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Conserved domains on  [gi|6606089|gb|AAF19057|]
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DNA-dependent RNA polymerase II RPB140, partial [Agaricus bisporus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-914 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: 973.66  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089      1 SEKVLIAQERMATNHVYVFAKAQPSPINFLAEIRSAveKGGKTiSQFQVKMfHRNQERSVSFTTIPYikvDIPIWVVFRG 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISS--RAGYR-AQVTVER-RKDGTIYVSFPAVPG---KIPFVILMRA 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     81 LGVISDRDILEHICYD--MQDaqmlEMLKPCIDDGFVIQDREVALDFIGNRgTTTGLSRERRIRYAQEILQKEMLPHVSM 158
Cdd:PRK08565  221 LGLETDRDIVYAVSLDpeIQQ----ELLPSLEQASSIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLGT 295

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    159 AEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLAL 238
Cdd:PRK08565  296 SPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRA 375

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    239 AVKHQTITNGLKYSLATGNWGDQkksmssKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 318
Cdd:PRK08565  376 IVRPDIITERIRHALATGNWVGG------RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFE 449

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    319 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSTSP-CTKVFVNGVWMGVHRDPANLVKTIKKLRRK 397
Cdd:PRK08565  450 TPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRRS 529

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    398 DDISPEVSV--VRDIREKELRIYTDAGRVCRPLFIVENQQLLLGKRHIRWLNSGsddegnEYKWEQLIKGGVIELLDAEE 475
Cdd:PRK08565  530 GKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEE 603

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    476 EETVMISMTPEDLensrlqaagvdphandgdfdpaarlkagTHAHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 555
Cdd:PRK08565  604 EENAYVALDPEDL----------------------------TPEH--THLEIWPPAILGITASIIPYPEHNQSPRNTYQA 653

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    556 AMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 635
Cdd:PRK08565  654 AMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA 733

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    636 RSIYYRSYMDLEKKSGIQQLEEFEKPtrDTTLRMKHG--TYDKLEDDGLIAPGTGVRGEDIIIGKTAPiPPDSEELGQRT 713
Cdd:PRK08565  734 RSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEELEELS 810

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    714 R-THTRRDVSTPLKSTEIGIVDQVLITTNSEGQKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVP 792
Cdd:PRK08565  811 LgLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVP 890

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    793 DLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLG 872
Cdd:PRK08565  891 DLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIG 970

                         890       900       910       920
                  ....*....|....*....|....*....|....*....|..
gi 6606089    873 PTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:PRK08565  971 VVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-914 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 973.66  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089      1 SEKVLIAQERMATNHVYVFAKAQPSPINFLAEIRSAveKGGKTiSQFQVKMfHRNQERSVSFTTIPYikvDIPIWVVFRG 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISS--RAGYR-AQVTVER-RKDGTIYVSFPAVPG---KIPFVILMRA 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     81 LGVISDRDILEHICYD--MQDaqmlEMLKPCIDDGFVIQDREVALDFIGNRgTTTGLSRERRIRYAQEILQKEMLPHVSM 158
Cdd:PRK08565  221 LGLETDRDIVYAVSLDpeIQQ----ELLPSLEQASSIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLGT 295

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    159 AEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLAL 238
Cdd:PRK08565  296 SPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRA 375

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    239 AVKHQTITNGLKYSLATGNWGDQkksmssKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 318
Cdd:PRK08565  376 IVRPDIITERIRHALATGNWVGG------RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFE 449

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    319 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSTSP-CTKVFVNGVWMGVHRDPANLVKTIKKLRRK 397
Cdd:PRK08565  450 TPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRRS 529

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    398 DDISPEVSV--VRDIREKELRIYTDAGRVCRPLFIVENQQLLLGKRHIRWLNSGsddegnEYKWEQLIKGGVIELLDAEE 475
Cdd:PRK08565  530 GKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEE 603

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    476 EETVMISMTPEDLensrlqaagvdphandgdfdpaarlkagTHAHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 555
Cdd:PRK08565  604 EENAYVALDPEDL----------------------------TPEH--THLEIWPPAILGITASIIPYPEHNQSPRNTYQA 653

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    556 AMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 635
Cdd:PRK08565  654 AMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA 733

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    636 RSIYYRSYMDLEKKSGIQQLEEFEKPtrDTTLRMKHG--TYDKLEDDGLIAPGTGVRGEDIIIGKTAPiPPDSEELGQRT 713
Cdd:PRK08565  734 RSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEELEELS 810

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    714 R-THTRRDVSTPLKSTEIGIVDQVLITTNSEGQKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVP 792
Cdd:PRK08565  811 LgLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVP 890

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    793 DLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLG 872
Cdd:PRK08565  891 DLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIG 970

                         890       900       910       920
                  ....*....|....*....|....*....|....*....|..
gi 6606089    873 PTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:PRK08565  971 VVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-914 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: 871.89  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    1 SEKVLIAQERMATNHVYVFakaqPSPINFLAEIRSAVEKGGKTISQFQVKMFHRNQERSVsftTIPYIKvdipiwvvfrg 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYV---RIDLKR----------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   81 lgvisdrdilehicydmqdaqmlemlkpciddgfviqdREVALDFIGNRGtttglsrerriryaqeilqkemlphvsmae 160
Cdd:cd00653 199 --------------------------------------QEEALKYIGKRF------------------------------ 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  161 gseskkaYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAV 240
Cdd:cd00653 211 -------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLI 283

