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Conserved domains on  [gi|45545355|gb|AAS67525|]
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DNA-dependent RNA polymerase II second largest subunit, partial [Ustilago maydis]

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

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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: 880.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355     1 SEKVLIAQERMAANHVYVFSKAPPAPVTFLAEIRSAVeKGGKTISTMqvklfsrnkEKTANNTIRATLPYIRNDIPIVIV 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYRAQVTV---------ERRKDGTIYVSFPAVPGKIPFVIL 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    81 FRALGIVPDREVLQHIcydFNDTPMLEMLKPCIEEAF-VIQDRDVALDFIGRRgTTTGLSRAKRTVYAQEILQKEMLPHI 159
Cdd:PRK08565  218 MRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHL 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   160 STSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHI 239
Cdd:PRK08565  294 GTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   240 QAAVKSSTITNGLRYSLATGNWGdqkkamQAKAGVSQVLNRFAFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCP 319
Cdd:PRK08565  374 RAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICP 447

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   320 AETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHA-KATKIFVNGVWMGTHDDPGQLVDTLRDLR 398
Cdd:PRK08565  448 FETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYiSWSRVYLNGRLIGYHPDGEELAEKIRELR 527

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   399 RKDDISHEVSV--VRDIRERELRIYTDASRVLRPVFIVNphDMSLLIKKRHVEMIgqpipETGEeFRWTHLVQEGVIEYL 476
Cdd:PRK08565  528 RSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE--NGKPKLTREHVEKL-----KKGE-LTFDDLVKMGVIEYL 599

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   477 DAEEEESVLICMSTTDLeqSREYkarngqinlnsadpsarlksvhtiapdtwTHCEIHPAMVLGICASIVPFPDHNQSPR 556
Cdd:PRK08565  600 DAEEEENAYVALDPEDL--TPEH-----------------------------THLEIWPPAILGITASIIPYPEHNQSPR 648

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   557 NVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSI 636
Cdd:PRK08565  649 NTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASI 728

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   637 DRGLFRSMYYRGYMAEEKKVGVMQLEEFEKPhrDTTIRMKHG--TYDKIDADGLCAPGTRVSGDDVIIGKTAPlPPDSEE 714
Cdd:PRK08565  729 ERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEE 805

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   715 L-GMRSKLHTKKDASVSLKSTENGIIDQVLVTTNSHGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSA 793
Cdd:PRK08565  806 LeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTE 885

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   794 EGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQA 873
Cdd:PRK08565  886 DGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKA 965

                         890
                  ....*....|....
gi 45545355   874 QVYLGPTYYQRLKH 887
Cdd:PRK08565  966 PIFIGVVYYQKLHH 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: 880.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355     1 SEKVLIAQERMAANHVYVFSKAPPAPVTFLAEIRSAVeKGGKTISTMqvklfsrnkEKTANNTIRATLPYIRNDIPIVIV 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYRAQVTV---------ERRKDGTIYVSFPAVPGKIPFVIL 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    81 FRALGIVPDREVLQHIcydFNDTPMLEMLKPCIEEAF-VIQDRDVALDFIGRRgTTTGLSRAKRTVYAQEILQKEMLPHI 159
Cdd:PRK08565  218 MRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHL 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   160 STSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHI 239
Cdd:PRK08565  294 GTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   240 QAAVKSSTITNGLRYSLATGNWGdqkkamQAKAGVSQVLNRFAFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCP 319
Cdd:PRK08565  374 RAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICP 447

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   320 AETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHA-KATKIFVNGVWMGTHDDPGQLVDTLRDLR 398
Cdd:PRK08565  448 FETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYiSWSRVYLNGRLIGYHPDGEELAEKIRELR 527

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   399 RKDDISHEVSV--VRDIRERELRIYTDASRVLRPVFIVNphDMSLLIKKRHVEMIgqpipETGEeFRWTHLVQEGVIEYL 476
Cdd:PRK08565  528 RSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE--NGKPKLTREHVEKL-----KKGE-LTFDDLVKMGVIEYL 599

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   477 DAEEEESVLICMSTTDLeqSREYkarngqinlnsadpsarlksvhtiapdtwTHCEIHPAMVLGICASIVPFPDHNQSPR 556
Cdd:PRK08565  600 DAEEEENAYVALDPEDL--TPEH-----------------------------THLEIWPPAILGITASIIPYPEHNQSPR 648

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   557 NVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSI 636
Cdd:PRK08565  649 NTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASI 728

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   637 DRGLFRSMYYRGYMAEEKKVGVMQLEEFEKPhrDTTIRMKHG--TYDKIDADGLCAPGTRVSGDDVIIGKTAPlPPDSEE 714
Cdd:PRK08565  729 ERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEE 805

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   715 L-GMRSKLHTKKDASVSLKSTENGIIDQVLVTTNSHGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSA 793
Cdd:PRK08565  806 LeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTE 885

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   794 EGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQA 873
Cdd:PRK08565  886 DGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKA 965

                         890
                  ....*....|....
gi 45545355   874 QVYLGPTYYQRLKH 887
Cdd:PRK08565  966 PIFIGVVYYQKLHH 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: 772.51  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   1 SEKVLIAQERMAANHVYVFSKAppapVTFLAEIRSAVEKGGKTISTMQVKLfsrnkeKTANNTIRATLPYIRndipiviv 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVEDSK----GKRIYTKTSIPSYSPYRGSWLEVKS------DKKKDRIYVRIDLKR-------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  81 fralgivpdrevlqhicydfndtpmlemlkpcieeafviqdRDVALDFIGRRGtttglsrakrtvyaqeilqkemlphis 160
Cdd:cd00653 199 -----------------------------------------QEEALKYIGKRF--------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 161 tsegsntkkaYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHIQ 240
Cdd:cd00653 211 ----------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQ 280

