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Conserved domains on  [gi|68131884|gb|AAY85220|]
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RNA polymerase II second largest subunit, partial [Berberis nervosa]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 1000145)

DNA-directed RNA polymerase subunit B family protein similar to fungal DNA-directed RNA polymerase II subunit RPB2

CATH:  3.90.1110.10|3.90.1070.20
EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0000428|GO:0008270|GO:0003677|GO:0006351
PubMed:  11839495
SCOP:  4003708

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-540 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: 658.96  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884     1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPSVIPTAHKIFVNGCWVGIHRNPELLVKTLRQLRR 80
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    81 QVDVNTEVGI--IRDFSLKELRLYTDYGRCSRPLFIVENQRLLIKKKDIralqqrESLDEG--GWHDLVAKGYIEYVDTE 156
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHV------EKLKKGelTFDDLVKMGVIEYLDAE 602

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   157 EEETTMISMTIDDLVNArtnpnetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMD 236
Cdd:PRK08565  603 EEENAYVALDPEDLTPE----------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTD 672

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   237 TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLV 316
Cdd:PRK08565  673 TRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQ 752

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   317 KEDFGRPNrENTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAPDETQGGVASQyTKRDHSTSLRHSESGM 393
Cdd:PRK08565  753 EDKIEIPE-PNVRGYRgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQ-ERRDTSVTVRHGEKGI 830

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   394 VDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIE 473
Cdd:PRK08565  831 VDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 910

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68131884   474 CIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:PRK08565  911 SIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKL 977
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-540 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 658.96  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884     1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPSVIPTAHKIFVNGCWVGIHRNPELLVKTLRQLRR 80
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    81 QVDVNTEVGI--IRDFSLKELRLYTDYGRCSRPLFIVENQRLLIKKKDIralqqrESLDEG--GWHDLVAKGYIEYVDTE 156
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHV------EKLKKGelTFDDLVKMGVIEYLDAE 602

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   157 EEETTMISMTIDDLVNArtnpnetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMD 236
Cdd:PRK08565  603 EEENAYVALDPEDLTPE----------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTD 672

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   237 TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLV 316
Cdd:PRK08565  673 TRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQ 752

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   317 KEDFGRPNrENTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAPDETQGGVASQyTKRDHSTSLRHSESGM 393
Cdd:PRK08565  753 EDKIEIPE-PNVRGYRgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQ-ERRDTSVTVRHGEKGI 830

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   394 VDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIE 473
Cdd:PRK08565  831 VDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 910

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68131884   474 CIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:PRK08565  911 SIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKL 977
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-540 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: 590.69  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   1 ETPEGQACGLVKNLALMVYITvgsaanpilefleewstenfeeispsviptahkifvngcwvgihrnpellvktlrqlrr 80
Cdd:cd00653 361 ETPEGENCGLVKNLALMARIS----------------------------------------------------------- 381

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  81 qvdvntevgiirdfslkelrlytdyGRCSRPLFIVENQrllikkkdiralqqresldeggwhdlvakgyieyvdteeeet 160
Cdd:cd00653 382 -------------------------GRIERPYRIVEKE------------------------------------------ 394

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 161 tmismtiddlvnartnpnetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAY 240
Cdd:cd00653 395 -----------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLY 451

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 241 VLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF 320
Cdd:cd00653 452 LLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT 531

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 321 grpnRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAPDE-TQGGVASQYTKRDHSTSLRHSESGMVDQVLL 399
Cdd:cd00653 532 ----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETEsTPIFGEKARDVRDTSLKYPGGEKGIVDDVKI 607

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 400 TT---NADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIM 476
Cdd:cd00653 608 FSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687

                       490       500       510       520       530       540
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 68131884 477 GKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:cd00653 688 GKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 55-540 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: 573.51  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    55 IFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGIIRDFSLKELRLYTDYGRCSRPLFIVENQRLLIKKKDIRALQQRE 134
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   135 SldegGWHDLVAKGYIEYVDTEEEETTMISMTIDDLvnartNPNetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPRNT 214
Cdd:TIGR03670  81 L----TWDDLVKQGVIEYLDAEEEENAYIALDPEEL-----TPE-----HTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   215 YQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDR 294
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   295 GFFRSLFFRSYRDEEKKMGTLVKEDFGRPNREnTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPiaP---DETQ 370
Cdd:TIGR03670 227 GLARSTFFRTYEAEERRYPGGQEDRFEIPEPD-VRGYRgEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP--PrflEELR 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   371 GGVASQYTKRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEG 450
Cdd:TIGR03670 304 EFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDG 383

