NCBI Conserved Domain Search

Conserved domains on [gi|45545349|gb|AAS67522|]

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DNA-dependent RNA polymerase II second largest subunit, partial [Taphrina deformans]

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;

1-936

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: 966.73 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349     1 SEKVIIAQERSAANMVQVFRKAPPSPVSYLAEIRSAIeKGSKlissMQIKLKAAKVGstgqTIAATLPYVKTDIPIVIVF 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYR----AQVTVERRKDG----TIYVSFPAVPGKIPFVILM 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    81 RALGVVPDRDILDHICYDAKDRQMLEmlkPCIEEAF-VIQDREVALDFIGKRgSAIGVTKEKRLRYAQDILQKEMLPHIT 159
Cdd:PRK08565  219 RALGLETDRDIVYAVSLDPEIQQELL---PSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLG 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   160 TSEGFETRKAFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKEFNLP 239
Cdd:PRK08565  295 TSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLR 374

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   240 LAVKHTTITNGLRYSLATGTWGDQkkqmnaRVGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPA 319
Cdd:PRK08565  375 AIVRPDIITERIRHALATGNWVGG------RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPF 448

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   320 ETPEGQACGLVKNLALMSYVSVGSASAPIIEFLEEWGMESLEDYNPSAGRPSTKIFVNGVWLGVHSDPGHLVKTLRSLRR 399
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   400 KTDISPEVSV--VRDIREKELRLFTDAGRVCRPLFVVhddesaeksEAGSLVLKKEHVQRMayskehpeDDEKFGWAQVL 477
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV---------ENGKPKLTREHVEKL--------KKGELTFDDLV 591

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   478 SNGIAEYLDAEEEETVMIAMTPDDLeATKHmmagyvepedekerkiaaeaakrlrpavnkaqhlwTHCEIHPSMILGICA 557
Cdd:PRK08565  592 KMGVIEYLDAEEEENAYVALDPEDL-TPEH-----------------------------------THLEIWPPAILGITA 635

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   558 SIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 637
Cdd:PRK08565  636 SIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGY 715

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   638 NQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQEFEKPTRETTMKMKRSTYDKLEDDGLVAPGTRVSGEDVIVG 717
Cdd:PRK08565  716 NIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIG 795

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   718 KTAGLLKDENLADLasRSATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGHKFVKVRIRATKIPQIGDKFASRHGQKGTIG 797
Cdd:PRK08565  796 KTSPPRFLEELEEL--SLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIG 873

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   798 VTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNLREQGYHSRGFEI 877
Cdd:PRK08565  874 MLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEV 953

                         890       900       910       920       930
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 45545349   878 MYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:PRK08565  954 MYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012

Name

Accession

Description

Interval

E-value

PRK08565

DNA-directed RNA polymerase subunit B; Provisional

1-936

0e+00

DNA-directed RNA polymerase subunit B; Provisional

Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 966.73 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349     1 SEKVIIAQERSAANMVQVFRKAPPSPVSYLAEIRSAIeKGSKlissMQIKLKAAKVGstgqTIAATLPYVKTDIPIVIVF 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYR----AQVTVERRKDG----TIYVSFPAVPGKIPFVILM 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    81 RALGVVPDRDILDHICYDAKDRQMLEmlkPCIEEAF-VIQDREVALDFIGKRgSAIGVTKEKRLRYAQDILQKEMLPHIT 159
Cdd:PRK08565  219 RALGLETDRDIVYAVSLDPEIQQELL---PSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLG 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   160 TSEGFETRKAFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKEFNLP 239
Cdd:PRK08565  295 TSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLR 374

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   240 LAVKHTTITNGLRYSLATGTWGDQkkqmnaRVGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPA 319
Cdd:PRK08565  375 AIVRPDIITERIRHALATGNWVGG------RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPF 448

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   320 ETPEGQACGLVKNLALMSYVSVGSASAPIIEFLEEWGMESLEDYNPSAGRPSTKIFVNGVWLGVHSDPGHLVKTLRSLRR 399
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   400 KTDISPEVSV--VRDIREKELRLFTDAGRVCRPLFVVhddesaeksEAGSLVLKKEHVQRMayskehpeDDEKFGWAQVL 477
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV---------ENGKPKLTREHVEKL--------KKGELTFDDLV 591

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   478 SNGIAEYLDAEEEETVMIAMTPDDLeATKHmmagyvepedekerkiaaeaakrlrpavnkaqhlwTHCEIHPSMILGICA 557
Cdd:PRK08565  592 KMGVIEYLDAEEEENAYVALDPEDL-TPEH-----------------------------------THLEIWPPAILGITA 635

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   558 SIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 637
Cdd:PRK08565  636 SIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGY 715

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   638 NQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQEFEKPTRETTMKMKRSTYDKLEDDGLVAPGTRVSGEDVIVG 717
Cdd:PRK08565  716 NIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIG 795

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   718 KTAGLLKDENLADLasRSATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGHKFVKVRIRATKIPQIGDKFASRHGQKGTIG 797
Cdd:PRK08565  796 KTSPPRFLEELEEL--SLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIG 873

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   798 VTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNLREQGYHSRGFEI 877
Cdd:PRK08565  874 MLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEV 953

                         890       900       910       920       930
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 45545349   878 MYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:PRK08565  954 MYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012

RNA_pol_B_RPB2

cd00653

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...