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 241 AAVKSSTITNGLRYSLATGNWGDQKKAMQaKAGVSQVLNRFAFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGMVCP 319
Cdd:cd00653 281 LLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICP 359

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 320 AETPEGQACGLVKNLSLMATVtvgtpsapivefleefgldslvdmqlahakatkifvNGvwmgthddpgqlvdtlrdlrr 399
Cdd:cd00653 360 IETPEGENCGLVKNLALMARI------------------------------------SG--------------------- 382

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 400 kddishevsvvrdirerelriytdasRVLRPVFIVnphdmsllikkrhvemigqpipetgeefrwthlvqegvieyldae 479
Cdd:cd00653 383 --------------------------RIERPYRIV--------------------------------------------- 391

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 480 eEESVlicmsttdleqsreykarngqinlnsadpsarlksvhtiapdtwTHCEIHPAMVLGICASIVPFPDHNQSPRNVY 559
Cdd:cd00653 392 -EKEV--------------------------------------------THIEISPSQILSVAASLIPFPEHNQSPRNLY 426

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 560 QSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 639
Cdd:cd00653 427 QSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRG 506

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 640 LFRSMYYRGYMAEEKKVGVMQLEEFekphRDTTIRMKHGTYDKIDADGLCAPGTRVSGDDVIIGKTAPLPPDSEELGMRS 719
Cdd:cd00653 507 FFRSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGE 582

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 720 KLHTKKDASVSLKSTENGIIDQVLVTT---NSHGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGV 796
Cdd:cd00653 583 KARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGI 662

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 797 TPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQAQVY 876
Cdd:cd00653 663 PPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIF 742

                       890
                ....*....|.
gi 45545355 877 LGPTYYQRLKH 887
Cdd:cd00653 743 VGPVYYQRLKH 753
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 374-887 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: 574.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   374 IFVNGVWMGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELRIYTDASRVLRPVFIVNphDMSLLIKKRHVEMIGQ 453
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVE--NGKPKLTREHVEKLKE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   454 pipetgEEFRWTHLVQEGVIEYLDAEEEESVLICMSTTDLeqSREYkarngqinlnsadpsarlksvhtiapdtwTHCEI 533
Cdd:TIGR03670  79 ------GELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL--TPEH-----------------------------THLEI 121

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   534 HPAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNA 613
Cdd:TIGR03670 122 DPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNF 201

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   614 IVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEKKVGVMQLEEFEKPhrDTTIRMKHG--TYDKIDADGLCAP 691
Cdd:TIGR03670 202 VVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLDEDGIVYP 279

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   692 GTRVSGDDVIIGKTAPlPPDSEELG-MRSKLHTKKDASVSLKSTENGIIDQVLVTTNSHGNKFVKVRVRSTRVPQTGDKF 770
Cdd:TIGR03670 280 EVEVKGGDVLIGKTSP-PRFLEELReFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKF 358

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   771 ASRHGQKGTIGITYRQEDMPFSAEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILR 850
Cdd:TIGR03670 359 ASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELL 438

                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 45545355   851 GLGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKH 887
Cdd:TIGR03670 439 KLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 542-887 3.53e-159

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: 470.09  E-value: 3.53e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   542 CASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYS 621
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   622 GYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEKKVGvmQLEE-FEKPhrdttIRMKHGTYDKIDADGLCAPGTRVSGDDV 700
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG--PIEEiTRDI-----PNVSEEALKKLDEDGIVRVGAEVKPGDI 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   701 IIGKTAPlPPDSEELGMR--SKLHTKKDASVSLKSTENGIIDQVLV-TTNSHGNKFVKVRVRSTRVPQTGDKFASRHGQK 777
Cdd:pfam00562 154 LVGKVGP-TELTKLLRAIfgEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   778 GTIGITYRQEDMPFSAEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTE--LTVEAVSSILRGLGYQ 855
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGasTEVEDIGELLEKAGYN 312

                         330       340       350
                  ....*....|....*....|....*....|..
gi 45545355   856 SRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKH 887
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-887 7.04e-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: 477.68  E-value: 7.04e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    1 SEKVLIAQERMAANHVYVFSKAPPAPVTFLAEIRSAveKGGKTIstmqvklFSRNKektaNNTIRATLPYIRnDIPIVIV 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE-------FETDK----DGTIYVRIDRKR-KIPVTVL 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   81 FRALGIVPDREVLQHicydFNDTPMLEMLKPCIEEAfVIQDRDVALDFIGRRGTTTGLSRAKRtvyAQEIL-------QK 153
Cdd:COG0085  183 LRALGLETDEEILEA----FGDDPIQEYILATLEKD-NTKTQEEALLEIYRKLRPGEPPTIER---AEQLLdnlffdpKR 254

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  154 EMLPHI-----------STSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRD 222
Cdd:COG0085  255 YDLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERV 334

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  223 VYRHLQKcvEEHREFHIQAAVKSSTITNGLRYSLATGnwgdqkkamqakaGVSQVLNRFAFASTLSHLRRTNT----PIG 298
Cdd:COG0085  335 VRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLS 399

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  299 RDgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMATVTvgtpsapivefleEFGldslvdmqlahakatki 374
Cdd:COG0085  400 RE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN-------------EYG----------------- 445

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  375 fvngvwmgthddpgqlvdtlrdlrrkddishevsvvrdirerelriytdasRVLRPVFIVnphdmslliKKRHVemigqp 454
Cdd:COG0085  446 ---------------------------------------------------FIETPYRKV---------ENGKV------ 459