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   451 ITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMI 530
Cdd:TIGR03670 384 IVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEI 463

                         490
                  ....*....|
gi 68131884   531 FLGPTYYQRL 540
Cdd:TIGR03670 464 FIGVIYYQKL 473
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 198-540 9.24e-169

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: 482.41  E-value: 9.24e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   198 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYS 277
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   278 GYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTlVKEDFGRPNREntmgmRHGSYDKLDDDGLAPPGTRVSGEDVI 357
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-IEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   358 IGKTTPIAPDE--TQGGVASQYTKRDHSTSLRHSESGMVDQVLL-TTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGT 434
Cdd:pfam00562 155 VGKVGPTELTKllRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   435 VGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT--DVTVDNISKALHKCGYQMR 512
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYY 314

                         330       340
                  ....*....|....*....|....*...
gi 68131884   513 GFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKL 342
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-540 6.09e-117

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: 369.05  E-value: 6.09e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    1 ETPEGQACGLVKNLALMVYITVgsaanpilefleewstenfeeispsviptahkifvngcwvgihrnpellvktlrqlrr 80
Cdd:COG0085  422 ETPEGPNIGLIGSLALYARVNE---------------------------------------------------------- 443

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   81 qvdvntevgiirdfslkelrlytdYGRCSRPLFIVENQRLLikkkdiralqqreslDEggwhdlvakgyIEYVDTEEEET 160
Cdd:COG0085  444 ------------------------YGFIETPYRKVENGKVT---------------DE-----------IEYLTADEEEN 473

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  161 TMIS----------MTIDDLVNARTNPNETYQL---YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIY 227
Cdd:COG0085  474 YYIAqanapldedgNFLEERVLVRYRGEEVLVPpeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLL 553

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  228 VTNYQLrmdtLAYVLY----------YPQKPLVttRAMEHLHFRQ------------LPAGINAIVAIACYSGYNQEDSV 285
Cdd:COG0085  554 RPEAPL----LHYPLQkfqrsnqgtcINQRPIV--RVGDRVEKGDvladgpatdngeLALGQNLLVAFMPWEGYNYEDAI 627

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  286 IMNQSSIDRGFFRSLFFRSYRDEEK--KMGtlvKEDFGR--PNrentmgmrHG--SYDKLDDDGLAPPGTRVSGEDVIIG 359
Cdd:COG0085  628 IISERLVKDDVLTSIHIEEYEIEARdtKLG---PEEITRdiPN--------VSeeALRNLDEDGIIRIGAEVKGGDILVG 696

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  360 KTTPiaPDETQ-----------GGVASQYtKRDHSTSLRHSESGMVDQVLLTTNADG-------LRFVKVRMRSVRIPQI 421
Cdd:COG0085  697 KVTP--KGETEltpeerllraiFGEKARE-VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEV 773

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  422 GDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNIS 501
Cdd:COG0085  774 GDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIR 853

                        570       580       590
                 ....*....|....*....|....*....|....*....
gi 68131884  502 KALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:COG0085  854 ELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKL 892
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-540 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 658.96  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884     1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEWSTENFEEISPSVIPTAHKIFVNGCWVGIHRNPELLVKTLRQLRR 80
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    81 QVDVNTEVGI--IRDFSLKELRLYTDYGRCSRPLFIVENQRLLIKKKDIralqqrESLDEG--GWHDLVAKGYIEYVDTE 156
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHV------EKLKKGelTFDDLVKMGVIEYLDAE 602

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   157 EEETTMISMTIDDLVNArtnpnetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMD 236
Cdd:PRK08565  603 EEENAYVALDPEDLTPE----------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTD 672

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   237 TLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLV 316
Cdd:PRK08565  673 TRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQ 752

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   317 KEDFGRPNrENTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP--IAPDETQGGVASQyTKRDHSTSLRHSESGM 393
Cdd:PRK08565  753 EDKIEIPE-PNVRGYRgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQ-ERRDTSVTVRHGEKGI 830

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   394 VDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIE 473
Cdd:PRK08565  831 VDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 910

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68131884   474 CIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:PRK08565  911 SIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKL 977
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-540 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: 590.69  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   1 ETPEGQACGLVKNLALMVYITvgsaanpilefleewstenfeeispsviptahkifvngcwvgihrnpellvktlrqlrr 80
Cdd:cd00653 361 ETPEGENCGLVKNLALMARIS----------------------------------------------------------- 381

