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Conserved domains on  [gi|89274920|gb|ABD65901|]
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RNA polymerase II second largest subunit, partial [Serendipita indica]

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;
1-651 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: 714.42  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920     1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISNGLKYSLATGNWGDQqnamssKAG*S 80
Cdd:PRK08565  330 YANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------RTGVS 403

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    81 QVLNRYTYASTLSHLRRTNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSYSAPVGEFLDE 160
Cdd:PRK08565  404 QLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYE 483

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   161 WGMEALEENAQSDRPS-TKVFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSV--VRDIREKELRIYTDSGRVCRPLF 237
Cdd:PRK08565  484 LGVVPVEEAREEEYISwSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLI 563

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   238 VVEKDKLLITPEQVARLRDEKddpagYRWDNLFKDGVVELLDAEEEETVMICMSPEDLdarssgqvyhTEDmydpssrvk 317
Cdd:PRK08565  564 VVENGKPKLTREHVEKLKKGE-----LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL----------TPE--------- 619

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   318 tiikagsYSHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALE 397
Cdd:PRK08565  620 -------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALE 692

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   398 WLKFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKTAGQITLEEFEKPsrDTTLRMKHGN- 476
Cdd:PRK08565  693 IIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGEe 770

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   477 -YDKLDDDGLIAPGMNVIGEDIIIGKTAPlPPDSQEL-GQRTDRHTRRDVSTPLKSTESGIIDHVLITVDGEGSKFVKIR 554
Cdd:PRK08565  771 yYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEELeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVR 849

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   555 VRSTRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPF 634
Cdd:PRK08565  850 VRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929

                         650
                  ....*....|....*..
gi 89274920   635 TDLTVEQVSHALRAAGY 651
Cdd:PRK08565  930 YGEPEEELRKELLKLGY 946
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-651 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 714.42  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920     1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISNGLKYSLATGNWGDQqnamssKAG*S 80
Cdd:PRK08565  330 YANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------RTGVS 403

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    81 QVLNRYTYASTLSHLRRTNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSYSAPVGEFLDE 160
Cdd:PRK08565  404 QLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYE 483

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   161 WGMEALEENAQSDRPS-TKVFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSV--VRDIREKELRIYTDSGRVCRPLF 237
Cdd:PRK08565  484 LGVVPVEEAREEEYISwSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLI 563

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   238 VVEKDKLLITPEQVARLRDEKddpagYRWDNLFKDGVVELLDAEEEETVMICMSPEDLdarssgqvyhTEDmydpssrvk 317
Cdd:PRK08565  564 VVENGKPKLTREHVEKLKKGE-----LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL----------TPE--------- 619

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   318 tiikagsYSHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALE 397
Cdd:PRK08565  620 -------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALE 692

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   398 WLKFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKTAGQITLEEFEKPsrDTTLRMKHGN- 476
Cdd:PRK08565  693 IIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGEe 770

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   477 -YDKLDDDGLIAPGMNVIGEDIIIGKTAPlPPDSQEL-GQRTDRHTRRDVSTPLKSTESGIIDHVLITVDGEGSKFVKIR 554
Cdd:PRK08565  771 yYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEELeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVR 849

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   555 VRSTRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPF 634
Cdd:PRK08565  850 VRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929

                         650
                  ....*....|....*..
gi 89274920   635 TDLTVEQVSHALRAAGY 651
Cdd:PRK08565  930 YGEPEEELRKELLKLGY 946
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-654 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: 671.20  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISNGLKYSLATGNWGDQQNAMSsKAG*S 80
Cdd:cd00653 236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLS 314

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  81 QVLNRYTYASTLSHLRRTNT-PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISvgsysapvgefld 159
Cdd:cd00653 315 QVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------- 381

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 160 ewgmealeenaqsdrpstkvflngvwmgvhreptqllntlkhlrrteaihpevsvvrdirekelriytdsGRVCRPLFVV 239
Cdd:cd00653 382 ----------------------------------------------------------------------GRIERPYRIV 391

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 240 EKDkllitpeqvarlrdekddpagyrwdnlfkdgvvelldaeeeetvmicmspedldarssgqvyhtedmydpssrvkti 319
Cdd:cd00653 392 EKE----------------------------------------------------------------------------- 394

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 320 ikagsYSHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALEWL 399
Cdd:cd00653 395 -----VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYI 469