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  455 ipeTGEefrwthlvqegvIEYLDAEEEESVLICMSTTDLEQsreykarNGQInLNSADPSARLKSVHTIAPDTWTHCEIH 534
Cdd:COG0085  460 ---TDE------------IEYLTADEEENYYIAQANAPLDE-------DGNF-LEERVLVRYRGEEVLVPPEEVDYMDVS 516

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  535 PAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNiqsradsmAHVLLYP--------------QKPLgtTRSME 600
Cdd:COG0085  517 PKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPI--VRVGD 586

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  601 HLR------------FRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEK--KVGvmqLEE--F 664
Cdd:COG0085  587 RVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARdtKLG---PEEitR 663

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  665 EKPHrdttirmkHG--TYDKIDADGLCAPGTRVSGDDVIIGKTAP-----LPPdsEELGMRS----KLHTKKDASVSLKS 733
Cdd:COG0085  664 DIPN--------VSeeALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTP--EERLLRAifgeKAREVRDTSLRVPH 733

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  734 TENGIIDQVLVTTNSHG-------NKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGVTPDIIINPHA 806
Cdd:COG0085  734 GEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLG 813

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  807 IPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLK 886
Cdd:COG0085  814 VPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLH 893


                 .
gi 45545355  887 H 887
Cdd:COG0085  894 H 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: 880.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355     1 SEKVLIAQERMAANHVYVFSKAPPAPVTFLAEIRSAVeKGGKTISTMqvklfsrnkEKTANNTIRATLPYIRNDIPIVIV 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYRAQVTV---------ERRKDGTIYVSFPAVPGKIPFVIL 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    81 FRALGIVPDREVLQHIcydFNDTPMLEMLKPCIEEAF-VIQDRDVALDFIGRRgTTTGLSRAKRTVYAQEILQKEMLPHI 159
Cdd:PRK08565  218 MRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHL 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   160 STSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHI 239
Cdd:PRK08565  294 GTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   240 QAAVKSSTITNGLRYSLATGNWGdqkkamQAKAGVSQVLNRFAFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGMVCP 319
Cdd:PRK08565  374 RAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICP 447

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   320 AETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGLDSLVDMQLAHA-KATKIFVNGVWMGTHDDPGQLVDTLRDLR 398
Cdd:PRK08565  448 FETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYiSWSRVYLNGRLIGYHPDGEELAEKIRELR 527

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   399 RKDDISHEVSV--VRDIRERELRIYTDASRVLRPVFIVNphDMSLLIKKRHVEMIgqpipETGEeFRWTHLVQEGVIEYL 476
Cdd:PRK08565  528 RSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE--NGKPKLTREHVEKL-----KKGE-LTFDDLVKMGVIEYL 599

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   477 DAEEEESVLICMSTTDLeqSREYkarngqinlnsadpsarlksvhtiapdtwTHCEIHPAMVLGICASIVPFPDHNQSPR 556
Cdd:PRK08565  600 DAEEEENAYVALDPEDL--TPEH-----------------------------THLEIWPPAILGITASIIPYPEHNQSPR 648

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   557 NVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSI 636
Cdd:PRK08565  649 NTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASI 728

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   637 DRGLFRSMYYRGYMAEEKKVGVMQLEEFEKPhrDTTIRMKHG--TYDKIDADGLCAPGTRVSGDDVIIGKTAPlPPDSEE 714
Cdd:PRK08565  729 ERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEE 805

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   715 L-GMRSKLHTKKDASVSLKSTENGIIDQVLVTTNSHGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSA 793
Cdd:PRK08565  806 LeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTE 885

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   794 EGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQA 873
Cdd:PRK08565  886 DGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKA 965

                         890
                  ....*....|....
gi 45545355   874 QVYLGPTYYQRLKH 887
Cdd:PRK08565  966 PIFIGVVYYQKLHH 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: 772.51  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   1 SEKVLIAQERMAANHVYVFSKAppapVTFLAEIRSAVEKGGKTISTMQVKLfsrnkeKTANNTIRATLPYIRndipiviv 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVEDSK----GKRIYTKTSIPSYSPYRGSWLEVKS------DKKKDRIYVRIDLKR-------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  81 fralgivpdrevlqhicydfndtpmlemlkpcieeafviqdRDVALDFIGRRGtttglsrakrtvyaqeilqkemlphis 160
Cdd:cd00653 199 -----------------------------------------QEEALKYIGKRF--------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 161 tsegsntkkaYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHREFHIQ 240
Cdd:cd00653 211 ----------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQ 280

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 241 AAVKSSTITNGLRYSLATGNWGDQKKAMQaKAGVSQVLNRFAFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGMVCP 319
Cdd:cd00653 281 LLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICP 359

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 320 AETPEGQACGLVKNLSLMATVtvgtpsapivefleefgldslvdmqlahakatkifvNGvwmgthddpgqlvdtlrdlrr 399
Cdd:cd00653 360 IETPEGENCGLVKNLALMARI------------------------------------SG--------------------- 382

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 400 kddishevsvvrdirerelriytdasRVLRPVFIVnphdmsllikkrhvemigqpipetgeefrwthlvqegvieyldae 479
Cdd:cd00653 383 --------------------------RIERPYRIV--------------------------------------------- 391

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 480 eEESVlicmsttdleqsreykarngqinlnsadpsarlksvhtiapdtwTHCEIHPAMVLGICASIVPFPDHNQSPRNVY 559
Cdd:cd00653 392 -EKEV--------------------------------------------THIEISPSQILSVAASLIPFPEHNQSPRNLY 426