1-936

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: 843.77 E-value: 0e+00

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   1 SEKVIIAQERSAANMVQVFrkapPSPVSYLAEIRSAIEKGSKLISSMQIKLKAAKvgstgQTIAATLPYVKtdipivivf 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK-----DRIYVRIDLKR--------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  81 ralgvvpdrdildhicydakdrqmlemlkpcieeafviqdREVALDFIGKRGsaigvtkekrlryaqdilqkemlphitt 160
Cdd:cd00653 199 ----------------------------------------QEEALKYIGKRF---------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 161 segfetrkaFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKEFNLPL 240
Cdd:cd00653 211 ---------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQL 281

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 241 AVKHTTITNGLRYSLATGTWGDQKKQMNaRVGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPA 319
Cdd:cd00653 282 LINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPI 360

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 320 ETPEGQACGLVKNLALMSYVSvgsasapiiefleewgmesledynpsagrpstkifvngvwlgvhsdpghlvktlrslrr 399
Cdd:cd00653 361 ETPEGENCGLVKNLALMARIS----------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 400 ktdispevsvvrdirekelrlftdaGRVCRPLFVVHDDesaekseagslvlkkehvqrmayskehpeddekfgwaqvlsn 479
Cdd:cd00653 382 -------------------------GRIERPYRIVEKE------------------------------------------ 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 480 giaeyldaeeeetvmiamtpddleatkhmmagyvepedekerkiaaeaakrlrpavnkaqhlWTHCEIHPSMILGICASI 559
Cdd:cd00653 395 --------------------------------------------------------------VTHIEISPSQILSVAASL 412

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 560 IPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQ 639
Cdd:cd00653 413 IPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNF 492

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 640 EDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQaqefEKPTRETTMKMKRSTYDKLEDDGLVAPGTRVSGEDVIVGKT 719
Cdd:cd00653 493 EDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGP----EEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKI 568

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 720 AglLKDENLADLASRSATQTKRDVSTQLRSTEAGIIDKVMVST---NSDGHKFVKVRIRATKIPQIGDKFASRHGQKGTI 796
Cdd:cd00653 569 T--PKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVI 646

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 797 GVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNLREQGYHSRGFE 876
Cdd:cd00653 647 SKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKE 726

                       890       900       910       920       930       940
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 877 IMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRF 786

rpoB_arch

TIGR03670

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...

374-936

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: 640.54 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   374 IFVNGVWLGVHSDPGHLVKTLRSLRRKTDISPEVSVVRDIREKELRLFTDAGRVCRPLFVVhddesaeksEAGSLVLKKE 453
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVV---------ENGKPKLTRE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   454 HVQRMAyskehpedDEKFGWAQVLSNGIAEYLDAEEEETVMIAMTPDDLeATKHmmagyvepedekerkiaaeaakrlrp 533
Cdd:TIGR03670  72 HVEKLK--------EGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL-TPEH-------------------------- 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   534 avnkaqhlwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSM 613
Cdd:TIGR03670 117 ---------THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   614 EYLKFRELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQEFEKPTRETTMKMKRST 693
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEA 267

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   694 YDKLEDDGLVAPGTRVSGEDVIVGKTAGLLKDENLADLASrsATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGHKFVKVR 773
Cdd:TIGR03670 268 YKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFGL--VTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVR 345

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   774 IRATKIPQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPF 853
Cdd:TIGR03670 346 VRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF 425

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   854 TDVTVEAVSNNLREQGYHSRGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGG 933
Cdd:TIGR03670 426 EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGG 505


                  ...
gi 45545349   934 LRF 936
Cdd:TIGR03670 506 LRF 508

RNA_pol_Rpb2_6

pfam00562

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...

556-930

5.39e-180

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: 524.79 E-value: 5.39e-180

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   556 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 635
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   636 GYNQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMnqaqeFEKPTRETTmKMKRSTYDKLEDDGLVAPGTRVSGEDVI 715
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-----IEEITRDIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   716 VGKTAGLLKDENLADLASRSAtQTKRDVSTQLRSTEAGIIDKVMV-STNSDGHKFVKVRIRATKIPQIGDKFASRHGQKG 794
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKA-RDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKG 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   795 TIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFT--DVTVEAVSNNLREQGYHS 872
Cdd:pfam00562 234 VVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNY 313

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 45545349   873 RGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRAR 930
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371

RpoB

COG0085

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...

1-936

9.23e-176

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: 536.61 E-value: 9.23e-176

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    1 SEKVIIAQERSAANMVQVFRKAPPSPVSYLAEIRSAieKGSKLISSMQIKlkaakvgstgQTIAATLPyVKTDIPIVIVF 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLEFETDKD----------GTIYVRID-RKRKIPVTVLL 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   81 RALGVVPDRDILDHIcydaKDRQMLEMLKPCIEEAfVIQDREVALDFIGKR---GSAigvtkeKRLRYAQDIL------- 150
Cdd:COG0085  184 RALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGEP------PTIERAEQLLdnlffdp 252

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  151 QKEMLPHI---------TTSEGFETR--KAFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLT 219
Cdd:COG0085  253 KRYDLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRME 332

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  220 KDIRQYMTKcvDSGKEFNLPLAVKHTTITNGLRYSLATGtwgdqkkqmnarvGVSQVLNRYTYASTLSHLRRTNT----P 295
Cdd:COG0085  333 RVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgG 397

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  296 IGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMSYVSvgsasapiiEFleewgmesledynpsagrps 371
Cdd:COG0085  398 LSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY-------------------- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  372 tkifvngvwlgvhsdpghlvktlrslrrktdispevsvvrdirekelrlftdaGRVCRPLFVVHDdesaekseagslvlk 451
Cdd:COG0085  445 -----------------------------------------------------GFIETPYRKVEN--------------- 456

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  452 kehvqrmayskehpeddekfGwaqVLSNGIaEYLDAEEEETVMIAMTPDDLeatkhmmagyvepeDEKERKIAAEAAKRL 531
Cdd:COG0085  457 --------------------G---KVTDEI-EYLTADEEENYYIAQANAPL--------------DEDGNFLEERVLVRY 498

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  532 R---PAVNKAQHlwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQvrmdtmanILYYP----- 603
Cdd:COG0085  499 RgeeVLVPPEEV--DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPlqkfq 568

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  604 ---------QKPLAttRSMEYLK------------FRELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRV 662
Cdd:COG0085  569 rsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEE 646