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 400 KFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKTagqiTLEEFEKPSRDTTLRMKHGNYDK 479
Cdd:cd00653 470 AFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRK----TKNGPEEITRGDIPNVSEEKLKN 545

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 480 LDDDGLIAPGMNVIGEDIIIGKTAPLPPDSQELGQRTDRHTRRDVSTPLKSTESGIIDHVLIT---VDGEGSKFVKIRVR 556
Cdd:cd00653 546 LDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDGGNKLVKVYIR 625

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 557 STRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTD 636
Cdd:cd00653 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDG 705

                       650
                ....*....|....*...
gi 89274920 637 LTVEQVSHALRAAGYQSR 654
Cdd:cd00653 706 AEEEDISELLGEAGLNYY 723
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 179-653 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: 529.98  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   179 VFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSVVRDIREKELRIYTDSGRVCRPLFVVEKDKLLITPEQVARLRDEK 258
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   259 ddpagYRWDNLFKDGVVELLDAEEEETVMICMSPEDLdarssgqvyhTEDmydpssrvktiikagsYSHCEIHPSMILGV 338
Cdd:TIGR03670  81 -----LTWDDLVKQGVIEYLDAEEEENAYIALDPEEL----------TPE----------------HTHLEIDPSAILGI 129

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   339 CASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALEWLKFRDLPAGQNAIVAILCYS 418
Cdd:TIGR03670 130 IASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYE 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   419 GYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKT--AGQitLEEFEKPSRDTTLRMKHGNYDKLDDDGLIAPGMNVIGED 496
Cdd:TIGR03670 210 GYNIEDALIMNKASIERGLARSTFFRTYEAEERRypGGQ--EDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGD 287

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   497 IIIGKTAplPP----DSQELGQRTDRhtRRDVSTPLKSTESGIIDHVLITVDGEGSKFVKIRVRSTRIPQVGDKFASRHG 572
Cdd:TIGR03670 288 VLIGKTS--PPrfleELREFGLVTER--RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHG 363

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   573 QKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTDLTVEQVSHALRAAGYQ 652
Cdd:TIGR03670 364 QKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFK 443


                  .
gi 89274920   653 S 653
Cdd:TIGR03670 444 P 444
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 339-652 2.11e-145

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: 426.95  E-value: 2.11e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   339 CASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALEWLKFRDLPAGQNAIVAILCYS 418
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   419 GYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKTAGQITlEEFEKPSRDttlrmKHGNYDKLDDDGLIAPGMNVIGEDII 498
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPIE-EITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   499 IGKTAPlPPDSQELGQRT--DRHTRRDVSTPLKSTESGIIDHVLI-TVDGEGSKFVKIRVRSTRIPQVGDKFASRHGQKG 575
Cdd:pfam00562 155 VGKVGP-TELTKLLRAIFgeKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKG 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 89274920   576 TIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFT--DLTVEQVSHALRAAGYQ 652
Cdd:pfam00562 234 VVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYN 312
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-653 9.14e-121

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: 382.92  E-value: 9.14e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVyRYlQKCVESGKAFDVGRAIKLGTISNGLKYSLATGnwgdqqnamsskaG*S 80
Cdd:COG0085  308 LGNRRVRLVGELLQNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLS 372

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   81 QVLNRYTYASTLSHLRRTNT----PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISvgsysa 152
Cdd:COG0085  373 QFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------ 442

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  153 pvgEFldewgmealeenaqsdrpstkvflngvwmgvhreptqllntlkhlrrteaihpevsvvrdirekelriytdsGRV 232
Cdd:COG0085  443 ---EY------------------------------------------------------------------------GFI 447

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  233 CRPLFVVEKdkllitpeqvARLRDEkddpagyrwdnlfkdgvVELLDAEEEETVMICMSPEDLDAR---SSGQV---YHT 306
Cdd:COG0085  448 ETPYRKVEN----------GKVTDE-----------------IEYLTADEEENYYIAQANAPLDEDgnfLEERVlvrYRG 500

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  307 EDMYDPSSRVKtiikagsysHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGislsnfLVRmdTMANILYYP 386
Cdd:COG0085  501 EEVLVPPEEVD---------YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVP------LLR--PEAPLLHYP 563