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  241 KHQTITNGLKYSLATGNWGDQKKSMSsKAGVSQVLNRYTYASTLSHLRRCNT-PLGREGKIAKPRQLHNTHWGMVCPAET 319
Cdd:cd00653 284 NSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIET 362

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  320 PEGQACGLVKNLALMSCISvgsysapviefleewglesleenahstspctkvfvngvwmgvhrdpanlvktikklrrkdd 399
Cdd:cd00653 363 PEGENCGLVKNLALMARIS------------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  400 ispevsvvrdirekelriytdaGRVCRPLFIVENQqlllgkrhirwlnsgsddegneykweqlikggvielldaeeeetv 479
Cdd:cd00653 382 ----------------------GRIERPYRIVEKE--------------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  480 mismtpedlensrlqaagvdphandgdfdpaarlkagthahtWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMAK 559
Cdd:cd00653 395 ------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQK 432

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  560 QAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIY 639
Cdd:cd00653 433 QAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIH 512

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  640 YRSYMDLEKKSGIQQleefEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRR 719
Cdd:cd00653 513 YKKYEIELRKTKNGP----EEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVR 588

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  720 DVSTPLKSTEIGIVDQVLITT---NSEGQKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVPDLII 796
Cdd:cd00653 589 DTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIIL 668

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  797 NPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPTYY 876
Cdd:cd00653 669 NPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYY 748

                       890       900       910
                ....*....|....*....|....*....|....*...
gi 6606089  877 QRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:cd00653 749 QRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRF 786
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 371-914 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: 665.57  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    371 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIYTDAGRVCRPLFIVENQQLLLGKRHIRWLNSGs 450
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    451 ddegnEYKWEQLIKGGVIELLDAEEEETVMISMTPEDLensrlqaagvdphandgdfdpaarlkagTHAHTwtHCEIHPS 530
Cdd:TIGR03670  80 -----ELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL----------------------------TPEHT--HLEIDPS 124

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    531 MILGICASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVA 610
Cdd:TIGR03670 125 AILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVA 204

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    611 ILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVR 690
Cdd:TIGR03670 205 VMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVK 284

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    691 GEDIIIGKTAPiPPDSEELGQRTR-THTRRDVSTPLKSTEIGIVDQVLITTNSEGQKFVKVRVRATRIPQIGDKFASCHG 769
Cdd:TIGR03670 285 GGDVLIGKTSP-PRFLEELREFGLvTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHG 363

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    770 QKGTVGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQ 849
Cdd:TIGR03670 364 QKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFK 443

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6606089    850 SRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:TIGR03670 444 PDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRF 508
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 536-908 0e+00

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 530.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    536 CASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 615
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    616 GYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGiqqleEFEKPTRDTTlRMKHGTYDKLEDDGLIAPGTGVRGEDII 695
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-----PIEEITRDIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    696 IGKTAPIPPDSE---ELGQRTRthTRRDVSTPLKSTEIGIVDQVLI-TTNSEGQKFVKVRVRATRIPQIGDKFASCHGQK 771
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    772 GTVGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--DLTVESVSTFLRQKGYQ 849
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYN 312

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 6606089    850 SRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSR 908
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-914 8.63e-179

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: 543.55  E-value: 8.63e-179
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     1 SEKVLIAQERMATNHVYVFAKAQPSPINFLAEIRSAveKGGKTIsqFQVkmfHRNQERSVSFTTipyiKVDIPIWVVFRG 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE--FET---DKDGTIYVRIDR----KRKIPVTVLLRA 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    81 LGVISDRDILEHICydmqDAQMLEMLKPCIDDGfVIQDREVALDFIGNR---GtttglsRERRIRYAQEIL-------QK 150
Cdd:COG0085  186 LGLETDEEILEAFG----DDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpG------EPPTIERAEQLLdnlffdpKR 254

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   151 EMLPHV-----------SMAEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKD 219
Cdd:COG0085  255 YDLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERV 334

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   220 V-YRylqkcVETHKEFNLALA--VKHQTITNGLKYSLATGnwgdqkksmsskaGVSQVLNRYTYASTLSHLRRCNT---- 292
Cdd:COG0085  335 VrER-----MTTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpg 396

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   293 PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISvgsysapviEFleewglesleenahstspc 368
Cdd:COG0085  397 GLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------------- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   369 tkvfvngvwmgvhrdpanlvktikklrrkddispevsvvrdirekelriytdaGRVCRPLFIVENQQLllgkrhirwlns 448
Cdd:COG0085  445 -----------------------------------------------------GFIETPYRKVENGKV------------ 459

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   449 gsDDEgneykweqlikggvIELLDAEEEETVMISMTPEDL-ENSRLQAAGVD-PHANDGDFDPAARLkagthahtwTHCE 526
Cdd:COG0085  460 --TDE--------------IEYLTADEEENYYIAQANAPLdEDGNFLEERVLvRYRGEEVLVPPEEV---------DYMD 514

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   527 IHPSMILGICASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNflirmdtmANILYYP--------------QKPLAttRS 592
Cdd:COG0085  515 VSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RV 584