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  663 YqDSEE---KIDMnqaqefEKPTRE---TTMKMKRstydKLEDDGLVAPGTRVSGEDVIVGKTA-----GLLKDENLADL 731
Cdd:COG0085  647 Y-EIEArdtKLGP------EEITRDipnVSEEALR----NLDEDGIIRIGAEVKGGDILVGKVTpkgetELTPEERLLRA 715

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  732 ASRSATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGH-------KFVKVRIRATKIPQIGDKFASRHGQKGTIGVTYRNED 804
Cdd:COG0085  716 IFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDelppgvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQED 795

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  805 MPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNLREQGYHSRGFEIMYNGHTG 884
Cdd:COG0085  796 MPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTG 875

                        970       980       990      1000      1010
                 ....*....|....*....|....*....|....*....|....*....|..
gi 45545349  885 RKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:COG0085  876 EPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927

Name

Accession

Description

Interval

E-value

PRK08565

DNA-directed RNA polymerase subunit B; Provisional

1-936

0e+00

DNA-directed RNA polymerase subunit B; Provisional

Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 966.73 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349     1 SEKVIIAQERSAANMVQVFRKAPPSPVSYLAEIRSAIeKGSKlissMQIKLKAAKVGstgqTIAATLPYVKTDIPIVIVF 80
Cdd:PRK08565  148 SERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSR-AGYR----AQVTVERRKDG----TIYVSFPAVPGKIPFVILM 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    81 RALGVVPDRDILDHICYDAKDRQMLEmlkPCIEEAF-VIQDREVALDFIGKRgSAIGVTKEKRLRYAQDILQKEMLPHIT 159
Cdd:PRK08565  219 RALGLETDRDIVYAVSLDPEIQQELL---PSLEQASsIAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLG 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   160 TSEGFETRKAFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKEFNLP 239
Cdd:PRK08565  295 TSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLR 374

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   240 LAVKHTTITNGLRYSLATGTWGDQkkqmnaRVGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPA 319
Cdd:PRK08565  375 AIVRPDIITERIRHALATGNWVGG------RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPF 448

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   320 ETPEGQACGLVKNLALMSYVSVGSASAPIIEFLEEWGMESLEDYNPSAGRPSTKIFVNGVWLGVHSDPGHLVKTLRSLRR 399
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   400 KTDISPEVSV--VRDIREKELRLFTDAGRVCRPLFVVhddesaeksEAGSLVLKKEHVQRMayskehpeDDEKFGWAQVL 477
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV---------ENGKPKLTREHVEKL--------KKGELTFDDLV 591

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   478 SNGIAEYLDAEEEETVMIAMTPDDLeATKHmmagyvepedekerkiaaeaakrlrpavnkaqhlwTHCEIHPSMILGICA 557
Cdd:PRK08565  592 KMGVIEYLDAEEEENAYVALDPEDL-TPEH-----------------------------------THLEIWPPAILGITA 635

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   558 SIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGY 637
Cdd:PRK08565  636 SIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGY 715

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   638 NQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQEFEKPTRETTMKMKRSTYDKLEDDGLVAPGTRVSGEDVIVG 717
Cdd:PRK08565  716 NIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIG 795

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   718 KTAGLLKDENLADLasRSATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGHKFVKVRIRATKIPQIGDKFASRHGQKGTIG 797
Cdd:PRK08565  796 KTSPPRFLEELEEL--SLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIG 873

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   798 VTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNLREQGYHSRGFEI 877
Cdd:PRK08565  874 MLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEV 953

                         890       900       910       920       930
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 45545349   878 MYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:PRK08565  954 MYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012

RNA_pol_B_RPB2

cd00653

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...

1-936

0e+00

Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 843.77 E-value: 0e+00

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   1 SEKVIIAQERSAANMVQVFrkapPSPVSYLAEIRSAIEKGSKLISSMQIKLKAAKvgstgQTIAATLPYVKtdipivivf 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK-----DRIYVRIDLKR--------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  81 ralgvvpdrdildhicydakdrqmlemlkpcieeafviqdREVALDFIGKRGsaigvtkekrlryaqdilqkemlphitt 160
Cdd:cd00653 199 ----------------------------------------QEEALKYIGKRF---------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 161 segfetrkaFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKEFNLPL 240
Cdd:cd00653 211 ---------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQL 281

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 241 AVKHTTITNGLRYSLATGTWGDQKKQMNaRVGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPA 319
Cdd:cd00653 282 LINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPI 360

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 320 ETPEGQACGLVKNLALMSYVSvgsasapiiefleewgmesledynpsagrpstkifvngvwlgvhsdpghlvktlrslrr 399
Cdd:cd00653 361 ETPEGENCGLVKNLALMARIS----------------------------------------------------------- 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 400 ktdispevsvvrdirekelrlftdaGRVCRPLFVVHDDesaekseagslvlkkehvqrmayskehpeddekfgwaqvlsn 479
Cdd:cd00653 382 -------------------------GRIERPYRIVEKE------------------------------------------ 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 480 giaeyldaeeeetvmiamtpddleatkhmmagyvepedekerkiaaeaakrlrpavnkaqhlWTHCEIHPSMILGICASI 559
Cdd:cd00653 395 --------------------------------------------------------------VTHIEISPSQILSVAASL 412

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 560 IPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQ 639
Cdd:cd00653 413 IPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNF 492

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 640 EDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQaqefEKPTRETTMKMKRSTYDKLEDDGLVAPGTRVSGEDVIVGKT 719
Cdd:cd00653 493 EDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGP----EEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKI 568

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 720 AglLKDENLADLASRSATQTKRDVSTQLRSTEAGIIDKVMVST---NSDGHKFVKVRIRATKIPQIGDKFASRHGQKGTI 796
Cdd:cd00653 569 T--PKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVI 646

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 797 GVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNLREQGYHSRGFE 876
Cdd:cd00653 647 SKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKE 726

                       890       900       910       920       930       940
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349 877 IMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRF 786

rpoB_arch

TIGR03670

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...