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  387 --------------QKPLAttRALEWLKFRD------------LPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRS 440
Cdd:COG0085  564 lqkfqrsnqgtcinQRPIV--RVGDRVEKGDvladgpatdngeLALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTS 641

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  441 IYYRSYM-DMEKTAG---QITleeFEKP--SRDTtlrmkhgnYDKLDDDGLIAPGMNVIGEDIIIGKTAP-----LPPDS 509
Cdd:COG0085  642 IHIEEYEiEARDTKLgpeEIT---RDIPnvSEEA--------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTPEE 710

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  510 QEL----GQRTdrHTRRDVSTPLKSTESGIIDHVLITVDGEGS-------KFVKIRVRSTRIPQVGDKFASRHGQKGTIG 578
Cdd:COG0085  711 RLLraifGEKA--REVRDTSLRVPHGEKGKVIDVKVFSREEGDelppgvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVIS 788

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 89274920  579 ILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTDLTVEQVSHALRAAGYQS 653
Cdd:COG0085  789 RILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPP 863
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-651 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 714.42  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920     1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISNGLKYSLATGNWGDQqnamssKAG*S 80
Cdd:PRK08565  330 YANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------RTGVS 403

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    81 QVLNRYTYASTLSHLRRTNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSYSAPVGEFLDE 160
Cdd:PRK08565  404 QLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYE 483

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   161 WGMEALEENAQSDRPS-TKVFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSV--VRDIREKELRIYTDSGRVCRPLF 237
Cdd:PRK08565  484 LGVVPVEEAREEEYISwSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLI 563

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   238 VVEKDKLLITPEQVARLRDEKddpagYRWDNLFKDGVVELLDAEEEETVMICMSPEDLdarssgqvyhTEDmydpssrvk 317
Cdd:PRK08565  564 VVENGKPKLTREHVEKLKKGE-----LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL----------TPE--------- 619

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   318 tiikagsYSHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALE 397
Cdd:PRK08565  620 -------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALE 692

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   398 WLKFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKTAGQITLEEFEKPsrDTTLRMKHGN- 476
Cdd:PRK08565  693 IIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGEe 770

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   477 -YDKLDDDGLIAPGMNVIGEDIIIGKTAPlPPDSQEL-GQRTDRHTRRDVSTPLKSTESGIIDHVLITVDGEGSKFVKIR 554
Cdd:PRK08565  771 yYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PRFLEELeELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVR 849

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   555 VRSTRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPF 634
Cdd:PRK08565  850 VRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929

                         650
                  ....*....|....*..
gi 89274920   635 TDLTVEQVSHALRAAGY 651
Cdd:PRK08565  930 YGEPEEELRKELLKLGY 946
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-654 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: 671.20  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISNGLKYSLATGNWGDQQNAMSsKAG*S 80
Cdd:cd00653 236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLS 314

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  81 QVLNRYTYASTLSHLRRTNT-PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISvgsysapvgefld 159
Cdd:cd00653 315 QVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------- 381

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 160 ewgmealeenaqsdrpstkvflngvwmgvhreptqllntlkhlrrteaihpevsvvrdirekelriytdsGRVCRPLFVV 239
Cdd:cd00653 382 ----------------------------------------------------------------------GRIERPYRIV 391

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 240 EKDkllitpeqvarlrdekddpagyrwdnlfkdgvvelldaeeeetvmicmspedldarssgqvyhtedmydpssrvkti 319
Cdd:cd00653 392 EKE----------------------------------------------------------------------------- 394

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 320 ikagsYSHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALEWL 399
Cdd:cd00653 395 -----VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYI 469

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 400 KFRDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKTagqiTLEEFEKPSRDTTLRMKHGNYDK 479
Cdd:cd00653 470 AFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRK----TKNGPEEITRGDIPNVSEEKLKN 545

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 480 LDDDGLIAPGMNVIGEDIIIGKTAPLPPDSQELGQRTDRHTRRDVSTPLKSTESGIIDHVLIT---VDGEGSKFVKIRVR 556
Cdd:cd00653 546 LDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDGGNKLVKVYIR 625

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920 557 STRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTD 636
Cdd:cd00653 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDG 705