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 560 QSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRG 639
Cdd:cd00653 427 QSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRG 506

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 640 LFRSMYYRGYMAEEKKVGVMQLEEFekphRDTTIRMKHGTYDKIDADGLCAPGTRVSGDDVIIGKTAPLPPDSEELGMRS 719
Cdd:cd00653 507 FFRSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGE 582

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 720 KLHTKKDASVSLKSTENGIIDQVLVTT---NSHGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGV 796
Cdd:cd00653 583 KARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGI 662

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355 797 TPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQAQVY 876
Cdd:cd00653 663 PPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIF 742

                       890
                ....*....|.
gi 45545355 877 LGPTYYQRLKH 887
Cdd:cd00653 743 VGPVYYQRLKH 753
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 374-887 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: 574.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   374 IFVNGVWMGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELRIYTDASRVLRPVFIVNphDMSLLIKKRHVEMIGQ 453
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVE--NGKPKLTREHVEKLKE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   454 pipetgEEFRWTHLVQEGVIEYLDAEEEESVLICMSTTDLeqSREYkarngqinlnsadpsarlksvhtiapdtwTHCEI 533
Cdd:TIGR03670  79 ------GELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL--TPEH-----------------------------THLEI 121

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   534 HPAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNA 613
Cdd:TIGR03670 122 DPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNF 201

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   614 IVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEKKVGVMQLEEFEKPhrDTTIRMKHG--TYDKIDADGLCAP 691
Cdd:TIGR03670 202 VVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLDEDGIVYP 279

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   692 GTRVSGDDVIIGKTAPlPPDSEELG-MRSKLHTKKDASVSLKSTENGIIDQVLVTTNSHGNKFVKVRVRSTRVPQTGDKF 770
Cdd:TIGR03670 280 EVEVKGGDVLIGKTSP-PRFLEELReFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKF 358

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   771 ASRHGQKGTIGITYRQEDMPFSAEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILR 850
Cdd:TIGR03670 359 ASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELL 438

                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 45545355   851 GLGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKH 887
Cdd:TIGR03670 439 KLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 370-887 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 548.41  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  370 KATKIFVNGVWMGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELRIYTDASRVLRPVFIVNphDMSLLIKKRHVE 449
Cdd:PRK07225   3 RKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVE--NGEPLLTEEHIE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  450 MIgqpipETGEeFRWTHLVQEGVIEYLDAEEEESVLICMSTTDLEqsreykarngqinlnsadpsarlksvhtiaPDTwT 529
Cdd:PRK07225  81 KL-----KNGE-LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT------------------------------EEH-T 123

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  530 HCEIHPAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPA 609
Cdd:PRK07225 124 HLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPA 203

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  610 GQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEKKVGVMQLEEFEKPhrDTTIRMKHG--TYDKIDADG 687
Cdd:PRK07225 204 GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIP--DKDVRGYRGeeAYRHLDEDG 281

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  688 LCAPGTRVSGDDVIIGKTAPlP-----PDSEELGMRSKlhtkKDASVSLKSTENGIIDQVLVTTNSHGNKFVKVRVRSTR 762
Cdd:PRK07225 282 LVNPETEVKEGDVLIGKTSP-PrfleePDDFGISPEKR----RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLR 356

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  763 VPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTV 842
Cdd:PRK07225 357 IPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDE 436

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*
gi 45545355  843 EAVSSILRGLGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKH 887
Cdd:PRK07225 437 EDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHH 481
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 542-887 3.53e-159

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: 470.09  E-value: 3.53e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   542 CASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNIQSRADSMAHVLLYPQKPLGTTRSMEHLRFRELPAGQNAIVAIMCYS 621
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   622 GYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEKKVGvmQLEE-FEKPhrdttIRMKHGTYDKIDADGLCAPGTRVSGDDV 700
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG--PIEEiTRDI-----PNVSEEALKKLDEDGIVRVGAEVKPGDI 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   701 IIGKTAPlPPDSEELGMR--SKLHTKKDASVSLKSTENGIIDQVLV-TTNSHGNKFVKVRVRSTRVPQTGDKFASRHGQK 777
Cdd:pfam00562 154 LVGKVGP-TELTKLLRAIfgEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   778 GTIGITYRQEDMPFSAEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTE--LTVEAVSSILRGLGYQ 855
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGasTEVEDIGELLEKAGYN 312

                         330       340       350
                  ....*....|....*....|....*....|..
gi 45545355   856 SRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKH 887
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-887 7.04e-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: 477.68  E-value: 7.04e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    1 SEKVLIAQERMAANHVYVFSKAPPAPVTFLAEIRSAveKGGKTIstmqvklFSRNKektaNNTIRATLPYIRnDIPIVIV 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLE-------FETDK----DGTIYVRIDRKR-KIPVTVL 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   81 FRALGIVPDREVLQHicydFNDTPMLEMLKPCIEEAfVIQDRDVALDFIGRRGTTTGLSRAKRtvyAQEIL-------QK 153
Cdd:COG0085  183 LRALGLETDEEILEA----FGDDPIQEYILATLEKD-NTKTQEEALLEIYRKLRPGEPPTIER---AEQLLdnlffdpKR 254

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  154 EMLPHI-----------STSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRD 222
Cdd:COG0085  255 YDLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERV 334

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  223 VYRHLQKcvEEHREFHIQAAVKSSTITNGLRYSLATGnwgdqkkamqakaGVSQVLNRFAFASTLSHLRRTNT----PIG 298
Cdd:COG0085  335 VRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLS 399

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  299 RDgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMATVTvgtpsapivefleEFGldslvdmqlahakatki 374
Cdd:COG0085  400 RE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN-------------EYG----------------- 445