374-936

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: 640.54 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   374 IFVNGVWLGVHSDPGHLVKTLRSLRRKTDISPEVSVVRDIREKELRLFTDAGRVCRPLFVVhddesaeksEAGSLVLKKE 453
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVV---------ENGKPKLTRE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   454 HVQRMAyskehpedDEKFGWAQVLSNGIAEYLDAEEEETVMIAMTPDDLeATKHmmagyvepedekerkiaaeaakrlrp 533
Cdd:TIGR03670  72 HVEKLK--------EGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL-TPEH-------------------------- 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   534 avnkaqhlwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSM 613
Cdd:TIGR03670 117 ---------THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   614 EYLKFRELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQEFEKPTRETTMKMKRST 693
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEA 267

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   694 YDKLEDDGLVAPGTRVSGEDVIVGKTAGLLKDENLADLASrsATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGHKFVKVR 773
Cdd:TIGR03670 268 YKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFGL--VTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVR 345

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   774 IRATKIPQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPF 853
Cdd:TIGR03670 346 VRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF 425

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   854 TDVTVEAVSNNLREQGYHSRGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGG 933
Cdd:TIGR03670 426 EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGG 505


                  ...
gi 45545349   934 LRF 936
Cdd:TIGR03670 506 LRF 508

PRK07225

DNA-directed RNA polymerase subunit B'; Validated

372-936

0e+00

DNA-directed RNA polymerase subunit B'; Validated

Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 611.19 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  372 TKIFVNGVWLGVHSDPGHLVKTLRSLRRKTDISPEVSVVRDIREKELRLFTDAGRVCRPLFVVHDdesaekseaGSLVLK 451
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN---------GEPLLT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  452 KEHVQRMAyskehpedDEKFGWAQVLSNGIAEYLDAEEEETVMIAMTPDDLEaTKHmmagyvepedekerkiaaeaakrl 531
Cdd:PRK07225  76 EEHIEKLK--------NGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT-EEH------------------------ 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  532 rpavnkaqhlwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTR 611
Cdd:PRK07225 123 -----------THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQ 191

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  612 SMEYLKFRELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMNQAQEFEKPTRETTMKMKR 691
Cdd:PRK07225 192 TQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGE 271

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  692 STYDKLEDDGLVAPGTRVSGEDVIVGKTAGLLKDENLADLASrsATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGHKFVK 771
Cdd:PRK07225 272 EAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFGI--SPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVK 349

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  772 VRIRATKIPQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDAT 851
Cdd:PRK07225 350 VRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGT 429

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  852 PFTDVTVEAVSNNLREQGYHSRGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARD 931
Cdd:PRK07225 430 AFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRARE 509


                 ....*
gi 45545349  932 GGLRF 936
Cdd:PRK07225 510 GGLRF 514

RNA_pol_Rpb2_6

pfam00562

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...

556-930

5.39e-180

Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 524.79 E-value: 5.39e-180

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   556 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYS 635
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   636 GYNQEDSMIMNQSSIDRGLFRSMFYRVYQDSEEKIDMnqaqeFEKPTRETTmKMKRSTYDKLEDDGLVAPGTRVSGEDVI 715
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-----IEEITRDIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   716 VGKTAGLLKDENLADLASRSAtQTKRDVSTQLRSTEAGIIDKVMV-STNSDGHKFVKVRIRATKIPQIGDKFASRHGQKG 794
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKA-RDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKG 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   795 TIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFT--DVTVEAVSNNLREQGYHS 872
Cdd:pfam00562 234 VVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNY 313

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 45545349   873 RGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRAR 930
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371

RpoB

COG0085

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...

1-936

9.23e-176

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: 536.61 E-value: 9.23e-176

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    1 SEKVIIAQERSAANMVQVFRKAPPSPVSYLAEIRSAieKGSKLISSMQIKlkaakvgstgQTIAATLPyVKTDIPIVIVF 80
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPS--RGAWLEFETDKD----------GTIYVRID-RKRKIPVTVLL 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   81 RALGVVPDRDILDHIcydaKDRQMLEMLKPCIEEAfVIQDREVALDFIGKR---GSAigvtkeKRLRYAQDIL------- 150
Cdd:COG0085  184 RALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGEP------PTIERAEQLLdnlffdp 252

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  151 QKEMLPHI---------TTSEGFETR--KAFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLT 219
Cdd:COG0085  253 KRYDLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRME 332

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  220 KDIRQYMTKcvDSGKEFNLPLAVKHTTITNGLRYSLATGtwgdqkkqmnarvGVSQVLNRYTYASTLSHLRRTNT----P 295
Cdd:COG0085  333 RVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgG 397

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  296 IGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMSYVSvgsasapiiEFleewgmesledynpsagrps 371
Cdd:COG0085  398 LSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY-------------------- 444

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  372 tkifvngvwlgvhsdpghlvktlrslrrktdispevsvvrdirekelrlftdaGRVCRPLFVVHDdesaekseagslvlk 451
Cdd:COG0085  445 -----------------------------------------------------GFIETPYRKVEN--------------- 456

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  452 kehvqrmayskehpeddekfGwaqVLSNGIaEYLDAEEEETVMIAMTPDDLeatkhmmagyvepeDEKERKIAAEAAKRL 531
Cdd:COG0085  457 --------------------G---KVTDEI-EYLTADEEENYYIAQANAPL--------------DEDGNFLEERVLVRY 498

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  532 R---PAVNKAQHlwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYQvrmdtmanILYYP----- 603
Cdd:COG0085  499 RgeeVLVPPEEV--DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPlqkfq 568

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  604 ---------QKPLAttRSMEYLK------------FRELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRV 662
Cdd:COG0085  569 rsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEE 646

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  663 YqDSEE---KIDMnqaqefEKPTRE---TTMKMKRstydKLEDDGLVAPGTRVSGEDVIVGKTA-----GLLKDENLADL 731
Cdd:COG0085  647 Y-EIEArdtKLGP------EEITRDipnVSEEALR----NLDEDGIIRIGAEVKGGDILVGKVTpkgetELTPEERLLRA 715

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  732 ASRSATQTKRDVSTQLRSTEAGIIDKVMVSTNSDGH-------KFVKVRIRATKIPQIGDKFASRHGQKGTIGVTYRNED 804
Cdd:COG0085  716 IFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDelppgvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQED 795

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  805 MPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNLREQGYHSRGFEIMYNGHTG 884
Cdd:COG0085  796 MPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTG 875

                        970       980       990      1000      1010
                 ....*....|....*....|....*....|....*....|....*....|..
gi 45545349  885 RKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:COG0085  876 EPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927

RNA_pol_Rpb2_1

pfam04563

RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...