                       650
                ....*....|....*...
gi 89274920 637 LTVEQVSHALRAAGYQSR 654
Cdd:cd00653 706 AEEEDISELLGEAGLNYY 723
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 179-653 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: 529.98  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   179 VFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSVVRDIREKELRIYTDSGRVCRPLFVVEKDKLLITPEQVARLRDEK 258
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   259 ddpagYRWDNLFKDGVVELLDAEEEETVMICMSPEDLdarssgqvyhTEDmydpssrvktiikagsYSHCEIHPSMILGV 338
Cdd:TIGR03670  81 -----LTWDDLVKQGVIEYLDAEEEENAYIALDPEEL----------TPE----------------HTHLEIDPSAILGI 129

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   339 CASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALEWLKFRDLPAGQNAIVAILCYS 418
Cdd:TIGR03670 130 IASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYE 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   419 GYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKT--AGQitLEEFEKPSRDTTLRMKHGNYDKLDDDGLIAPGMNVIGED 496
Cdd:TIGR03670 210 GYNIEDALIMNKASIERGLARSTFFRTYEAEERRypGGQ--EDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGD 287

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   497 IIIGKTAplPP----DSQELGQRTDRhtRRDVSTPLKSTESGIIDHVLITVDGEGSKFVKIRVRSTRIPQVGDKFASRHG 572
Cdd:TIGR03670 288 VLIGKTS--PPrfleELREFGLVTER--RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHG 363

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   573 QKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTDLTVEQVSHALRAAGYQ 652
Cdd:TIGR03670 364 QKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFK 443


                  .
gi 89274920   653 S 653
Cdd:TIGR03670 444 P 444
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 177-653 7.89e-174

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 508.35  E-value: 7.89e-174
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  177 TKVFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSVVRDIREKELRIYTDSGRVCRPLFVVEKDKLLITPEQVARLRD 256
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  257 EKDDpagyrWDNLFKDGVVELLDAEEEETVMICMSPEDLdarssgqvyhTEDmydpssrvktiikagsYSHCEIHPSMIL 336
Cdd:PRK07225  85 GELT-----FDDLVKQGVIEYLDAEEEENAYIAVYEEDL----------TEE----------------HTHLEIDPSLIL 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  337 GVCASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALEWLKFRDLPAGQNAIVAILC 416
Cdd:PRK07225 134 GIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMS 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  417 YSGYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKT--AGQItlEEFEKPSRDttLRMKHGN--YDKLDDDGLIAPGMNV 492
Cdd:PRK07225 214 YEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRypGGQE--DRFEIPDKD--VRGYRGEeaYRHLDEDGLVNPETEV 289

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  493 IGEDIIIGKTAPlP-----PDsqELGQRTDRhtRRDVSTPLKSTESGIIDHVLITVDGEGSKFVKIRVRSTRIPQVGDKF 567
Cdd:PRK07225 290 KEGDVLIGKTSP-PrfleePD--DFGISPEK--RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKF 364

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  568 ASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTDLTVEQVSHALR 647
Cdd:PRK07225 365 ASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALE 444


                 ....*.
gi 89274920  648 AAGYQS 653
Cdd:PRK07225 445 KLGFEH 450
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 339-652 2.11e-145

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: 426.95  E-value: 2.11e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   339 CASIVPFPDHNQSPRNTYQSAMGKQAMGISLSNFLVRMDTMANILYYPQKPLATTRALEWLKFRDLPAGQNAIVAILCYS 418
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   419 GYNQEDSVIMNQSSIDRGLFRSIYYRSYMDMEKTAGQITlEEFEKPSRDttlrmKHGNYDKLDDDGLIAPGMNVIGEDII 498
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPIE-EITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   499 IGKTAPlPPDSQELGQRT--DRHTRRDVSTPLKSTESGIIDHVLI-TVDGEGSKFVKIRVRSTRIPQVGDKFASRHGQKG 575
Cdd:pfam00562 155 VGKVGP-TELTKLLRAIFgeKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKG 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 89274920   576 TIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFT--DLTVEQVSHALRAAGYQ 652
Cdd:pfam00562 234 VVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYN 312
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-653 9.14e-121

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: 382.92  E-value: 9.14e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVyRYlQKCVESGKAFDVGRAIKLGTISNGLKYSLATGnwgdqqnamsskaG*S 80
Cdd:COG0085  308 LGNRRVRLVGELLQNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLS 372

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   81 QVLNRYTYASTLSHLRRTNT----PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISvgsysa 152
Cdd:COG0085  373 QFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------ 442

