK14844  903 LVGKVTPkpslsLPPETKLLmtifGEKsfdcadsslytspdvegtvidVQVFTRRGVEenerallikqkeiNDFEKERDY 982

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   738 IVD-----------QVLVTT-NQDGLKF---------------------------------------------------- 753
Cdd:PRK14844  983 IINvtseyfydelkKLLINSgSQDREKFdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegyd 1062

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545331   754 --------VKIRIRSTRIPQVGDKFASRHGQKGTVGITYRHEDMPFTAEGITPDIIINPHAIPSRMTIGHLIECLLS--- 822
Cdd:PRK14844 1063 lpqgvsmsVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwac 1142


                  ....*....
gi 45545331   823 -KLATLIGN 830
Cdd:PRK14844 1143 kKLGEKVGN 1151
 
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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