1-249

7.82e-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: 7.82e-105

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349     1 SEKVIIAQERSAANMVQVFRKAPPSPVSYLAEIRSAIEKGSKLISSMQIKLKAakvGSTGQTIAATLPYVKTDIPIVIVF 80
Cdd:pfam04563 146 SEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLE---YLSNGTIYFKFPYIKKEIPIVIIL 222

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    81 RALGVVPDRDILDHICYDAKDRQMLEMLKPCIEEAFVI--QDREVALDFIGKRGSAI---GVTKEKRLRYAQDILQKEML 155
Cdd:pfam04563 223 RALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVL 302

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   156 PHITTSEGFETRKAFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCVDSGKE 235
Cdd:pfam04563 303 PHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDD 382

                         250
                  ....*....|....
gi 45545349   236 FNLPLAVKHTTITN 249
Cdd:pfam04563 383 LMLQLLVNAKPITS 396

PRK09606

DNA-directed RNA polymerase subunit B''; Validated

1-358

2.82e-75

DNA-directed RNA polymerase subunit B''; Validated

Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 255.26 E-value: 2.82e-75

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    1 SEKVIIAQERSAANMVqvfrkappspvsyLAEIrsaIEKGSKLIssmqiklKAAKVGSTGQ--------------TIAAT 66
Cdd:PRK09606 153 SERVLMTLEDLAPNKI-------------LVEK---DERYGDRI-------EVAKVFSQRRgyralvtvernrdgLLEVS 209

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   67 LPYVKTDIPIVIVFRALGVVPDRDILDHIcydAKDRQMLEMLKPCIEEAfVIQDREVALDFIGKRGsAIGVTKEKRLRYA 146
Cdd:PRK09606 210 FPSVPGSIPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYIGKRV-APGQTKEYRIKRA 284

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  147 QDILQKEMLPHITTSEGFETRKAFFLGYMVHRLLLCALERRDPDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDI---- 222
Cdd:PRK09606 285 EYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVkyql 364

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349  223 -RQYMtkcvdSGKEFNLPLAVKHTTITNGLRYSLATGTWgdqkkqMNARVGVSQVLNRYTYASTLSHLRRTNTPIGRDGK 301
Cdd:PRK09606 365 eRANM-----RNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQP 433

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 45545349  302 IAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYVSVGSASAPIIEFLEEWGME 358
Cdd:PRK09606 434 HFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490

rpoB

TIGR02013

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...

190-936

6.39e-55

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: 207.21 E-value: 6.39e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    190 DDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKcvdsgKEFNlplAVKHTTITNGLRYSLATgtwgdqkKQMNA 269
Cdd:TIGR02013  319 DDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMST-----QDTD---TLTPQDLINAKPISAAI-------KEFFG 383

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    270 RVGVSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLAlmSYVSV---G 342
Cdd:TIGR02013  384 SSQLSQFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS--TYARVneyG 461

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    343 SASAPIIEFLEEWGMESLEDYNPSAGRPSTKIFVNG-VWLGvhsDPGHLVKTLRSLRRKTDI---SPEVSVVRDIREKEL 418
Cdd:TIGR02013  462 FIETPYRKVKDGKVVVTDEIDYLTADEEDNYVIAQAnAPLD---ENGRFVEDLVVARYRGEItlvSPDQVDYMDVSPKQV 538

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    419 rlfTDAGRVCRPlFVVHDDesAEKSEAGSlvlkkeHVQRMAYSKEHPEddekfgwAQVLSNGIaEYLDAEEEETVMIAMT 498
Cdd:TIGR02013  539 ---VSVAASLIP-FLEHDD--ANRALMGS------NMQRQAVPLLRSE-------APLVGTGM-EAKVARDSGAVIVAKR 598

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    499 PddleatkhmmaGYVEPEDEKERKIAAEAAkrlrpavnkaqhlwthceihpsmilgicasiipfPDHNQSPRNTYQsamg 578
Cdd:TIGR02013  599 G-----------GVVEYVDAKRIVIRYDED----------------------------------EEEPDGGIDIYR---- 629

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    579 kqamgvfLTNYQ-VRMDTMANilyypQKP-------------LATTRSMEylkFRELPAGQNAIVAILCYSGYNQEDSMI 644
Cdd:TIGR02013  630 -------LLKYQrSNQDTCIN-----QRPivsvgdrveagdvLADGPSTD---LGELALGRNVLVAFMPWNGYNYEDAIL 694

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    645 MNQSSIDRGLFRSMfyrvyqdseekidmnQAQEFEKPTRETTMKMKRSTYD----------KLEDDGLVAPGTRVSGEDV 714
Cdd:TIGR02013  695 ISERLVKDDVFTSI---------------HIEEYEVEARDTKLGPEEITRDipnvseealrNLDENGIVRIGAEVKAGDI 759

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    715 IVGKTA-----GLLKDENLAdlasRSATQTK----RDVSTQLRSTEAGIIDKVMVSTNSDG-------HKFVKVRIRATK 778
Cdd:TIGR02013  760 LVGKVTpkgetELTPEEKLL----RAIFGEKardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKR 835

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    779 IPQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQLSKVGSLSGFEGD--ATP-FTD 855
Cdd:TIGR02013  836 KIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDG 915

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    856 VTVEAVSNNLREQGYHSRGFEIMYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLR 935
Cdd:TIGR02013  916 ASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQR 995


                   .
gi 45545349    936 F 936
Cdd:TIGR02013  996 F 996

RNA_pol_Rpb2_2

pfam04561

RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...