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  153 pvgEFldewgmealeenaqsdrpstkvflngvwmgvhreptqllntlkhlrrteaihpevsvvrdirekelriytdsGRV 232
Cdd:COG0085  443 ---EY------------------------------------------------------------------------GFI 447

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  233 CRPLFVVEKdkllitpeqvARLRDEkddpagyrwdnlfkdgvVELLDAEEEETVMICMSPEDLDAR---SSGQV---YHT 306
Cdd:COG0085  448 ETPYRKVEN----------GKVTDE-----------------IEYLTADEEENYYIAQANAPLDEDgnfLEERVlvrYRG 500

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  307 EDMYDPSSRVKtiikagsysHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMGislsnfLVRmdTMANILYYP 386
Cdd:COG0085  501 EEVLVPPEEVD---------YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVP------LLR--PEAPLLHYP 563

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  387 --------------QKPLAttRALEWLKFRD------------LPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRS 440
Cdd:COG0085  564 lqkfqrsnqgtcinQRPIV--RVGDRVEKGDvladgpatdngeLALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTS 641

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  441 IYYRSYM-DMEKTAG---QITleeFEKP--SRDTtlrmkhgnYDKLDDDGLIAPGMNVIGEDIIIGKTAP-----LPPDS 509
Cdd:COG0085  642 IHIEEYEiEARDTKLgpeEIT---RDIPnvSEEA--------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTPEE 710

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920  510 QEL----GQRTdrHTRRDVSTPLKSTESGIIDHVLITVDGEGS-------KFVKIRVRSTRIPQVGDKFASRHGQKGTIG 578
Cdd:COG0085  711 RLLraifGEKA--REVRDTSLRVPHGEKGKVIDVKVFSREEGDelppgvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVIS 788

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 89274920  579 ILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVATLNGQEGDATPFTDLTVEQVSHALRAAGYQS 653
Cdd:COG0085  789 RILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPP 863
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 4-164 1.43e-35

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 140.47  E-value: 1.43e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    4 KRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISNGLKYSLATGNWgdqqnaMSSKAG*SQVL 83
Cdd:PRK09606 336 KRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLL 409

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   84 NRYTYASTLSHLRRTNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISVGSYSAPVGEFLDEWGM 163
Cdd:PRK09606 410 DRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGV 489


                 .
gi 89274920  164 E 164
Cdd:PRK09606 490 E 490
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 80-651 2.66e-35

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: 143.26  E-value: 2.66e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920     80 SQVLNRYTYASTLSHLRRTNT--P--LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACISvgsysapvg 155
Cdd:TIGR02013  388 SQFMDQTNPLAELTHKRRLSAlgPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN--------- 458

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    156 efldEWGmealeenaqsdrpstkvFLngvwmgvhreptqllntlkhlrrtEAIHPEVSVVRDIREKELRIYTdsgrvcrp 235
Cdd:TIGR02013  459 ----EYG-----------------FI------------------------ETPYRKVKDGKVVVTDEIDYLT-------- 485

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    236 lfVVEKDKLLITPEQVARlrDEkddpagyrwDNLFKDGVVElldaeeeetvmicmspedldARSSGqvyhtEDMYDPSSR 315
Cdd:TIGR02013  486 --ADEEDNYVIAQANAPL--DE---------NGRFVEDLVV--------------------ARYRG-----EITLVSPDQ 527

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    316 VktiikagsySHCEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAMG----------------------------- 366
Cdd:TIGR02013  528 V---------DYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPllrseaplvgtgmeakvardsgavivakr 598

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    367 ------ISLSNFLVR-----MDTMANILYYP--------------QKPL-----------------ATTRAlewlkfrDL 404
Cdd:TIGR02013  599 ggvveyVDAKRIVIRydedeEEPDGGIDIYRllkyqrsnqdtcinQRPIvsvgdrveagdvladgpSTDLG-------EL 671

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    405 PAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYyrsymdmektagqitLEEFEKPSRDTtlrmKHG--------- 475
Cdd:TIGR02013  672 ALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIH---------------IEEYEVEARDT----KLGpeeitrdip 732