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  81 qvdvntevgiirdfslkelrlytdyGRCSRPLFIVENQrllikkkdiralqqresldeggwhdlvakgyieyvdteeeet 160
Cdd:cd00653 382 -------------------------GRIERPYRIVEKE------------------------------------------ 394

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 161 tmismtiddlvnartnpnetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAY 240
Cdd:cd00653 395 -----------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLY 451

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 241 VLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDF 320
Cdd:cd00653 452 LLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT 531

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 321 grpnRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIAPDE-TQGGVASQYTKRDHSTSLRHSESGMVDQVLL 399
Cdd:cd00653 532 ----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETEsTPIFGEKARDVRDTSLKYPGGEKGIVDDVKI 607

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884 400 TT---NADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIM 476
Cdd:cd00653 608 FSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687

                       490       500       510       520       530       540
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 68131884 477 GKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:cd00653 688 GKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 55-540 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: 573.51  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    55 IFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGIIRDFSLKELRLYTDYGRCSRPLFIVENQRLLIKKKDIRALQQRE 134
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   135 SldegGWHDLVAKGYIEYVDTEEEETTMISMTIDDLvnartNPNetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPRNT 214
Cdd:TIGR03670  81 L----TWDDLVKQGVIEYLDAEEEENAYIALDPEEL-----TPE-----HTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   215 YQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDR 294
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   295 GFFRSLFFRSYRDEEKKMGTLVKEDFGRPNREnTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPiaP---DETQ 370
Cdd:TIGR03670 227 GLARSTFFRTYEAEERRYPGGQEDRFEIPEPD-VRGYRgEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP--PrflEELR 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   371 GGVASQYTKRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEG 450
Cdd:TIGR03670 304 EFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDG 383

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   451 ITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTAMI 530
Cdd:TIGR03670 384 IVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEI 463

                         490
                  ....*....|
gi 68131884   531 FLGPTYYQRL 540
Cdd:TIGR03670 464 FIGVIYYQKL 473
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 54-540 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 558.81  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   54 KIFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGI-IRDFSlKELRLYTDYGRCSRPLFIVENQRLLIKKKDIRALQQ 132
Cdd:PRK07225   6 KVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVsYKEET-NEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  133 RESldegGWHDLVAKGYIEYVDTEEEETTMISMTIDDLvnartNPNetyqlYTHCEIHPSLILGVCASIIPFPDHNQSPR 212
Cdd:PRK07225  85 GEL----TFDDLVKQGVIEYLDAEEEENAYIAVYEEDL-----TEE-----HTHLEIDPSLILGIGAGMIPYPEHNASPR 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  213 NTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSI 292
Cdd:PRK07225 151 ITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASI 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  293 DRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPNRENTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPI----APDE 368
Cdd:PRK07225 231 ERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPrfleEPDD 310

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  369 TqGGVASQytKRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTM 448
Cdd:PRK07225 311 F-GISPEK--RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTE 387

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  449 EGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRKLTA 528
Cdd:PRK07225 388 SGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEA 467

                        490
                 ....*....|..
gi 68131884  529 MIFLGPTYYQRL 540
Cdd:PRK07225 468 EIFVGVIYYQKL 479
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 198-540 9.24e-169

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: 482.41  E-value: 9.24e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   198 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQLRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYS 277
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   278 GYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTlVKEDFGRPNREntmgmRHGSYDKLDDDGLAPPGTRVSGEDVI 357
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-IEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   358 IGKTTPIAPDE--TQGGVASQYTKRDHSTSLRHSESGMVDQVLL-TTNADGLRFVKVRMRSVRIPQIGDKFSSRHGQKGT 434
Cdd:pfam00562 155 VGKVGPTELTKllRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   435 VGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT--DVTVDNISKALHKCGYQMR 512
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYY 314

                         330       340
                  ....*....|....*....|....*...
gi 68131884   513 GFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKL 342
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-540 6.09e-117

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: 369.05  E-value: 6.09e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    1 ETPEGQACGLVKNLALMVYITVgsaanpilefleewstenfeeispsviptahkifvngcwvgihrnpellvktlrqlrr 80
Cdd:COG0085  422 ETPEGPNIGLIGSLALYARVNE---------------------------------------------------------- 443