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   593 MEYLK------------FRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYrsymdlekksgiqqlEEFEK 660
Cdd:COG0085  585 GDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHI---------------EEYEI 649

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   661 PTRDTTLRMKHGT----------YDKLEDDGLIAPGTGVRGEDIIIGKTAP---IPPDSEE------LGQRTRThtRRDV 721
Cdd:COG0085  650 EARDTKLGPEEITrdipnvseeaLRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEErllraiFGEKARE--VRDT 727

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   722 STPLKSTEIGIVDQVLITTNSEG-------QKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVPDL 794
Cdd:COG0085  728 SLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDI 807

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   795 IINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPT 874
Cdd:COG0085  808 VLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYM 887

                        970       980       990      1000
                 ....*....|....*....|....*....|....*....|
gi 6606089   875 YYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:COG0085  888 YYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-914 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 973.66  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089      1 SEKVLIAQERMATNHVYVFAKAQPSPINFLAEIRSAveKGGKTiSQFQVKMfHRNQERSVSFTTIPYikvDIPIWVVFRG 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISS--RAGYR-AQVTVER-RKDGTIYVSFPAVPG---KIPFVILMRA 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     81 LGVISDRDILEHICYD--MQDaqmlEMLKPCIDDGFVIQDREVALDFIGNRgTTTGLSRERRIRYAQEILQKEMLPHVSM 158
Cdd:PRK08565  221 LGLETDRDIVYAVSLDpeIQQ----ELLPSLEQASSIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLGT 295

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    159 AEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLAL 238
Cdd:PRK08565  296 SPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRA 375

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    239 AVKHQTITNGLKYSLATGNWGDQkksmssKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAE 318
Cdd:PRK08565  376 IVRPDIITERIRHALATGNWVGG------RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFE 449

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    319 TPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLESLEENAHSTSP-CTKVFVNGVWMGVHRDPANLVKTIKKLRRK 397
Cdd:PRK08565  450 TPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRRS 529

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    398 DDISPEVSV--VRDIREKELRIYTDAGRVCRPLFIVENQQLLLGKRHIRWLNSGsddegnEYKWEQLIKGGVIELLDAEE 475
Cdd:PRK08565  530 GKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEE 603

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    476 EETVMISMTPEDLensrlqaagvdphandgdfdpaarlkagTHAHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 555
Cdd:PRK08565  604 EENAYVALDPEDL----------------------------TPEH--THLEIWPPAILGITASIIPYPEHNQSPRNTYQA 653

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    556 AMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 635
Cdd:PRK08565  654 AMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA 733

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    636 RSIYYRSYMDLEKKSGIQQLEEFEKPtrDTTLRMKHG--TYDKLEDDGLIAPGTGVRGEDIIIGKTAPiPPDSEELGQRT 713
Cdd:PRK08565  734 RSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEELEELS 810

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    714 R-THTRRDVSTPLKSTEIGIVDQVLITTNSEGQKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVP 792
Cdd:PRK08565  811 LgLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVP 890

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    793 DLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLG 872
Cdd:PRK08565  891 DLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIG 970

                         890       900       910       920
                  ....*....|....*....|....*....|....*....|..
gi 6606089    873 PTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:PRK08565  971 VVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-914 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: 871.89  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    1 SEKVLIAQERMATNHVYVFakaqPSPINFLAEIRSAVEKGGKTISQFQVKMFHRNQERSVsftTIPYIKvdipiwvvfrg 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYV---RIDLKR----------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   81 lgvisdrdilehicydmqdaqmlemlkpciddgfviqdREVALDFIGNRGtttglsrerriryaqeilqkemlphvsmae 160
Cdd:cd00653 199 --------------------------------------QEEALKYIGKRF------------------------------ 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  161 gseskkaYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFNLALAV 240
Cdd:cd00653 211 -------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLI 283

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  241 KHQTITNGLKYSLATGNWGDQKKSMSsKAGVSQVLNRYTYASTLSHLRRCNT-PLGREGKIAKPRQLHNTHWGMVCPAET 319
Cdd:cd00653 284 NSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIET 362

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  320 PEGQACGLVKNLALMSCISvgsysapviefleewglesleenahstspctkvfvngvwmgvhrdpanlvktikklrrkdd 399
Cdd:cd00653 363 PEGENCGLVKNLALMARIS------------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  400 ispevsvvrdirekelriytdaGRVCRPLFIVENQqlllgkrhirwlnsgsddegneykweqlikggvielldaeeeetv 479
Cdd:cd00653 382 ----------------------GRIERPYRIVEKE--------------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  480 mismtpedlensrlqaagvdphandgdfdpaarlkagthahtWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMAK 559
Cdd:cd00653 395 ------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQK 432

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  560 QAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIY 639
Cdd:cd00653 433 QAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIH 512

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  640 YRSYMDLEKKSGIQQleefEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAPIPPDSEELGQRTRTHTRR 719
Cdd:cd00653 513 YKKYEIELRKTKNGP----EEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVR 588

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  720 DVSTPLKSTEIGIVDQVLITT---NSEGQKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVPDLII 796
Cdd:cd00653 589 DTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIIL 668