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  375 fvngvwmgthddpgqlvdtlrdlrrkddishevsvvrdirerelriytdasRVLRPVFIVnphdmslliKKRHVemigqp 454
Cdd:COG0085  446 ---------------------------------------------------FIETPYRKV---------ENGKV------ 459

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  455 ipeTGEefrwthlvqegvIEYLDAEEEESVLICMSTTDLEQsreykarNGQInLNSADPSARLKSVHTIAPDTWTHCEIH 534
Cdd:COG0085  460 ---TDE------------IEYLTADEEENYYIAQANAPLDE-------DGNF-LEERVLVRYRGEEVLVPPEEVDYMDVS 516

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  535 PAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAIGIPISNiqsradsmAHVLLYP--------------QKPLgtTRSME 600
Cdd:COG0085  517 PKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPI--VRVGD 586

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  601 HLR------------FRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEK--KVGvmqLEE--F 664
Cdd:COG0085  587 RVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARdtKLG---PEEitR 663

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  665 EKPHrdttirmkHG--TYDKIDADGLCAPGTRVSGDDVIIGKTAP-----LPPdsEELGMRS----KLHTKKDASVSLKS 733
Cdd:COG0085  664 DIPN--------VSeeALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTP--EERLLRAifgeKAREVRDTSLRVPH 733

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  734 TENGIIDQVLVTTNSHG-------NKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGVTPDIIINPHA 806
Cdd:COG0085  734 GEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLG 813

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  807 IPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLK 886
Cdd:COG0085  814 VPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLH 893


                 .
gi 45545355  887 H 887
Cdd:COG0085  894 H 894
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-250 2.95e-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: 331.27  E-value: 2.95e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355     1 SEKVLIAQERMAANHVYVFSKAPPAPVTFLAEIRSAVEKGGKTISTMQVKLfsrnKEKTANNTIRATLPYIRNDIPIVIV 80
Cdd:pfam04563 146 SEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNV----LEYLSNGTIYFKFPYIKKEIPIVII 221

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    81 FRALGIVPDREVLQHICYDFNDTPMLEMLKPCIEEAFVI--QDRDVALDFIGRRGTT---TGLSRAKRTVYAQEILQKEM 155
Cdd:pfam04563 222 LRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQKEV 301

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   156 LPHISTSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEHR 235
Cdd:pfam04563 302 LPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPD 381

                         250
                  ....*....|....*
gi 45545355   236 EFHIQAAVKSSTITN 250
Cdd:pfam04563 382 DLMLQLLVNAKPITS 396
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-358 8.71e-78

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 261.42  E-value: 8.71e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    1 SEKVLIAQERMAANHVYVfskappapvtflaeirsavEKGGKTISTMQV-KLFSRNK--------EKTANNTIRATLPYI 71
Cdd:PRK09606 153 SERVLMTLEDLAPNKILV-------------------EKDERYGDRIEVaKVFSQRRgyralvtvERNRDGLLEVSFPSV 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   72 RNDIPIVIVFRALGIVPDREVLQHICYDFNdtPMLEMLkPCIEEAfVIQDRDVALDFIGRRGTTtGLSRAKRTVYAQEIL 151
Cdd:PRK09606 214 PGSIPFVILMRALGLETDEEIVEAVSDDPE--IVKFML-ENLEEA-EVDTQEEALEYIGKRVAP-GQTKEYRIKRAEYVI 288

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  152 QKEMLPHISTSEGSNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCV 231
Cdd:PRK09606 289 DRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERAN 368

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355  232 EEHREFHIQAAVKSSTITNGLRYSLATGNWgdqkkaMQAKAGVSQVLNRFAFASTLSHLRRTNTPIGRDGKIAKPRQLHN 311
Cdd:PRK09606 369 MRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHP 442

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*..
gi 45545355  312 THWGMVCPAETPEGQACGLVKNLSLMATVTVGTPSAPIVEFLEEFGL 358
Cdd:PRK09606 443 TQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGV 489
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-202 9.17e-52

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: 179.08  E-value: 9.17e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    12 AANHVYVFSKAPPAPVTflaeirsavekGGKTISTMQVKLfSRNKEKTANNTIRATLPYIRNDIPIVIVFRALGIVPDRE 91
Cdd:pfam04561   1 RSNGIYVEKELDKNGII-----------ATYTSSLISNRG-SWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDRE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    92 VLQHICYDFNDTPMLEMLKPCIEEAFVIQDRDVALDFIGrRGTTTGLSRAKRTVYAQEILQK-----EMLPHISTSEG-- 164
Cdd:pfam04561  69 ILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEPfe 147

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 45545355   165 SNTKKAYFFGYMIHRLLLAALDRREIDDRDHFGKKRID 202
Cdd:pfam04561 148 NERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 189-887 4.64e-49

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: 188.72  E-value: 4.64e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    189 EIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQkcVEEHREFHIQAAVKSSTITNGLRYSLATGNwgdqkkam 268
Cdd:TIGR02013  317 EIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMS--TQDTDTLTPQDLINAKPISAAIKEFFGSSQ-------- 386

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    269 qakagVSQVLNRFAFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMATVTvgt 344
Cdd:TIGR02013  387 -----LSQFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN--- 458

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    345 psapivefleEFGldslvdmqlahakatkifvngvwmgthddpgqlvdtlrdlrrkddishevsvvrdirerelriytda 424
Cdd:TIGR02013  459 ----------EYG------------------------------------------------------------------- 461