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    476 -----NYDKLDDDGLIAPGMNVIGEDIIIGKTAP-----LPPDSQEL----GQRTdRHTRrDVSTPLKSTESGIIDHVLI 541
Cdd:TIGR02013  733 nvseeALRNLDENGIVRIGAEVKAGDILVGKVTPkgeteLTPEEKLLraifGEKA-RDVR-DTSLRVPPGVEGTVIDVKV 810

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    542 TVDGEG-------SKFVKIRVRSTRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLV 614
Cdd:TIGR02013  811 FSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIL 890

                          650       660       670       680
                   ....*....|....*....|....*....|....*....|
gi 89274920    615 ECLLSKVATLNGQEGD--ATP-FTDLTVEQVSHALRAAGY 651
Cdd:TIGR02013  891 ETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGL 930
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 179-240 1.69e-31

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: 116.70  E-value: 1.69e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 89274920   179 VFLNGVWMGVHREPTQLLNTLKHLRRTEAIHPEVSVVRDIREKELRIYTDSGRVCRPLFVVE 240
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 81-143 1.02e-30

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


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 114.55  E-value: 1.02e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 89274920    81 QVLNRYTYASTLSHLRRTNTP---LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMA 143
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPrggLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-618 1.39e-29

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 125.20  E-value: 1.39e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920     1 FGKKRLDLAGPLLSTLFRMLFRkvvkdvyRYLQKCVESGKAFDVGRAIKLGTISNGLKYSLATGNWGDQQnamsskag*S 80
Cdd:CHL00207  303 LKNRRVRSVGELLQNQFRIGLK-------RLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQ--------LS 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    81 QVLNRYTYASTLSHLRRTNTpLGREG----KIAKP-RQLHNTHWGMVCPAETPEGQACGLVKnlSLMACISVGSYSapvg 155
Cdd:CHL00207  368 QYMDQTNPLSELTHKRRISI-LGPGGldkdRISFAvRDIHPSHYGRICPIETPEGPNCGLIG--SLATNARINKFG---- 440

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   156 eFLDEwgmealeenaqsdrPSTKVFLNGVwmgvhreptqllntlkhlrrteaihpevsvvrdiREKELRIYTDSgrvcrp 235
Cdd:CHL00207  441 -FIET--------------PFYKVINGKV----------------------------------KKFGNPIYLTA------ 465

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   236 lfvVEKDKLLITPEQVArlrdekddpagYRWDNLFKDGVVELLDAEEEETVMIcmspedldarssgqvyhtedmydpsSR 315
Cdd:CHL00207  466 ---DSEDLYRIAPNDIN-----------LNKNNYFKKNIIPVRYKQEFKTVNP-------------------------SK 506

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   316 VKTIikagsyshcEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAM------------------------------ 365
Cdd:CHL00207  507 VDFI---------AISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVpllypekpivgtgyekqialdsgmtiislt 577

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   366 -GI--SLSNF--LVRMDTMANILYYPQKPLATT-------RALEW----------------LKFRDLPAGQNAIVAILCY 417
Cdd:CHL00207  578 eGIvvSVSAYkiIIQDDNNRYIHYYLQKYQRSNqntcinyRPIVWvgekinigqiladgsdIDNSELALGQNVLVAYMPW 657

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   418 SGYNQEDSVIMNQSSIDRGLFRSIYYRSYmdmektagQITLEEFEKPSRDTTLRM-KHGNYD--KLDDDGLIAPGMNVIG 494
Cdd:CHL00207  658 EGYNFEDAILINKRLVYEDLFTSIHIEKY--------EIELRQTKLGSEEITRNIpNVSEYSlkNLDENGIISIGSKVLA 729

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   495 EDIIIGKTAPLPPDSQ----ELGQRTDRHTRRDV---STPLKSTESGIIDHVLITVDGEGSK-----FVKIRV--RSTRI 560
Cdd:CHL00207  730 GDILVGKITPKGESDQlpegKLLRAIFGEKAKDVkdtSLRMPNGGYGRVIKVEIFSRSKGDElkfgyYLKIRVfiAQIRK 809

                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 89274920   561 PQVGDKFASRHGQKGTIG-ILYRQeDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLL 618
Cdd:CHL00207  810 IQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLL 867
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 407-651 5.82e-28

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 120.21  E-value: 5.82e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   407 GQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYyrsymdmektagqitLEEFEKPSRDTtlrmKHGNYD-------- 478
Cdd:PRK00405  716 GQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIH---------------IEEYEIEARDT----KLGPEEitrdipnv 776