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089  797 NPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPTYY 876
Cdd:cd00653 669 NPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYY 748

                       890       900       910
                ....*....|....*....|....*....|....*...
gi 6606089  877 QRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:cd00653 749 QRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRF 786
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 371-914 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: 665.57  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    371 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIYTDAGRVCRPLFIVENQQLLLGKRHIRWLNSGs 450
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    451 ddegnEYKWEQLIKGGVIELLDAEEEETVMISMTPEDLensrlqaagvdphandgdfdpaarlkagTHAHTwtHCEIHPS 530
Cdd:TIGR03670  80 -----ELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL----------------------------TPEHT--HLEIDPS 124

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    531 MILGICASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVA 610
Cdd:TIGR03670 125 AILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVA 204

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    611 ILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDTTLRMKHGTYDKLEDDGLIAPGTGVR 690
Cdd:TIGR03670 205 VMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVK 284

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    691 GEDIIIGKTAPiPPDSEELGQRTR-THTRRDVSTPLKSTEIGIVDQVLITTNSEGQKFVKVRVRATRIPQIGDKFASCHG 769
Cdd:TIGR03670 285 GGDVLIGKTSP-PRFLEELREFGLvTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHG 363

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    770 QKGTVGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQ 849
Cdd:TIGR03670 364 QKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFK 443

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6606089    850 SRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:TIGR03670 444 PDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRF 508
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 369-914 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 636.62  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   369 TKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIYTDAGRVCRPLFIVENQQLLLGKRHIRWLNS 448
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   449 GsddegnEYKWEQLIKGGVIELLDAEEEETVMISMTPEDLensrlqaagvdphandgdfdpaarlkagTHAHTwtHCEIH 528
Cdd:PRK07225  85 G------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL----------------------------TEEHT--HLEID 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   529 PSMILGICASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAI 608
Cdd:PRK07225 129 PSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFV 208

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   609 VAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGIQQLEEFEKPTRDttLRMKHG--TYDKLEDDGLIAPG 686
Cdd:PRK07225 209 VAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKD--VRGYRGeeAYRHLDEDGLVNPE 286

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   687 TGVRGEDIIIGKTAPiP-----PDSEELGqrtrTHTRRDVSTPLKSTEIGIVDQVLITTNSEGQKFVKVRVRATRIPQIG 761
Cdd:PRK07225 287 TEVKEGDVLIGKTSP-PrfleePDDFGIS----PEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELG 361

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   762 DKFASCHGQKGTVGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVST 841
Cdd:PRK07225 362 DKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLRE 441

                        490       500       510       520       530       540       550
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6606089   842 FLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:PRK07225 442 ALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRF 514
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 536-908 0e+00

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 530.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    536 CASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNFLIRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 615
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    616 GYNQEDSVIMNQSSIDRGLFRSIYYRSYMDLEKKSGiqqleEFEKPTRDTTlRMKHGTYDKLEDDGLIAPGTGVRGEDII 695
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-----PIEEITRDIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    696 IGKTAPIPPDSE---ELGQRTRthTRRDVSTPLKSTEIGIVDQVLI-TTNSEGQKFVKVRVRATRIPQIGDKFASCHGQK 771
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    772 GTVGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFT--DLTVESVSTFLRQKGYQ 849
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYN 312

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 6606089    850 SRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSR 908
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-914 8.63e-179

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: 543.55  E-value: 8.63e-179
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     1 SEKVLIAQERMATNHVYVFAKAQPSPINFLAEIRSAveKGGKTIsqFQVkmfHRNQERSVSFTTipyiKVDIPIWVVFRG 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE--FET---DKDGTIYVRIDR----KRKIPVTVLLRA 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    81 LGVISDRDILEHICydmqDAQMLEMLKPCIDDGfVIQDREVALDFIGNR---GtttglsRERRIRYAQEIL-------QK 150
Cdd:COG0085  186 LGLETDEEILEAFG----DDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpG------EPPTIERAEQLLdnlffdpKR 254

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   151 EMLPHV-----------SMAEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKD 219
Cdd:COG0085  255 YDLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERV 334

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   220 V-YRylqkcVETHKEFNLALA--VKHQTITNGLKYSLATGnwgdqkksmsskaGVSQVLNRYTYASTLSHLRRCNT---- 292
Cdd:COG0085  335 VrER-----MTTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpg 396

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   293 PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISvgsysapviEFleewglesleenahstspc 368
Cdd:COG0085  397 GLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------------- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   369 tkvfvngvwmgvhrdpanlvktikklrrkddispevsvvrdirekelriytdaGRVCRPLFIVENQQLllgkrhirwlns 448
Cdd:COG0085  445 -----------------------------------------------------GFIETPYRKVENGKV------------ 459

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   449 gsDDEgneykweqlikggvIELLDAEEEETVMISMTPEDL-ENSRLQAAGVD-PHANDGDFDPAARLkagthahtwTHCE 526
Cdd:COG0085  460 --TDE--------------IEYLTADEEENYYIAQANAPLdEDGNFLEERVLvRYRGEEVLVPPEEV---------DYMD 514

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   527 IHPSMILGICASIIPFPDHNQSPRNTYQSAMAKQAMGIYLTNflirmdtmANILYYP--------------QKPLAttRS 592
Cdd:COG0085  515 VSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RV 584

