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Conserved domains on  [gi|544346191|ref|NP_001269705|]
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DNA-directed RNA polymerase I subunit RPA2 isoform 5 [Homo sapiens]

Protein Classification

RNA_pol_B_RPB2 and RNA_pol_Rpa2_4 domain-containing protein( domain architecture ID 13591551)

RNA_pol_B_RPB2 and RNA_pol_Rpa2_4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 130-922 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: 932.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 130 EKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIF 209
Cdd:cd00653  208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLL 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 210 TMGIDLTKPFEYLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPV 289
Cdd:cd00653  283 INSKPITSGIKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPI 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 290 HTPDGEPCGLMNHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrh 369
Cdd:cd00653  361 ETPEGENCGLVKNLALMARIS----------------------------------------------------------- 381

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 370 fkvlrekrippwmevvlipmtgkpslypglflfttpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQE 449
Cdd:cd00653  382 ------------------------------------------------------GRIERPYRIVE--------KEVTHIE 399

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 450 LFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTN 529
Cdd:cd00653  400 ISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQN 479

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 530 AIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQ 609
Cdd:cd00653  480 AIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVE 559

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 610 YGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASR 675
Cdd:cd00653  560 PGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASR 639

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 676 HGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEml 755
Cdd:cd00653  640 HGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE-- 717

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 756 kaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALL 835
Cdd:cd00653  718 --AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALI 795

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 836 AHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAM 915
Cdd:cd00653  796 AHGAAYLLQERLTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSM 859


                 ....*..
gi 544346191 916 NIKVKLD 922
Cdd:cd00653  860 NIDPRLK 866
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 352-410 8.68e-24

RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.


:

Pssm-ID: 462028  Cd Length: 58  Bit Score: 94.86  E-value: 8.68e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 544346191  352 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 410
Cdd:pfam06883   1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
RNA_pol_Rpb2_1 super family cl38164
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 9-205 9.08e-24

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.


The actual alignment was detected with superfamily member pfam04563:

Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 104.77  E-value: 9.08e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191    9 SAVNMnLHYLENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQ 88
Cdd:pfam04563 192 SWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-ELICYDVNDQQLQEELLPSLEEGFKIRIQTQEQ 267

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   89 VLNYLGECFRVKLNV-PDWYPNEQAAEFLFNQCICIHLK----SNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 163
Cdd:pfam04563 268 ALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRL 347

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 544346191  164 LTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQK-----TSVSMNTDNL 205
Cdd:pfam04563 348 RLAGPLLASLFRVLFKKLVRDVRERLQKVLGSpddlmLQLLVNAKPI 394
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 130-922 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: 932.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 130 EKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIF 209
Cdd:cd00653  208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLL 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 210 TMGIDLTKPFEYLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPV 289
Cdd:cd00653  283 INSKPITSGIKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPI 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 290 HTPDGEPCGLMNHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrh 369
Cdd:cd00653  361 ETPEGENCGLVKNLALMARIS----------------------------------------------------------- 381

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 370 fkvlrekrippwmevvlipmtgkpslypglflfttpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQE 449
Cdd:cd00653  382 ------------------------------------------------------GRIERPYRIVE--------KEVTHIE 399

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 450 LFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTN 529
Cdd:cd00653  400 ISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQN 479

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 530 AIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQ 609
Cdd:cd00653  480 AIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVE 559

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 610 YGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASR 675
Cdd:cd00653  560 PGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASR 639

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 676 HGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEml 755
Cdd:cd00653  640 HGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE-- 717

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 756 kaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALL 835
Cdd:cd00653  718 --AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALI 795

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 836 AHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAM 915
Cdd:cd00653  796 AHGAAYLLQERLTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSM 859


                 ....*..
gi 544346191 916 NIKVKLD 922
Cdd:cd00653  860 NIDPRLK 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 459-818 0e+00

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


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 530.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  459 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 538
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  539 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 617
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  618 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 682
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  683 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 762
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 544346191  763 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 818
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 85-923 1.23e-173

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 533.77  E-value: 1.23e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   85 TQKQVLNYLGEcfRVKLNVPDWYPNEQAAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVN 160
Cdd:PRK08565  256 TVEDALDYIGK--RVAIGQPREYRIERAEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYAN 332