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   479 ------KLDDDGLIAPGMNVIGEDIIIGKTAP-----LPPDSQEL----GQRTdRHTRrDVSTPLKSTESGI-IDHVLIT 542
Cdd:PRK00405  777 seealrNLDESGIVRIGAEVKPGDILVGKVTPkgeteLTPEEKLLraifGEKA-RDVK-DTSLRVPHGEEGTvIDVKVFT 854

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   543 VDGEGS-------KFVKIRVRSTRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVE 615
Cdd:PRK00405  855 RIEQGDelppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILE 934

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 89274920   616 CLLSKVATLNGQEGdATP-FTDLTVEQVSHALRAAGY 651
Cdd:PRK00405  935 THLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGL 970
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 266-332 2.92e-22

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: 89.91  E-value: 2.92e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 89274920   266 WDNLFKDGVVELLDAEEEETVMICMSPEDLDARSSGQvyhtedmydpssrvKTIIKAGSYSHCEIHP 332
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE--------------REGPYAHTYTHCEIHP 53
rpoB CHL00001
RNA polymerase beta subunit
 407-634 4.10e-22

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 101.90  E-value: 4.10e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   407 GQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYYRSYmdmEKTAgQITLEEFEK-----PSRDTTLrMKHgnydkLD 481
Cdd:CHL00001  652 GKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY---EIQT-HVTSQGPERitkeiPHLEAHL-LRN-----LD 721

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   482 DDGLIAPGMNVIGEDIIIGKTAPLPPDSQE-----------LGQRTDrhTRRDvsTPLKSTESG---IIDHVLITVDG-- 545
Cdd:CHL00001  722 KNGIVMLGSWVETGDILVGKLTPQEAEESSyapegrllraiFGIQVS--TSKE--TCLKLPIGGrgrVIDVRWIQKKGgs 797

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   546 -EGSKFVKIRVRSTRIPQVGDKFASRHGQKGTIG-ILYRQeDMPFSADGIVPDLIINPHAIPSRMTIGHLVECLLSKVAT 623
Cdd:CHL00001  798 sYNPETIHVYILQKREIQVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGD 876

                         250
                  ....*....|.
gi 89274920   624 LNGQEGDATPF 634
Cdd:CHL00001  877 LLNRHYRIAPF 887
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
80-628 4.89e-16

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 82.66  E-value: 4.89e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    80 SQVLNRYTYASTLSHLRRTNTpLGrEGKIAK------PRQLHNTHWGMVCPAETPEGQACGLVKNLSLMacisvgsysap 153
Cdd:PRK09603  526 SQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLSTF----------- 592

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   154 vgefldewgmealeenaqsdrpsTKVflngvwmgvhreptqllNTLKHLrrtEAihPEVSVVRDIREKELrIYtdsgrvc 233
Cdd:PRK09603  593 -----------------------TRV-----------------NDLGFI---EA--PYKKVVDGKVVGET-IY------- 619

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   234 rpLFVVEKDKLLITPEQVArlrdekddpagyrwdnLFKDGVVElldaeeeetvmicmspEDL-DARSSGQVYHTEdmydp 312
Cdd:PRK09603  620 --LTAIQEDSHIIAPASTP----------------IDEEGNIL----------------GDLiETRVEGEIVLNE----- 660

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   313 SSRVKTIikagsyshcEIHPSMILGVCASIVPFPDHNQSPRNTYQSAMGKQAM----------GISLSNFLVR------- 375
Cdd:PRK09603  661 KSKVTLM---------DLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivGTGIEKIIARdswgaik 731

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   376 --------------------MDTMANILYYP-QKPLATTRALEW-----------------------LKFRDLPAGQNAI 411
Cdd:PRK09603  732 anragvvekidskniyilgeGKEEAYIDAYSlQKNLRTNQNTSFnqvpivkvgdkveagqiiadgpsMDRGELALGKNVR 811

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   412 VAILCYSGYNQEDSVIMNQSSIDRGLFRS--IYYRSYMDMEKTAGqitLEEFEKPSRDTtlrmKHGNYDKLDDDGLIAPG 489
Cdd:PRK09603  812 VAFMPWNGYNFEDAIVVSERITKDDIFTSthIYEKEVDARELKHG---VEEFTADIPDV----KEEALAHLDESGIVKVG 884