12-201

6.88e-55

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: 188.32 E-value: 6.88e-55

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    12 AANMVQVFRKAPPSPVSylaeirsaiekGSKLISSMQIKLKAAKVGSTGQTIAATLPYVKTDIPIVIVFRALGVVPDRDI 91
Cdd:pfam04561   1 RSNGIYVEKELDKNGII-----------ATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREI 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349    92 LDHICYDAKDRQMLEMLKPCIEEAFVIQDREVALDFIGKrGSAIGVTKEKRLRYAQDILQK-----EMLPHITTSEGFET 166
Cdd:pfam04561  70 LDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEPFEN 148

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 45545349   167 R--KAFFLGYMVHRLLLCALERRDPDDRDHFGKKRID 201
Cdd:pfam04561 149 ErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185

rpoB

CHL00207

RNA polymerase beta subunit; Provisional

189-936

6.94e-51

RNA polymerase beta subunit; Provisional

Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 194.54 E-value: 6.94e-51

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   189 PDDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKCV-DSGKEFNLplaVKHTTITNGLRYSLATGTwgdqkkqm 267
Cdd:CHL00207  297 FDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDiDSLSKFNL---INPKPLIALIREFFGSSQ-------- 365

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   268 narvgVSQVLNRYTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLAlmsyvsvgs 343
Cdd:CHL00207  366 -----LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA--------- 431

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   344 asapiiefleewgmesledynpsagrpsTKIFVNgvwlgvhsdpghlvktlrslrrktdispevsvvrdirekelrlftD 423
Cdd:CHL00207  432 ----------------------------TNARIN---------------------------------------------K 438

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   424 AGRVCRPLFVVHDdesaekseagslvlkkehvqrmayskehpeddekfgwAQVLSNGIAEYLDAEEEETVMIAMTPDDLE 503
Cdd:CHL00207  439 FGFIETPFYKVIN-------------------------------------GKVKKFGNPIYLTADSEDLYRIAPNDINLN 481

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   504 ATKHMMAGYVEPEDEKERKIaaeaakrlrpaVNKAQHlwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMG 583
Cdd:CHL00207  482 KNNYFKKNIIPVRYKQEFKT-----------VNPSKV--DFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVP 548

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   584 ---------------------------------VFLTNYQVRMDTMAN--ILYYPQK-------------P--------- 606
Cdd:CHL00207  549 llypekpivgtgyekqialdsgmtiisltegivVSVSAYKIIIQDDNNryIHYYLQKyqrsnqntcinyrPivwvgekin 628

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   607 ----LATTRSMeylKFRELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRVYqdseeKIDMNQAQEF-EKP 681
Cdd:CHL00207  629 igqiLADGSDI---DNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-----EIELRQTKLGsEEI 700

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   682 TRETTmKMKRSTYDKLEDDGLVAPGTRVSGEDVIVGK-----TAGLLKDENLADLASRSATQTKRDVSTQLRSTEAG-II 755
Cdd:CHL00207  701 TRNIP-NVSEYSLKNLDENGIISIGSKVLAGDILVGKitpkgESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGrVI 779

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   756 D-KVMVSTNSDGHKF---VKVRIRATKIP--QIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTV 829
Cdd:CHL00207  780 KvEIFSRSKGDELKFgyyLKIRVFIAQIRkiQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNV 859

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   830 AHLVECQLSKVGSLSGFEGDATPFTDV----TVEAVSNNLREQGYHSRGFEIMYN-----------GHTGRKLMAQVFLG 894
Cdd:CHL00207  860 GQLFECLLGLAGDNLNKRFKILPFDEMygseYSRILINNKLNQASIKNNEYWLFNsyhpgkmvlrdGRTGYKFKNPVTVG 939

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|..
gi 45545349   895 PTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:CHL00207  940 IAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRF 981

rpoB

PRK00405

DNA-directed RNA polymerase subunit beta; Reviewed

620-936

2.00e-35

DNA-directed RNA polymerase subunit beta; Reviewed

Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 146.01 E-value: 2.00e-35

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   620 ELPAGQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMfyrvyqdseeKIDmnqaqEFEKPTRETTMKMKRSTYD---- 695
Cdd:PRK00405  712 ELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSI----------HIE-----EYEIEARDTKLGPEEITRDipnv 776

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   696 ------KLEDDGLVAPGTRVSGEDVIVGK---------TAgllkDENLadLasRSATQTK-RDV-STQLR--STEAGIID 756
Cdd:PRK00405  777 seealrNLDESGIVRIGAEVKPGDILVGKvtpkgetelTP----EEKL--L--RAIFGEKaRDVkDTSLRvpHGEEGTVI 848

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   757 KVMVST-NSDG-------HKFVKVRIrATK--IpQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSR 826
Cdd:PRK00405  849 DVKVFTrIEQGdelppgvNKLVKVYI-AQKrkI-QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSR 926

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   827 MTVAHLVECQLSKVGSLSG--FegdATP-FTDVTVEAVSNNLREQGYHSRGFEIMYNGHTGRKLMAQVFLGPTYYQRLKH 903
Cdd:PRK00405  927 MNIGQILETHLGWAAKGLGikF---ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHH 1003

                         330       340       350
                  ....*....|....*....|....*....|...
gi 45545349   904 LVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:PRK00405 1004 LVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRF 1036

RNA_pol_Rpb2_4

pfam04566

RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...