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  161 QEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSvSMNTDNLMRiftMGIdLTKPFEYLFATGN-LRSKTGLG-LLq 238
Cdd:PRK08565  333 KRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGR-KLDLRAIVR---PDI-ITERIRHALATGNwVGGRTGVSqLL- 406

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  239 dsglcvvaDKLNFIRYLSHFRCV----HRG-ADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVvTQF 313
Cdd:PRK08565  407 --------DRTNYLSTLSHLRRVvsplSRGqPHFE------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI-SVG 471

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  314 VYTASIPALLCNLGVTPIDGAPHRSYSECYPVLLDGVMVGWVDKDLApgIADSLRHFKvlREKRIPPWMEVVLIPMTGKP 393
Cdd:PRK08565  472 VDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEE--LAEKIRELR--RSGKISDEVNVAYIETGEIN 547

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  394 SLYpglfLFTTPCRLVRPVQNLALGKEELIGTM-EQIFMNVAIFEDEVFAGV------------------------TTHQ 448
Cdd:PRK08565  548 EVY----VNCDSGRVRRPLIVVENGKPKLTREHvEKLKKGELTFDDLVKMGVieyldaeeeenayvaldpedltpeHTHL 623

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  449 ELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGT 528
Cdd:PRK08565  624 EIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQ 703

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  529 NAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK----QGD-----SSLVFGIKPgdPRVLQKLD 597
Cdd:PRK08565  704 NAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypggQEDkieipEPNVRGYRG--EEYYRKLD 776

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  598 DDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMR 661
Cdd:PRK08565  777 EDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGEKGIVDTVLITESPEGN---KLVKVRVR 851

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  662 VPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFif 741
Cdd:PRK08565  852 DLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF-- 929

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  742 seENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQ 821
Cdd:PRK08565  930 --YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRARE 1007

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  822 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekppPSWSAMRNRKYNCTLCSRSDTIDTVSV 901
Cdd:PRK08565 1008 GGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH----------IAWYDRRKNKYVCPIHGDKGNISPVEV 1077

                         890       900
                  ....*....|....*....|..
gi 544346191  902 PYVFRYFVAELAAMNIKVKLDV 923
Cdd:PRK08565 1078 SYAFKLLLQELMSMGISPRLKL 1099
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 345-923 4.68e-147

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: 448.32  E-value: 4.68e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  345 VLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGK 419
Cdd:TIGR03670   1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  420 EELigtmEQIFMNVAIFEDEVFAGVT------------------------THQELFPHSLLSVIANFIPFSDHNQSPRNM 475
Cdd:TIGR03670  71 EHV----EKLKEGELTWDDLVKQGVIeyldaeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  476 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 555
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  556 GFAHGS---VYKSEFID----LSEKIKQGDSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYL 618
Cdd:TIGR03670 227 GLARSTffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELR 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  619 NLNTGE------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMP 692
Cdd:TIGR03670 304 EFGLVTerrrdtSVTV--RHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMP 378

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  693 FTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGI 772
Cdd:TIGR03670 379 FTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGI 454

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  773 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 852
Cdd:TIGR03670 455 TGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346191  853 RSVAHVCVKCGSLlspllekpppSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 923
Cdd:TIGR03670 535 KYVVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 446-921 1.98e-104

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: 347.48  E-value: 1.98e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  446 THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLV 511
Cdd:COG0085   511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIV 582

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  512 R--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----K 573
Cdd:COG0085   583 RvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearD 653

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  574 IKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSK---- 633
Cdd:COG0085   654 TKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrd 726

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  634 --------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPD 701
Cdd:COG0085   727 tslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVD 806

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  702 ILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEAD 780
Cdd:COG0085   807 IVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNP 881

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  781 IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCV 860
Cdd:COG0085   882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346191  861 kcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAELAAMNIKVKL 921
Cdd:COG0085   962 ---------YE---------AIVK--------GENIPEPGIPESFKVLLKELQSLGLDVEV 996
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 352-410 8.68e-24

RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.