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   81 qvdvntevgiirdfslkelrlytdYGRCSRPLFIVENQRLLikkkdiralqqreslDEggwhdlvakgyIEYVDTEEEET 160
Cdd:COG0085  444 ------------------------YGFIETPYRKVENGKVT---------------DE-----------IEYLTADEEEN 473

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  161 TMIS----------MTIDDLVNARTNPNETYQL---YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIY 227
Cdd:COG0085  474 YYIAqanapldedgNFLEERVLVRYRGEEVLVPpeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLL 553

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  228 VTNYQLrmdtLAYVLY----------YPQKPLVttRAMEHLHFRQ------------LPAGINAIVAIACYSGYNQEDSV 285
Cdd:COG0085  554 RPEAPL----LHYPLQkfqrsnqgtcINQRPIV--RVGDRVEKGDvladgpatdngeLALGQNLLVAFMPWEGYNYEDAI 627

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  286 IMNQSSIDRGFFRSLFFRSYRDEEK--KMGtlvKEDFGR--PNrentmgmrHG--SYDKLDDDGLAPPGTRVSGEDVIIG 359
Cdd:COG0085  628 IISERLVKDDVLTSIHIEEYEIEARdtKLG---PEEITRdiPN--------VSeeALRNLDEDGIIRIGAEVKGGDILVG 696

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  360 KTTPiaPDETQ-----------GGVASQYtKRDHSTSLRHSESGMVDQVLLTTNADG-------LRFVKVRMRSVRIPQI 421
Cdd:COG0085  697 KVTP--KGETEltpeerllraiFGEKARE-VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEV 773

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884  422 GDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNIS 501
Cdd:COG0085  774 GDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIR 853

                        570       580       590
                 ....*....|....*....|....*....|....*....
gi 68131884  502 KALHKCGYQMRGFETMYNGHTGRKLTAMIFLGPTYYQRL 540
Cdd:COG0085  854 ELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKL 892
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 150-540 2.10e-40

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: 156.75  E-value: 2.10e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    150 IEYVDTEEEETTMIS----------MTIDDLVNARTNPNETYQL---YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQ 216
Cdd:TIGR02013  481 IDYLTADEEDNYVIAqanapldengRFVEDLVVARYRGEITLVSpdqVDYMDVSPKQVVSVAASLIPFLEHDDANRALMG 560

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    217 SAMGKQAM----------------------------------------GIYVTNYQLRMDTLAYVLYYP----------- 245
Cdd:TIGR02013  561 SNMQRQAVpllrseaplvgtgmeakvardsgavivakrggvveyvdakRIVIRYDEDEEEPDGGIDIYRllkyqrsnqdt 640

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    246 ---QKPLVTT-------------RAMEHlhfRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE- 308
Cdd:TIGR02013  641 cinQRPIVSVgdrveagdvladgPSTDL---GELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEa 717

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    309 -EKKMGtlvKEDFGR--PN-RENTMgmrhgsyDKLDDDGLAPPGTRVSGEDVIIGKTTP-----IAPDETQ-----GGVA 374
Cdd:TIGR02013  718 rDTKLG---PEEITRdiPNvSEEAL-------RNLDENGIVRIGAEVKAGDILVGKVTPkgeteLTPEEKLlraifGEKA 787

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    375 SQYtkRDHSTSLRHSESGMVDQVLLTTNADG-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWT 447
Cdd:TIGR02013  788 RDV--RDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFL 865

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884    448 MEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD--ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 524
Cdd:TIGR02013  866 EDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGE 945

                          490
                   ....*....|....*.
gi 68131884    525 KLTAMIFLGPTYYQRL 540
Cdd:TIGR02013  946 QFDRPVTVGYMYMLKL 961
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 55-116 4.20e-27

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: 103.60  E-value: 4.20e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 68131884    55 IFVNGCWVGIHRNPELLVKTLRQLRRQVDVNTEVGIIRDFSLKELRLYTDYGRCSRPLFIVE 116
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 189-540 5.62e-27

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 115.96  E-value: 5.62e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   189 IHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------GI--YVTNYQLRM 235
Cdd:CHL00207  512 ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVpllypekpivgtgyekqialdsgmtiislteGIvvSVSAYKIII 591

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   236 --DTLAYVLYYPQK-------------PLV-------------TTRAMEHlhfRQLPAGINAIVAIACYSGYNQEDSVIM 287
Cdd:CHL00207  592 qdDNNRYIHYYLQKyqrsnqntcinyrPIVwvgekinigqilaDGSDIDN---SELALGQNVLVAYMPWEGYNFEDAILI 668