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    425 srvlrpvFIVNPHdmsllikkRHVEmigqpiPETGeefrwthlVQEGVIEYLDAEEEESVLICMSTTDLEQsreykarNG 504
Cdd:TIGR02013  462 -------FIETPY--------RKVK------DGKV--------VVTDEIDYLTADEEDNYVIAQANAPLDE-------NG 505

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    505 QINLNSAdpSARLKS-VHTIAPDTWTHCEIHPAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAIGI-----PI------ 572
Cdd:TIGR02013  506 RFVEDLV--VARYRGeITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLlrseaPLvgtgme 583

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    573 ------------------------SNIQSRADS-----MAHVLLYP--------------QKP-------------LGTT 596
Cdd:TIGR02013  584 akvardsgavivakrggvveyvdaKRIVIRYDEdeeepDGGIDIYRllkyqrsnqdtcinQRPivsvgdrveagdvLADG 663

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    597 RSMEHlrfRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYyrgymaeekkvgvmqLEEFEKPHRDTtirmK 676
Cdd:TIGR02013  664 PSTDL---GELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIH---------------IEEYEVEARDT----K 721

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    677 HG----TYD----------KIDADGLCAPGTRVSGDDVIIGKTAP-----LPPdsEELGMRSKLHTK----KDASVSLKS 733
Cdd:TIGR02013  722 LGpeeiTRDipnvseealrNLDENGIVRIGAEVKAGDILVGKVTPkgeteLTP--EEKLLRAIFGEKardvRDTSLRVPP 799

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    734 TENGIIDQVLVTTNSHG-------NKFVKVRVRSTRVPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGVTPDIIINPHA 806
Cdd:TIGR02013  800 GVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLG 879

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355    807 IPSRMTIGHLVECLLSKVAALSGQEGD--ATP-FTELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQ 883
Cdd:TIGR02013  880 VPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYML 959


                   ....
gi 45545355    884 RLKH 887
Cdd:TIGR02013  960 KLHH 963
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 189-887 7.12e-31

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 130.99  E-value: 7.12e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   189 EIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVyrhlqkcveehREfhiqaavksstitnglRYSLAtgnwgDQKKAM 268
Cdd:PRK00405  362 EVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAV-----------RE----------------RMSLQ-----DLDTLT 409

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   269 -----QAKAgVSQVLNRFaFAST--------------LSHLRRTNT--PIG----------RDgkiakprqLHNTHWGMV 317
Cdd:PRK00405  410 pqdliNAKP-VVAAIKEF-FGSSqlsqfmdqtnplseLTHKRRLSAlgPGGltreragfevRD--------VHPTHYGRI 479

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   318 CPAETPEGQACGLVKNLSLMATVtvgtpsapiveflEEFGldslvdmqlahakatkifvngvwmgthddpgqlvdtlrdl 397
Cdd:PRK00405  480 CPIETPEGPNIGLINSLATYARV-------------NEYG---------------------------------------- 506

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   398 rrkddishevsvvrdirerelriytdasrvlrpvFIVNPHdmsLLIKKRHVemigqpipeTGEefrwthlvqegvIEYLD 477
Cdd:PRK00405  507 ----------------------------------FIETPY---RKVVDGKV---------TDE------------IVYLT 528

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   478 AEEEESVLICMSTTDLEQsreykarNGQInlnsADP--SARLKS-VHTIAPDTWTHCEIHPAMVLGICASIVPFPDHNQS 554
Cdd:PRK00405  529 ADEEDNYVIAQANAPLDE-------DGRF----VDElvTARYKGeFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDA 597

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   555 PRnvyqsA-MGkqaigipiSNIQSRAdsmahV-LLYPQKPL-GTtrSMEH------------------------------ 601
Cdd:PRK00405  598 NR-----AlMG--------SNMQRQA-----VpLLRPEAPLvGT--GMERrvardsgavvvakrdgvveyvdasrivvrv 657

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   602 ---------------LRFR-----------------------------------ELPAGQNAIVAIMCYSGYNQEDSVIM 631
Cdd:PRK00405  658 eeldpgedgvdiynlIKFQrsnqntcinqrpivkvgdrvekgdvladgpstdngELALGQNVLVAFMPWNGYNFEDAILI 737

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   632 NQSSIDRGLFRSMYyrgymaeekkvgvmqLEEFEKPHRDTtirmKHG----TYD----------KIDADGLCAPGTRVSG 697
Cdd:PRK00405  738 SERLVKEDVFTSIH---------------IEEYEIEARDT----KLGpeeiTRDipnvseealrNLDESGIVRIGAEVKP 798

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   698 DDVIIGKTAP-----LPPdsEELGMRS----KLHTKKDASVSLKSTENGIIDQVLVTTN-------SHG-NKFVKVRVRS 760
Cdd:PRK00405  799 GDILVGKVTPkgeteLTP--EEKLLRAifgeKARDVKDTSLRVPHGEEGTVIDVKVFTRieqgdelPPGvNKLVKVYIAQ 876

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   761 TRVPQTGDKFASRHGQKGTIGITYRQEDMPFSAEGvTP-DIIINPHAIPSRMTIGHLVECLLSKVAALSGQEGdATP-FT 838
Cdd:PRK00405  877 KRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDG-TPvDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKF-ATPvFD 954

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|....*....
gi 45545355   839 ELTVEAVSSILRGLGYQSRGLEVMYHGHTGRKLQAQVYLGPTYYQRLKH 887
Cdd:PRK00405  955 GAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHH 1003
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 177-887 2.08e-29

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 126.36  E-value: 2.08e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   177 IHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVeehrefhIQAAVKSSTITNGLRYSL 256
Cdd:CHL00207  284 IDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICD-------IDSLSKFNLINPKPLIAL 356