374-434

8.75e-33

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: 120.93 E-value: 8.75e-33

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545349   374 IFVNGVWLGVHSDPGHLVKTLRSLRRKTDISPEVSVVRDIREKELRLFTDAGRVCRPLFVV 434
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIV 61

rpoB

CHL00001

RNA polymerase beta subunit

190-935

1.96e-32

RNA polymerase beta subunit

Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 136.19 E-value: 1.96e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   190 DDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTKcvdsgkefnlplAVKHTTI--TNGLRYSLA-TGTWgdqkKQ 266
Cdd:CHL00001  304 DDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICG------------AIRRKLIptPQNLVTSTPlTTTY----ES 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   267 MNARVGVSQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLALmsYVSVG 342
Cdd:CHL00001  368 FFGSHPLSQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAI--HARIG 445

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   343 SasapiiefleeWGmeSLEdynpsagrpstkifvngvwlgvhsdpghlvktlrslrrktdiSP--EVSVvrdiREKELRL 420
Cdd:CHL00001  446 H-----------WG--SLE------------------------------------------SPfyEISE----RSKEERM 466

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   421 FtdagrvcrplfvvhddesaekseagslvlkkehvqrmayskehpeddekfgwaqvlsngiaeYLDAEEEETVMIAmTPD 500
Cdd:CHL00001  467 V--------------------------------------------------------------YLSPSEDEYYMIA-AGN 483

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   501 DLEATkhmmagyvepEDEKERKIAaeaakrlrPAVNKAQHLWTHCE------IHPSMILGICASIIPFPDHNQSPRNTYQ 574
Cdd:CHL00001  484 SLALN----------QGIQEEQVV--------PARYRQEFLTIAWEqihlrsIFPFQYFSIGASLIPFLEHNDANRALMG 545

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   575 SAMGKQAMGVFLTNY---------QVRMD------------------------TMANILYYP--------------QKPl 607
Cdd:CHL00001  546 SNMQRQAVPLSRSEKcivgtglerQVALDsgvvaiaehegkiiytdtdkiilsGNGDTLSIPlvmyqrsnkntcmhQKP- 624

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   608 aTTRSMEYLKFRELPA------------GQNAIVAILCYSGYNQEDSMIMNQSSIDRGLFRSMFYRVYqdsEEKIDMNQa 675
Cdd:CHL00001  625 -QVRRGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY---EIQTHVTS- 699

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   676 QEFEKPTRETTmKMKRSTYDKLEDDGLVAPGTRVSGEDVIVGKTAGLLKDENLADLASRS-------ATQTKRDVSTQLR 748
Cdd:CHL00001  700 QGPERITKEIP-HLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLlraifgiQVSTSKETCLKLP 778

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   749 STEAG-IIDKVMVS---TNSDGHKFVKVRI-RATKIpQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAI 823
Cdd:CHL00001  779 IGGRGrVIDVRWIQkkgGSSYNPETIHVYIlQKREI-QVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGV 857

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   824 PSRMTVAHLVECQLSKVGSLSGFEGDATPFTDVTVEAVSNNL--------REQGYHSRGFE-------IMYNGHTGRKLM 888
Cdd:CHL00001  858 PSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLvfselyeaSKQTANPWVFEpeypgksRLFDGRTGDPFE 937

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|....*..
gi 45545349   889 AQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLR 935
Cdd:CHL00001  938 QPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQR 984

PRK09603

DNA-directed RNA polymerase subunit beta/beta';

190-936

5.21e-32

DNA-directed RNA polymerase subunit beta/beta';

Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 135.82 E-value: 5.21e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   190 DDRDHFGKKRIDLAGPLLA-----GLFRMlfKRLTKDIRQYMTKCVDSGKEFNLplaVKHTTITNGLRYSLATGTwgdqk 264
Cdd:PRK09603  455 DDRDHLGNRRIRAVGELLAnelhsGLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ----- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   265 kqmnarvgVSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYV 339
Cdd:PRK09603  525 --------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV 595

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   340 S-VGSASAPIIEFLEewGMESLEDYNPSAGR--------PSTKIFVNGVWLGVHSDP---GHLVKTLRSLRRKTDISPev 407
Cdd:PRK09603  596 NdLGFIEAPYKKVVD--GKVVGETIYLTAIQedshiiapASTPIDEEGNILGDLIETrveGEIVLNEKSKVTLMDLSS-- 671

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   408 svvrdirekelRLFTDAGRVCRPlFVVHDDesAEKSEAGSlvlkkeHVQRMAYSKEHPEddekfgwAQVLSNGIaeylda 487
Cdd:PRK09603  672 -----------SMLVGVAASLIP-FLEHDD--ANRALMGT------NMQRQAVPLLRSD-------APIVGTGI------ 718

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   488 eeEETVmiamTPDDLEATKHMMAGYVEPEDEKERKIAAEaakrlrpavNKAQHLWTHCEIHPSMilgicasiipfpdhnQ 567
Cdd:PRK09603  719 --EKII----ARDSWGAIKANRAGVVEKIDSKNIYILGE---------GKEEAYIDAYSLQKNL---------------R 768

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   568 SPRNTYQSAMGKQAMGVFLTNYQVrmdtmanilyypqkpLATTRSMEYlkfRELPAGQNAIVAILCYSGYNQEDSMIMNQ 647
Cdd:PRK09603  769 TNQNTSFNQVPIVKVGDKVEAGQI---------------IADGPSMDR---GELALGKNVRVAFMPWNGYNFEDAIVVSE 830

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   648 SSIDRGLFRSMfyRVYqdsEEKIDmnqAQEFEKPTRETTMKM---KRSTYDKLEDDGLVAPGTRVSGEDVIVGKT----- 719
Cdd:PRK09603  831 RITKDDIFTST--HIY---EKEVD---ARELKHGVEEFTADIpdvKEEALAHLDESGIVKVGTYVSAGMILVGKTspkge 902

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   720 -----------------AGLLKDENL----------------------ADLASRSATQTKRDV----------------- 743
Cdd:PRK09603  903 ikstpeerllraifgdkAGHVVNKSLycppslegtvidvkvftkkgyeKDARVLSAYEEEKAKldmehfdrltmlnreel 982