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   288 NQSSIDRGFFRSLFFRSYrDEEKKMGTLVKEDFGR--PNrentmgMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIA 365
Cdd:CHL00207  669 NKRLVYEDLFTSIHIEKY-EIELRQTKLGSEEITRniPN------VSEYSLKNLDENGIISIGSKVLAGDILVGKITPKG 741

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   366 PDETQGGVASQY-----TKRD-HSTSLRHS--ESGMVDQVLLTTNADGLRF-------VKVRMRSVRIPQIGDKFSSRHG 430
Cdd:CHL00207  742 ESDQLPEGKLLRaifgeKAKDvKDTSLRMPngGYGRVIKVEIFSRSKGDELkfgyylkIRVFIAQIRKIQVGDKLAGRHG 821

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   431 QKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKAL----HK 506
Cdd:CHL00207  822 NKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILinnkLN 901

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 68131884   507 CGYQMRGFETMYN-----------GHTGRKLTAMIFLGPTYYQRL 540
Cdd:CHL00207  902 QASIKNNEYWLFNsyhpgkmvlrdGRTGYKFKNPVTVGIAYMLKL 946
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 266-525 7.76e-26

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 112.50  E-value: 7.76e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   266 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSY----RDeeKKMGtlvKEDFGR--PNRENTMgMRHgsydkL 339
Cdd:PRK00405  716 GQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYeieaRD--TKLG---PEEITRdiPNVSEEA-LRN-----L 784

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   340 DDDGLAPPGTRVSGEDVIIGKTTPIApdETQ------------GGVASQYtkRDhsTSLR--HSESGMV-DQVLLTTNAD 404
Cdd:PRK00405  785 DESGIVRIGAEVKPGDILVGKVTPKG--ETEltpeekllraifGEKARDV--KD--TSLRvpHGEEGTViDVKVFTRIEQ 858

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   405 G-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWtMEGITP-DIIVNPHAIPSRMTIGQLIECIM 476
Cdd:PRK00405  859 GdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPY-LEDGTPvDIVLNPLGVPSRMNIGQILETHL 937

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 68131884   477 GKVAAHMGKEGdATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRK 525
Cdd:PRK00405  938 GWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEP 986
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 141-191 2.85e-20

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: 84.13  E-value: 2.85e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 68131884   141 WHDLVAKGYIEYVDTEEEETTMISMTIDDLVNARTNPNETY--QLYTHCEIHP 191
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREGPyaHTYTHCEIHP 53
rpoB CHL00001
RNA polymerase beta subunit
 262-492 2.37e-18

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 88.81  E-value: 2.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   262 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYrDEEKKMGTLVKEDFGR--PNRENTMgMRHgsydkL 339
Cdd:CHL00001  648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERITKeiPHLEAHL-LRN-----L 720

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   340 DDDGLAPPGTRVSGEDVIIGKTTPIAPDETQ------------GGVASqyTKRDhsTSLRhsesgmvdqvlLTTNADGlR 407
Cdd:CHL00001  721 DKNGIVMLGSWVETGDILVGKLTPQEAEESSyapegrllraifGIQVS--TSKE--TCLK-----------LPIGGRG-R 784

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   408 FVKVRM-----------RSVRI-------PQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIG 469
Cdd:CHL00001  785 VIDVRWiqkkggssynpETIHVyilqkreIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVG 864

                         250       260
                  ....*....|....*....|...
gi 68131884   470 QLIECIMGKVAAHMGKEGDATPF 492
Cdd:CHL00001  865 QIFECLLGLAGDLLNRHYRIAPF 887
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
406-486 3.79e-14

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 75.73  E-value: 3.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131884   406 LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGK 485
Cdd:PRK09603 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGK 1154


                  .
gi 68131884   486 E 486
Cdd:PRK09603 1155 Q 1155
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
420-486 2.15e-11

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 66.95  E-value: 2.15e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68131884   420 QIGDKFSSRHGQKGTVGMTYTQEDMPWTMEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE 486
Cdd:PRK14844 1082 QPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEK 1148
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-35 4.19e-07

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 52.64  E-value: 4.19e-07
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 68131884    1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEE 35
Cdd:PRK09606 452 ETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-17 4.05e-05

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: 41.74  E-value: 4.05e-05
                          10
                  ....*....|....*..
gi 68131884     1 ETPEGQACGLVKNLALM 17
Cdd:pfam04565  49 ETPEGPNCGLVKHLALY 65
 
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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