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   257 ATGNWGDQKkamqakagVSQVLNRFAFASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGMVCPAETPEGQACGLVK 332
Cdd:CHL00207  357 IREFFGSSQ--------LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIG 428

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   333 NLslmatvtvgtpsapivefleefgldslvdmqlahakATKIFVNgvwmgthddpgqlvdtlrdlRRKddishevsvvrd 412
Cdd:CHL00207  429 SL------------------------------------ATNARIN--------------------KFG------------ 440

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   413 irerelriytdasrvlrpvFIVNPHdmsLLIKKRHVEMIGQPIpetgeefrwthlvqegvieYLDAEEEEsvlicmsttd 492
Cdd:CHL00207  441 -------------------FIETPF---YKVINGKVKKFGNPI-------------------YLTADSED---------- 469

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   493 leqsrEYKARNGQINLNSADpsaRLKSVH----------TIAPDTWTHCEIHPAMVLGICASIVPFPDHNQSPRNVYQSA 562
Cdd:CHL00207  470 -----LYRIAPNDINLNKNN---YFKKNIipvrykqefkTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSN 541

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   563 MGKQAIGI-----PI------------SN--IQSRADSMA------------------HVLLYP-----------QKP-- 592
Cdd:CHL00207  542 MQRQAVPLlypekPIvgtgyekqialdSGmtIISLTEGIVvsvsaykiiiqddnnryiHYYLQKyqrsnqntcinYRPiv 621

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   593 -----------LGTTRSMEHlrfRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYYRGYmaeekKVGVMQL 661
Cdd:CHL00207  622 wvgekinigqiLADGSDIDN---SELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-----EIELRQT 693

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   662 EEFekPHRDTTIRMKHGTYD--KIDADGLCAPGTRVSGDDVIIGKTAPLPpDSEELGmRSKL---------HTKKDASVS 730
Cdd:CHL00207  694 KLG--SEEITRNIPNVSEYSlkNLDENGIISIGSKVLAGDILVGKITPKG-ESDQLP-EGKLlraifgekaKDVKDTSLR 769

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   731 LKSTENGIIDQVLVTTNSHGNKF-------VKVRVRSTRVPQTGDKFASRHGQKGTIG-ITYRQeDMPFSAEGVTPDIII 802
Cdd:CHL00207  770 MPNGGYGRVIKVEIFSRSKGDELkfgyylkIRVFIAQIRKIQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDGTPPDIIL 848

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   803 NPHAIPSRMTIGHLVECLLSKVAALSGQEGDATPFTELTVEAVS-----------SILRGLGY----QSRGLEVMYHGHT 867
Cdd:CHL00207  849 NPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSrilinnklnqaSIKNNEYWlfnsYHPGKMVLRDGRT 928

                         810       820
                  ....*....|....*....|
gi 45545355   868 GRKLQAQVYLGPTYYQRLKH 887
Cdd:CHL00207  929 GYKFKNPVTVGIAYMLKLIH 948
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 374-435 4.38e-29

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: 110.15  E-value: 4.38e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545355   374 IFVNGVWMGTHDDPGQLVDTLRDLRRKDDISHEVSVVRDIRERELRIYTDASRVLRPVFIVN 435
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 276-338 9.51e-29

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: 109.54  E-value: 9.51e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45545355   276 QVLNRFAFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMA 338
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
189-831 3.61e-23

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 106.55  E-value: 3.61e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   189 EIDDRDHFGKKRIDLGGPLMAN-----LFRMlfRKVTRDVYRHLQKCVEEHREFHIqaaVKSSTITNGLRYSLATGNwgd 263
Cdd:PRK09603  453 KIDDRDHLGNRRIRAVGELLANelhsgLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ--- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   264 qkkamqakagVSQVLNRFAFASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMA 338
Cdd:PRK09603  525 ----------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   339 TVTvgtpsapivefleefgldslvDMQLAHAKATKIfVNGvwmgthddpgqlvdtlrdlrrkddishevsvvrdirerel 418
Cdd:PRK09603  594 RVN---------------------DLGFIEAPYKKV-VDG---------------------------------------- 611

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   419 riytdasrvlrpvfivnphdmsllikkrhvemigqpipetgeefrwtHLVQEGVieYLDAEEEESVLICMSTTDLEQSRE 498
Cdd:PRK09603  612 -----------------------------------------------KVVGETI--YLTAIQEDSHIIAPASTPIDEEGN 642

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   499 YKA------RNGQINLNSadpsarlKSVHTIApdtwthcEIHPAMVLGICASIVPFPDHNQSPRNVYQSAMGKQAI---- 568
Cdd:PRK09603  643 ILGdlietrVEGEIVLNE-------KSKVTLM-------DLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllr 708

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   569 ------GIPISNIQSR---------------------------ADSMAHVLLYP-QKPLGTTR----------------- 597
Cdd:PRK09603  709 sdapivGTGIEKIIARdswgaikanragvvekidskniyilgeGKEEAYIDAYSlQKNLRTNQntsfnqvpivkvgdkve 788

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   598 ---------SMEHlrfRELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRS--MYYRGYMAEEKKVGVmqlEEFEK 666
Cdd:PRK09603  789 agqiiadgpSMDR---GELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSthIYEKEVDARELKHGV---EEFTA 862

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   667 PHRDTtirmKHGTYDKIDADGLCAPGTRVSGDDVIIGKTAP---LPPDSEELGMRS------------------------ 719
Cdd:PRK09603  863 DIPDV----KEEALAHLDESGIVKVGTYVSAGMILVGKTSPkgeIKSTPEERLLRAifgdkaghvvnkslycppslegtv 938