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   593 MEYLK------------FRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYrsymdlekksgiqqlEEFEK 660
Cdd:COG0085  585 GDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHI---------------EEYEI 649

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   661 PTRDTTLRMKHGT----------YDKLEDDGLIAPGTGVRGEDIIIGKTAP---IPPDSEE------LGQRTRThtRRDV 721
Cdd:COG0085  650 EARDTKLGPEEITrdipnvseeaLRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEErllraiFGEKARE--VRDT 727

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   722 STPLKSTEIGIVDQVLITTNSEG-------QKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVPDL 794
Cdd:COG0085  728 SLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDI 807

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   795 IINPHAIPSRMTIGHLVECLLSKVATLIGNEGDATPFTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPT 874
Cdd:COG0085  808 VLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYM 887

                        970       980       990      1000
                 ....*....|....*....|....*....|....*....|
gi 6606089   875 YYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:COG0085  888 YYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-247 3.03e-99

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: 315.86  E-value: 3.03e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089      1 SEKVLIAQERMATNHVYVFAKAQPSPINFLAEIRSAVEKGGKTISQFQVKMFHRNQERSVSFTtIPYIKVDIPIWVVFRG 80
Cdd:pfam04563 146 SEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLEYLSNGTIYFK-FPYIKKEIPIVIILRA 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     81 LGVISDRDILEHICYDMQDAQMLEMLKPCIDDGFVI--QDREVALDFIGNRGTT---TGLSRERRIRYAQEILQKEMLPH 155
Cdd:pfam04563 225 LGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQKEVLPH 304

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    156 VSMAEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQKCVETHKEFN 235
Cdd:pfam04563 305 LGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLM 384

                         250
                  ....*....|..
gi 6606089    236 LALAVKHQTITN 247
Cdd:pfam04563 385 LQLLVNAKPITS 396
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-356 1.19e-73

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 250.64  E-value: 1.19e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     1 SEKVLIAQERMATNHVYVfakaqpspinflaeirsavEKGGKTISQFQV-KMFHRNQ--------ERS------VSFtti 65
Cdd:PRK09606 153 SERVLMTLEDLAPNKILV-------------------EKDERYGDRIEVaKVFSQRRgyralvtvERNrdglleVSF--- 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    66 PYIKVDIPIWVVFRGLGVISDRDILEHICYD----MQDAQMLEMLKpciddgfvIQDREVALDFIGNRGTTtGLSRERRI 141
Cdd:PRK09606 211 PSVPGSIPFVILMRALGLETDEEIVEAVSDDpeivKFMLENLEEAE--------VDTQEEALEYIGKRVAP-GQTKEYRI 281

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   142 RYAQEILQKEMLPHVSMAEGSESKKAYFFGYMIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVY 221
Cdd:PRK09606 282 KRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVK 361

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089   222 RYLQKCVETHKEFNLALAVKHQTITNGLKYSLATGNWgdqkksMSSKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIA 301
Cdd:PRK09606 362 YQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHF 435

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 6606089   302 KPRQLHNTHWGMVCPAETPEGQACGLVKNLALMSCISVGSYSAPVIEFLEEWGLE 356
Cdd:PRK09606 436 EARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 186-914 1.16e-58

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: 218.38  E-value: 1.16e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     186 ELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLqkcveTHKEFNlalAVKHQTITNGLKYSLATgnwgdqkKSM 265
Cdd:TIGR02013  317 EIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM-----STQDTD---TLTPQDLINAKPISAAI-------KEF 381

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     266 SSKAGVSQVLNRYTYASTLSHLRRCNT--P--LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLAlmscisvgS 341
Cdd:TIGR02013  382 FGSSQLSQFMDQTNPLAELTHKRRLSAlgPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS--------T 453

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     342 YsAPVIE--FLEewglesleenahstSPCTKVfVNGVwmgvhrdpanlvktikklrrkddispevsvvrdirekelriyt 419
Cdd:TIGR02013  454 Y-ARVNEygFIE--------------TPYRKV-KDGK------------------------------------------- 474

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     420 dagrvcrplfivenqqlllgkrhirwlnsGSDDEGNEYkweqlikggvielLDAEEEETVMISM--TPEDlENSRLQAAG 497
Cdd:TIGR02013  475 -----------------------------VVVTDEIDY-------------LTADEEDNYVIAQanAPLD-ENGRFVEDL 511

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     498 VdPHANDGDFDPAARlkagthaHTWTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMAKQAM--------------- 562
Cdd:TIGR02013  512 V-VARYRGEITLVSP-------DQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgme 583

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     563 -------------------------GIYLTNFLIRMDTMANILYYP--------------QKP-------------LATT 590
Cdd:TIGR02013  584 akvardsgavivakrggvveyvdakRIVIRYDEDEEEPDGGIDIYRllkyqrsnqdtcinQRPivsvgdrveagdvLADG 663

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     591 RSMEylkFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYyrsymdlekksgiqqLEEFEKPTRDTTLRMK 670
Cdd:TIGR02013  664 PSTD---LGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIH---------------IEEYEVEARDTKLGPE 725