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   744 -------STQLRSTEAGIIDKV------------------------------------MVSTN--------SDGH----- 767
Cdd:PRK09603  983 lrvssllSQAILEEPFSHNGKDykegdqipkeeiasinrftlaslvkkyskevqnhyeITKNNfleqkkvlGEEHeekls 1062

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   768 -------------KFVKVRIRATKIPQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVE 834
Cdd:PRK09603 1063 ilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILE 1142

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   835 CQLSKVGSLSG------FEGDATPFTD------------------VTVEAVSNNLREQ--GYH---SRG----------- 874
Cdd:PRK09603 1143 MHLGLVGKEFGkqiasmLEDKTKDFAKelrakmleianainekdpLTIHALENCSDEEllEYAkdwSKGvkmaipvfegi 1222

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   875 --------FEI----------MYNGHTGRKLMAQVFLGPTYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:PRK09603 1223 sqekfyklFELakiamdgkmdLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRF 1302

RNA_pol_Rpb2_3

pfam04565

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...

275-338

3.72e-30

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

Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 113.39 E-value: 3.72e-30

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45545349   275 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSY 338
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67

PRK14844

DNA-directed RNA polymerase subunit beta/beta';

190-936

1.29e-22

DNA-directed RNA polymerase subunit beta/beta';

Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 105.09 E-value: 1.29e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   190 DDRDHFGKKRIDLAGPLLAGLFRMLFKRLTKDIRQYMTkcVDSGKEFNLPLAVKHTTITNGLRYSLATGTwgdqkkqmna 269
Cdd:PRK14844  464 DDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMS--TSSLDKVSPSDFINPKVLTNVLRDFFNSSQ---------- 531

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   270 rvgVSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMSYVS-VGSA 344
Cdd:PRK14844  532 ---LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkYGFI 608

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   345 SAPI-----------IEFLE--EWGMESLEDynPSAGRPSTKIFVNGVWLGVHSdpGHLVKTLRSLRRKTDISPEVSVvr 411
Cdd:PRK14844  609 ESPYrkvvnrvvtdqIEYLSaiDEGLYYIAD--TSAKLDENNCFVDDMLYCRYA--GSFVMVSSDQVSYIDVSPKQVI-- 682

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   412 direkelrlftdagRVCRPLFVVHDDESAEKSEAGSlvlkkeHVQRMAYSKEHPEddekfgwAQVLSNGIAEYLdAEEEE 491
Cdd:PRK14844  683 --------------SVAASLIPFLENDDANRALMGS------NMQRQAVPLLKPT-------APLVATGMESFV-ASGSG 734

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   492 TVMIAMTpddleatkhmmAGYVEPEDEKERKIAAEAAKRLRPAVNKAQHLwthceihpsmilgicasiipfpdhNQSPRN 571
Cdd:PRK14844  735 AVVLAKR-----------DGIVDSSDSNSIVIRAFDKERVNYLDVDIYHL------------------------RKFQRS 779

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   572 TYQSAMGKQAMgVFLTNYQVRMDTMANilyypqKPLATTRsmeylkfrELPAGQNAIVAILCYSGYNQEDSMIMNQSSID 651
Cdd:PRK14844  780 NHNTCINQKPL-VCVGDYVKEGDVIAD------GPAINSG--------ELALGQNLLVAFMSWQGYNFEDSIIISSEVVK 844

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   652 RGLFRSmfyrVYQDSEEKIDMNQAQEFEKPTRETTMKMKRSTYdKLEDDGLVAPGTRVSGEDVIVGKT------------ 719
Cdd:PRK14844  845 KDLFTS----IHIEEFECVVHDTPLGSEKITRAIPGVNEENLY-HLDDSGIVKIGTRVGPGYILVGKVtpkpslslppet 919

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   720 ---------------------------------------------AGLLKDENLADLASR-------------------- 734
Cdd:PRK14844  920 kllmtifgeksfdcadsslytspdvegtvidvqvftrrgveenerALLIKQKEINDFEKErdyiinvtseyfydelkkll 999

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   735 --SATQTK------------------RDVSTQLRSTEAGIIDKV---------MVSTNSDGHKF-------VKVRIRATK 778
Cdd:PRK14844 1000 inSGSQDRekfdsiereqwwgiglknQSISEQVKSLKKDFDEKVshaiaqfkrKVEKLHEGYDLpqgvsmsVKVFIAVKH 1079

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   779 IPQIGDKFASRHGQKGTIGVTYRNEDMPFTSEGIVPDLIINPHAIPSRMTVAHLVECQL--------SKVGSL------- 843
Cdd:PRK14844 1080 SLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVgwackklgEKVGNIldeinki 1159

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   844 -------------SGFEGDATPFTD------------------------------VTVE--------------------- 859
Cdd:PRK14844 1160 ksafckgirslndDNFTKFAAAYLDnkkienidddeitasvlntpnknalndelnELVEnylnscksaysnlrnflievy 1239

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545349   860 ------AVSNNLRE--------------------------------------QGYHSRGFEIMYNGHTGRKLMAQVFLGP 895
Cdd:PRK14844 1240 scgsnvSICNNIRDisdnnliefarklrdgipvaapvfegpkdeqiaklfelAGLDNSGQAVLYDGCSGEKFDRKVTVGY 1319

                         970       980       990      1000
                  ....*....|....*....|....*....|....*....|.
gi 45545349   896 TYYQRLKHLVDDKIHARARGPMQILTRQPVEGRARDGGLRF 936
Cdd:PRK14844 1320 MYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRF 1360

RNA_pol_Rpb2_5

pfam04567

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...

473-549

2.35e-19

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: 82.20 E-value: 2.35e-19

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45545349   473 WAQVLSNGIAEYLDAEEEETVMIAMTPDDLEATKHMMAGYvepedekerkiaaeaakrlrpavnKAQHLWTHCEIHP 549
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG------------------------PYAHTYTHCEIHP 53

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