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   720 ---KLHTKK-------------------------------------------------DASVSLKS-------------- 733
Cdd:PRK09603  939 idvKVFTKKgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileePFSHNGKDykegdqipkeeias 1018

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   734 -----------------------TENGIIDQVLVTTNSHGNKF----------------VKVRVRSTRVPQTGDKFASRH 774
Cdd:PRK09603 1019 inrftlaslvkkyskevqnhyeiTKNNFLEQKKVLGEEHEEKLsilekddilpngvikkVKLYIATKRKLKVGDKMAGRH 1098

                         810       820       830       840       850
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 45545355   775 GQKGTIGITYRQEDMPFSAEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAALSGQE 831
Cdd:PRK09603 1099 GNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQ 1155
rpoB CHL00001
RNA polymerase beta subunit
 606-839 6.51e-21

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 98.82  E-value: 6.51e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   606 ELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDRGLFRSMYYRGYMAEEKkvgvMQLEEFEK-----PHRDTTIrMKHgty 680
Cdd:CHL00001  648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTH----VTSQGPERitkeiPHLEAHL-LRN--- 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   681 dkIDADGLCAPGTRVSGDDVIIGKTAPLPPDSEELGMRSKL---------HTKKDASVSLKSTENG-IIDQVLVT---TN 747
Cdd:CHL00001  720 --LDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLlraifgiqvSTSKETCLKLPIGGRGrVIDVRWIQkkgGS 797

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   748 SHGNKFVKVRVRSTRVPQTGDKFASRHGQKGTIG-ITYRQeDMPFSAEGVTPDIIINPHAIPSRMTIGHLVECLLSKVAA 826
Cdd:CHL00001  798 SYNPETIHVYILQKREIQVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGD 876

                         250
                  ....*....|...
gi 45545355   827 LSGQEGDATPFTE 839
Cdd:CHL00001  877 LLNRHYRIAPFDE 889
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 464-535 1.95e-18

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: 79.51  E-value: 1.95e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45545355   464 WTHLVQEGVIEYLDAEEEESVLICMSTTDLEQS-REYKarngqinlnsadpsarlksvHTIAPDTWTHCEIHP 535
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREER--------------------EGPYAHTYTHCEIHP 53
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
176-818 1.93e-16

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 84.67  E-value: 1.93e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   176 MIHRLLLAALDRREIDDRDHFGKKRIDLGGPLMANLFRMLFRKVTRDVYRHLQKCVEEhrEFHIQAAVKSSTITNGLRys 255
Cdd:PRK14844  449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLD--KVSPSDFINPKVLTNVLR-- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   256 latgnwgDQKKAMQakagVSQVLNRFAFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGMVCPAETPEGQACGLV 331
Cdd:PRK14844  525 -------DFFNSSQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLI 593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   332 KNLSLMATVT-VGTPSAPIVEFLEEFGLD-----SLVDMQLAHAKATKIFVngvwmgthDDPGQLVDTLRDLRRKDDI-- 403
Cdd:PRK14844  594 NSLAIYARINkYGFIESPYRKVVNRVVTDqieylSAIDEGLYYIADTSAKL--------DENNCFVDDMLYCRYAGSFvm 665

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   404 --SHEVSVVrDIRERELrIYTDASrvLRPVFIVNPHDMSLL---IKKRHVEMIGQPIPetgeefrwthLVQEGVIEYLDA 478
Cdd:PRK14844  666 vsSDQVSYI-DVSPKQV-ISVAAS--LIPFLENDDANRALMgsnMQRQAVPLLKPTAP----------LVATGMESFVAS 731

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   479 EEEESVLicmsttdleqsreykARNGQInLNSADPSARLKSVHTIAPDTWTHCEIHPAmvlgicasivpfpdhNQSPRNV 558
Cdd:PRK14844  732 GSGAVVL---------------AKRDGI-VDSSDSNSIVIRAFDKERVNYLDVDIYHL---------------RKFQRSN 780

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   559 YQSAMGKQAIgIPISNIQSRADSMAHvllYPQKPLGttrsmehlrfrELPAGQNAIVAIMCYSGYNQEDSVIMNQSSIDR 638
Cdd:PRK14844  781 HNTCINQKPL-VCVGDYVKEGDVIAD---GPAINSG-----------ELALGQNLLVAFMSWQGYNFEDSIIISSEVVKK 845

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   639 GLFRSMYyrgymaeekkvgvmqLEEFEKPHRDTTI------RMKHGTYDK----IDADGLCAPGTRVSGDDVIIGKTAP- 707
Cdd:PRK14844  846 DLFTSIH---------------IEEFECVVHDTPLgsekitRAIPGVNEEnlyhLDDSGIVKIGTRVGPGYILVGKVTPk 910

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   708 ----LPPDSEEL----GMRS------KLHTKKDA--------------------SVSLKSTE--------NGIID----- 740
Cdd:PRK14844  911 pslsLPPETKLLmtifGEKSfdcadsSLYTSPDVegtvidvqvftrrgveenerALLIKQKEindfekerDYIINvtsey 990

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545355   741 ------QVLVTTNSHG------------------NKFVKVRVRSTR--------------------------VPQ----- 765
Cdd:PRK14844  991 fydelkKLLINSGSQDrekfdsiereqwwgiglkNQSISEQVKSLKkdfdekvshaiaqfkrkveklhegydLPQgvsms 1070

                         730       740       750       760       770       780
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45545355   766 ------------TGDKFASRHGQKGTIGITYRQEDMPFSAEGVTPDIIINPHAIPSRMTIGHLVE 818
Cdd:PRK14844 1071 vkvfiavkhslqPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILE 1135
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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