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     671 HGTYD----------KLEDDGLIAPGTGVRGEDIIIGKTAP---IPPDSEE------LGQRTRThtRRDVSTPLKSTEIG 731
Cdd:TIGR02013  726 EITRDipnvseealrNLDENGIVRIGAEVKAGDILVGKVTPkgeTELTPEEkllraiFGEKARD--VRDTSLRVPPGVEG 803

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     732 IVDQVLITTNSEGQ-------KFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVPDLIINPHAIPSR 804
Cdd:TIGR02013  804 TVIDVKVFSREQGDelppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     805 MTIGHLVECLLSKVATLIGNEGD--ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKH 881
Cdd:TIGR02013  884 MNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHH 963

                          810       820       830
                   ....*....|....*....|....*....|...
gi 6606089     882 MVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:TIGR02013  964 LVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 996
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-199 4.11e-48

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: 169.06  E-value: 4.11e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     12 ATNHVYVFAKAQPSPINF-----LAEIRSAV---EKGGKTIsqfqvkMFHRnqersvsfttiPYIKVDIPIWVVFRGLGV 83
Cdd:pfam04561   1 RSNGIYVEKELDKNGIIAtytssLISNRGSWlklEIDGKTL------IWSR-----------PSKKRKIPIVIFLKALGL 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089     84 ISDRDILEHICYDMQDAQMLEMLKPCIDDGFVIQDREVALDFIGNrGTTTGLSRERRIRYAQEILQK-----EMLPHVSM 158
Cdd:pfam04561  64 VSDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGL 142

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 6606089    159 AEGSESK--KAYFFGYMIHRLLLAALERRELDDRDHFGKKRLD 199
Cdd:pfam04561 143 NEPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 174-914 1.19e-46

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 181.44  E-value: 1.19e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    174 IHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRM----LFRKLTKDVYrylqKCV-ETHKEFNLalavkhqtITNG 248
Cdd:CHL00207  284 IDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIglkrLERILRNRMT----ICDiDSLSKFNL--------INPK 351

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    249 LKYSLATGNWGdqkksmSSKagVSQVLNRYTYASTLSHLRRCNTpLGREG----KIAKP-RQLHNTHWGMVCPAETPEGQ 323
Cdd:CHL00207  352 PLIALIREFFG------SSQ--LSQYMDQTNPLSELTHKRRISI-LGPGGldkdRISFAvRDIHPSHYGRICPIETPEGP 422

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    324 ACGLVKNLAlmSCISVGSYSapvieFLEewglesleenahstSPCTKVFVNGVWmgVHRDPANLVKTIKKLRRkddISPE 403
Cdd:CHL00207  423 NCGLIGSLA--TNARINKFG-----FIE--------------TPFYKVINGKVK--KFGNPIYLTADSEDLYR---IAPN 476

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    404 vsvvrDIREKElriytdagrvcrplfivenqqlllgkrhirwlnsgsddegneykwEQLIKGGVIELLDAEEEETVMISM 483
Cdd:CHL00207  477 -----DINLNK---------------------------------------------NNYFKKNIIPVRYKQEFKTVNPSK 506

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    484 tpedlensrlqaagVDPHAndgdfdpaarlkagthahtwthceIHPSMILGICASIIPFPDHNQSPRNTYQSAMAKQAM- 562
Cdd:CHL00207  507 --------------VDFIA------------------------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVp 548

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    563 ------------------------------GI--YLTNFLIRMDTMAN--ILYYPQK-------------P--------- 586
Cdd:CHL00207  549 llypekpivgtgyekqialdsgmtiislteGIvvSVSAYKIIIQDDNNryIHYYLQKyqrsnqntcinyrPivwvgekin 628

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    587 ----LATTRSMeylKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYmDLEkksgIQQLEEF-EKP 661
Cdd:CHL00207  629 igqiLADGSDI---DNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-EIE----LRQTKLGsEEI 700

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    662 TRDTTLRMKHGTYdKLEDDGLIAPGTGVRGEDIIIGKTAPIP----PDSEELGQRTRTHTRRDV---STPLKSTEIGIVD 734
Cdd:CHL00207  701 TRNIPNVSEYSLK-NLDENGIISIGSKVLAGDILVGKITPKGesdqLPEGKLLRAIFGEKAKDVkdtSLRMPNGGYGRVI 779

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    735 QVLITTNSEGQKF-------VKVRVRATRIPQIGDKFASCHGQKGTVG-ITYRQeDMPFTAEGIVPDLIINPHAIPSRMT 806
Cdd:CHL00207  780 KVEIFSRSKGDELkfgyylkIRVFIAQIRKIQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMN 858

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    807 IGHLVECLLSKVATLIGNEGDATPFTDL-TVESVSTFLRQKGYQSR--------------GLEVMYHGHTGRKLQAQIYL 871
Cdd:CHL00207  859 VGQLFECLLGLAGDNLNKRFKILPFDEMyGSEYSRILINNKLNQASiknneywlfnsyhpGKMVLRDGRTGYKFKNPVTV 938

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|...
gi 6606089    872 GPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:CHL00207  939 GIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRF 981
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 600-914 1.18e-41

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 165.66  E-value: 1.18e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    600 ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYyrsymdlekksgiqqLEEFEKPTRDTtlrmKHG----TYD 675
Cdd:PRK00405  712 ELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIH---------------IEEYEIEARDT----KLGpeeiTRD 772