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   490 MNVIGEDIIIGKTAP---LPPDSQE------LGQRTDRHTRRDVSTPlKSTESGIIDHVLITVDG--------------- 545
Cdd:PRK09603  885 TYVSAGMILVGKTSPkgeIKSTPEErllraiFGDKAGHVVNKSLYCP-PSLEGTVIDVKVFTKKGyekdarvlsayeeek 963

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   546 -------------------------------------------EGS---------------------------------- 548
Cdd:PRK09603  964 akldmehfdrltmlnreellrvssllsqaileepfshngkdykEGDqipkeeiasinrftlaslvkkyskevqnhyeitk 1043

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   549 --------------------------------KFVKIRVRSTRIPQVGDKFASRHGQKGTIGILYRQEDMPFSADGIVPD 596
Cdd:PRK09603 1044 nnfleqkkvlgeeheeklsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVD 1123

                         730       740       750
                  ....*....|....*....|....*....|..
gi 89274920   597 LIINPHAIPSRMTIGHLVECLLSKVATLNGQE 628
Cdd:PRK09603 1124 IVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQ 1155
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
80-615 5.47e-16

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 82.36  E-value: 5.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920    80 SQVLNRYTYASTLSHLRRTNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMACIS-VGSYSAPV 154
Cdd:PRK14844  533 SQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkYGFIESPY 612

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   155 GEFLDEWGMEALEenaqsdrpstkvFLNGVWMGVHreptqllntlkHLRRTEAihpevsvvrdiREKELRIYTDSGRVCR 234
Cdd:PRK14844  613 RKVVNRVVTDQIE------------YLSAIDEGLY-----------YIADTSA-----------KLDENNCFVDDMLYCR 658

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   235 ---PLFVVEKDKLL---ITPEQVARLRD------EKDDPAGYRWDNLFKDGVVELLdaeEEETVMICMSPEDLDARSSGQ 302
Cdd:PRK14844  659 yagSFVMVSSDQVSyidVSPKQVISVAAslipflENDDANRALMGSNMQRQAVPLL---KPTAPLVATGMESFVASGSGA 735

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   303 VY--HTEDMYDPSSRVKTIIKAGSYSHCEIhpsmiLGVcaSIVPFPDHNQSPRNTYQSamgkQAMGISLSNFLVRMDTMA 380
Cdd:PRK14844  736 VVlaKRDGIVDSSDSNSIVIRAFDKERVNY-----LDV--DIYHLRKFQRSNHNTCIN----QKPLVCVGDYVKEGDVIA 804

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   381 NilyypqKPLATTRalewlkfrDLPAGQNAIVAILCYSGYNQEDSVIMNQSSIDRGLFRSIYyrsymdmektagqitLEE 460
Cdd:PRK14844  805 D------GPAINSG--------ELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIH---------------IEE 855

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   461 FEKPSRDTTLR----------MKHGNYDKLDDDGLIAPGMNVIGEDIIIGKTAP-----LPPDSQEL----GQRT----- 516
Cdd:PRK14844  856 FECVVHDTPLGsekitraipgVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPkpslsLPPETKLLmtifGEKSfdcad 935

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   517 ---------------------------------------DRHTRRD---------------------------------- 523
Cdd:PRK14844  936 sslytspdvegtvidvqvftrrgveenerallikqkeinDFEKERDyiinvtseyfydelkkllinsgsqdrekfdsier 1015

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274920   524 ------------VSTPLKSTESGIIDHVLITVDG---------EG-------SKFVKIRVRSTRIPQVGDKFASRHGQKG 575
Cdd:PRK14844 1016 eqwwgiglknqsISEQVKSLKKDFDEKVSHAIAQfkrkveklhEGydlpqgvSMSVKVFIAVKHSLQPGDKMAGRHGNKG 1095

                         650       660       670       680
                  ....*....|....*....|....*....|....*....|
gi 89274920   576 TIGILYRQEDMPFSADGIVPDLIINPHAIPSRMTIGHLVE 615
Cdd:PRK14844 1096 VISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILE 1135
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-55 1.61e-13

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: 72.80  E-value: 1.61e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 89274920     1 FGKKRLDLAGPLLSTLFRMLFRKVVKDVYRYLQKCVESGKAFDVGRAIKLGTISN 55
Cdd:pfam04563 342 LGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
 
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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