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    676 ----------KLEDDGLIAPGTGVRGEDIIIGKTAP---IPPDSEE------LGQRTRTHtrRDVSTPLKSTEIGIV-DQ 735
Cdd:PRK00405  773 ipnvseealrNLDESGIVRIGAEVKPGDILVGKVTPkgeTELTPEEkllraiFGEKARDV--KDTSLRVPHGEEGTViDV 850

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    736 VLITTNSEG-------QKFVKVRVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIG 808
Cdd:PRK00405  851 KVFTRIEQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIG 930

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    809 HLVECLLSKVATLIGNEGdATP-FTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKHMVDDKI 887
Cdd:PRK00405  931 QILETHLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKI 1009

                         330       340
                  ....*....|....*....|....*..
gi 6606089    888 HSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:PRK00405 1010 HARSTGPYSLVTQQPLGGKAQFGGQRF 1036
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 371-432 7.31e-34

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: 123.63  E-value: 7.31e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6606089    371 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRIYTDAGRVCRPLFIVE 432
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
rpoB CHL00001
RNA polymerase beta subunit
 600-913 8.16e-32

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 134.26  E-value: 8.16e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    600 ELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYmDLEKKSGIQQLEEFEK--PTRDTTLrMKHgtydkL 677
Cdd:CHL00001  648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERITKeiPHLEAHL-LRN-----L 720

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    678 EDDGLIAPGTGVRGEDIIIGKTAP-IPPDSEE----------LGQRTRThTRrdvSTPLKsTEIG----IVDQVLIT--- 739
Cdd:CHL00001  721 DKNGIVMLGSWVETGDILVGKLTPqEAEESSYapegrllraiFGIQVST-SK---ETCLK-LPIGgrgrVIDVRWIQkkg 795

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    740 TNSEGQKFVKVRVRATRIPQIGDKFASCHGQKGTVG-ITYRQeDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKV 818
Cdd:CHL00001  796 GSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLA 874

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    819 ATLIGNEGDATPFTDLTVESVSTFL---------RQKGY------QSRGLEVMYHGHTGRKLQAQIYLGPTYYQRLKHMV 883
Cdd:CHL00001  875 GDLLNRHYRIAPFDERYEQEASRKLvfselyeasKQTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQV 954

                         330       340       350
                  ....*....|....*....|....*....|
gi 6606089    884 DDKIHSRARGPVQILTRQPVEGRSRDGGLR 913
Cdd:CHL00001  955 DDKIHARSSGPYALVTQQPLRGRSKQGGQR 984
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 273-335 2.37e-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: 114.16  E-value: 2.37e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6606089    273 QVLNRYTYASTLSHLRRCNTP---LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMS 335
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPrggLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
186-914 4.53e-30

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 129.27  E-value: 4.53e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    186 ELDDRDHFGKKRLDLAGPLLAN-----LFRMlfRKLTKDVYRYLQKCVETHKEFNLalaVKHQTITNGLKYSLATGNwgd 260
Cdd:PRK09603  453 KIDDRDHLGNRRIRAVGELLANelhsgLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ--- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    261 qkksmsskagVSQVLNRYTYASTLSHLRRCNTpLGrEGKIAK------PRQLHNTHWGMVCPAETPEGQACGLVKNLALM 334
Cdd:PRK09603  525 ----------LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLSTF 592

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    335 SCISVgsysapvIEFLEewglesleenahstSPCTKVfVNGVwmgvhrdpanlvktikklrrkddISPEVSVVRDIREKe 414
Cdd:PRK09603  593 TRVND-------LGFIE--------------APYKKV-VDGK-----------------------VVGETIYLTAIQED- 626

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    415 lriytdaGRVCRPLfivenqqlllgkrhirwlNSGSDDEGNeykweqlIKGgviELLDAEEEETVMISmtpedlENSRLQ 494
Cdd:PRK09603  627 -------SHIIAPA------------------STPIDEEGN-------ILG---DLIETRVEGEIVLN------EKSKVT 665

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    495 AAgvdphandgdfdpaarlkagthahtwthcEIHPSMILGICASIIPFPDHNQSPRNTYQSAMAKQAM------------ 562
Cdd:PRK09603  666 LM-----------------------------DLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgt 716

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    563 ----------------------------GIYLtnfLIRMDTMANILYYP-QKPLATTRSMEY------------------ 595
Cdd:PRK09603  717 giekiiardswgaikanragvvekidskNIYI---LGEGKEEAYIDAYSlQKNLRTNQNTSFnqvpivkvgdkveagqii 793

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    596 -----LKFRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRS--IYYRSYMDLEKKSGIqqlEEFekpTRDTTlR 668
Cdd:PRK09603  794 adgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSthIYEKEVDARELKHGV---EEF---TADIP-D 866

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    669 MKHGTYDKLEDDGLIAPGTGVRGEDIIIGKTAP------------------------------IPPDSE----------- 707
Cdd:PRK09603  867 VKEEALAHLDESGIVKVGTYVSAGMILVGKTSPkgeikstpeerllraifgdkaghvvnkslyCPPSLEgtvidvkvftk 946

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    708 ---ELGQRTRT-------------HTR----------------------RDVSTPLKS---------TEIGIVDQVLITT 740
Cdd:PRK09603  947 kgyEKDARVLSayeeekakldmehFDRltmlnreellrvssllsqaileEPFSHNGKDykegdqipkEEIASINRFTLAS 1026

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    741 -----NSEGQ---------------------------------------KFVKVRVRATRIPQIGDKFASCHGQKGTVGI 776
Cdd:PRK09603 1027 lvkkySKEVQnhyeitknnfleqkkvlgeeheeklsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSN 1106

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    777 TYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLIG-----------------------------NEGD 827
Cdd:PRK09603 1107 IVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGkqiasmledktkdfakelrakmleianaiNEKD 1186

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    828 ----------------------------ATP-FTDLTVESVSTFLRQKGYQSRGLEVMYHGHTGRKLQAQIYLGPTYYQR 878
Cdd:PRK09603 1187 pltihalencsdeelleyakdwskgvkmAIPvFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIK 1266

                         970       980       990
                  ....*....|....*....|....*....|....*.
gi 6606089    879 LKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:PRK09603 1267 LHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRF 1302
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 459-529 4.31e-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: 92.99  E-value: 4.31e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6606089    459 WEQLIKGGVIELLDAEEEETVMISMTPEDLENSRLQAagvdphandgdfdpaarlKAGTHAHTWTHCEIHP 529
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCEIHP 53
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
173-914 1.24e-19

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 95.46  E-value: 1.24e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    173 MIHRLLLAALERRELDDRDHFGKKRLDLAGPLLANLFRMLFRKLTKDVYRYLQkcVETHKEFNLALAVKHQTITNGLKys 252
Cdd:PRK14844  449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMS--TSSLDKVSPSDFINPKVLTNVLR-- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    253 latgnwgdqkkSMSSKAGVSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLV 328
Cdd:PRK14844  525 -----------DFFNSSQLSQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLI 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    329 KNLALMSciSVGSYSapvieFLEewglesleenahstSPCTKVfVNGVwmgvhrdpanlvktikklrrkddISPEVSVVR 408
Cdd:PRK14844  594 NSLAIYA--RINKYG-----FIE--------------SPYRKV-VNRV-----------------------VTDQIEYLS 628

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    409 DIREKELRIYTDAGRvcrplfIVENQQLLLGKRHIRWLNSGSDDEGNEYKWEQLIKGGVIELLDAeeeetvMISMTPEDL 488
Cdd:PRK14844  629 AIDEGLYYIADTSAK------LDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAAS------LIPFLENDD 696

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    489 ENSRLQAAGVDPHANDgDFDPAARLkAGTHAHTWThCEIHPSMILGICASIIPFPDHNQSPRNTY-QSAMAKQAMGIYLT 567
Cdd:PRK14844  697 ANRALMGSNMQRQAVP-LLKPTAPL-VATGMESFV-ASGSGAVVLAKRDGIVDSSDSNSIVIRAFdKERVNYLDVDIYHL 773

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    568 NFLIRMDTMANIlyyPQKPLatTRSMEYLK------------FRELPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLF 635
Cdd:PRK14844  774 RKFQRSNHNTCI---NQKPL--VCVGDYVKegdviadgpainSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLF 848

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    636 RSIYyrsymdlekksgiqqLEEFEKPTRDTTL------RMKHGTYDK----LEDDGLIAPGTGVRGEDIIIGKTAP---- 701
Cdd:PRK14844  849 TSIH---------------IEEFECVVHDTPLgsekitRAIPGVNEEnlyhLDDSGIVKIGTRVGPGYILVGKVTPkpsl 913

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    702 -IPPDSEEL----GQRT---------------------RTHTRRDVSTP-----LKSTE-----------IGIVDQ---- 735
Cdd:PRK14844  914 sLPPETKLLmtifGEKSfdcadsslytspdvegtvidvQVFTRRGVEENerallIKQKEindfekerdyiINVTSEyfyd 993

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    736 ----VLITTNSEGQK-------------------------------------------------------------FVKV 750
Cdd:PRK14844  994 elkkLLINSGSQDREkfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydlpqgvsmSVKV 1073

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    751 RVRATRIPQIGDKFASCHGQKGTVGITYRQEDMPFTAEGIVPDLIINPHAIPSRMTIGHLVEC--------LLSKVATLI 822
Cdd:PRK14844 1074 FIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILEThvgwackkLGEKVGNIL 1153

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    823 G----------------NEGDATPF------------------------------------------------------- 831
Cdd:PRK14844 1154 DeinkiksafckgirslNDDNFTKFaaayldnkkienidddeitasvlntpnknalndelnelvenylnscksaysnlrn 1233

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6606089    832 ---------TDLTV-----------------------------------ESVSTFLRQKGYQSRGLEVMYHGHTGRKLQA 867
Cdd:PRK14844 1234 flievyscgSNVSIcnnirdisdnnliefarklrdgipvaapvfegpkdEQIAKLFELAGLDNSGQAVLYDGCSGEKFDR 1313

                         970       980       990      1000
                  ....*....|....*....|....*....|....*....|....*..
gi 6606089    868 QIYLGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRF 914
Cdd:PRK14844 1314 KVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRF 1360
 
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.
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