Pssm-ID: 462028  Cd Length: 58  Bit Score: 94.86  E-value: 8.68e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 544346191  352 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 410
Cdd:pfam06883   1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 9-205 9.08e-24

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: 104.77  E-value: 9.08e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191    9 SAVNMnLHYLENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQ 88
Cdd:pfam04563 192 SWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-ELICYDVNDQQLQEELLPSLEEGFKIRIQTQEQ 267

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   89 VLNYLGECFRVKLNV-PDWYPNEQAAEFLFNQCICIHLK----SNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 163
Cdd:pfam04563 268 ALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRL 347

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 544346191  164 LTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQK-----TSVSMNTDNL 205
Cdd:pfam04563 348 RLAGPLLASLFRVLFKKLVRDVRERLQKVLGSpddlmLQLLVNAKPI 394
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 130-922 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: 932.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 130 EKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIF 209
Cdd:cd00653  208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLL 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 210 TMGIDLTKPFEYLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPV 289
Cdd:cd00653  283 INSKPITSGIKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPI 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 290 HTPDGEPCGLMNHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrh 369
Cdd:cd00653  361 ETPEGENCGLVKNLALMARIS----------------------------------------------------------- 381

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 370 fkvlrekrippwmevvlipmtgkpslypglflfttpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQE 449
Cdd:cd00653  382 ------------------------------------------------------GRIERPYRIVE--------KEVTHIE 399

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 450 LFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTN 529
Cdd:cd00653  400 ISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQN 479

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 530 AIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQ 609
Cdd:cd00653  480 AIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVE 559

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 610 YGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASR 675
Cdd:cd00653  560 PGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASR 639

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 676 HGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEml 755
Cdd:cd00653  640 HGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE-- 717

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 756 kaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALL 835
Cdd:cd00653  718 --AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALI 795

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 836 AHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAM 915
Cdd:cd00653  796 AHGAAYLLQERLTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSM 859


                 ....*..
gi 544346191 916 NIKVKLD 922
Cdd:cd00653  860 NIDPRLK 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 459-818 0e+00

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


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 530.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  459 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 538
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  539 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 617
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  618 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 682
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  683 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 762
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 544346191  763 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 818
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 85-923 1.23e-173

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 533.77  E-value: 1.23e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   85 TQKQVLNYLGEcfRVKLNVPDWYPNEQAAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVN 160
Cdd:PRK08565  256 TVEDALDYIGK--RVAIGQPREYRIERAEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYAN 332

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  161 QEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSvSMNTDNLMRiftMGIdLTKPFEYLFATGN-LRSKTGLG-LLq 238
Cdd:PRK08565  333 KRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGR-KLDLRAIVR---PDI-ITERIRHALATGNwVGGRTGVSqLL- 406

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  239 dsglcvvaDKLNFIRYLSHFRCV----HRG-ADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVvTQF 313
Cdd:PRK08565  407 --------DRTNYLSTLSHLRRVvsplSRGqPHFE------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI-SVG 471

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  314 VYTASIPALLCNLGVTPIDGAPHRSYSECYPVLLDGVMVGWVDKDLApgIADSLRHFKvlREKRIPPWMEVVLIPMTGKP 393
Cdd:PRK08565  472 VDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEE--LAEKIRELR--RSGKISDEVNVAYIETGEIN 547

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  394 SLYpglfLFTTPCRLVRPVQNLALGKEELIGTM-EQIFMNVAIFEDEVFAGV------------------------TTHQ 448
Cdd:PRK08565  548 EVY----VNCDSGRVRRPLIVVENGKPKLTREHvEKLKKGELTFDDLVKMGVieyldaeeeenayvaldpedltpeHTHL 623

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  449 ELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGT 528
Cdd:PRK08565  624 EIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQ 703

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  529 NAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK----QGD-----SSLVFGIKPgdPRVLQKLD 597
Cdd:PRK08565  704 NAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypggQEDkieipEPNVRGYRG--EEYYRKLD 776

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  598 DDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMR 661
Cdd:PRK08565  777 EDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGEKGIVDTVLITESPEGN---KLVKVRVR 851

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  662 VPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFif 741
Cdd:PRK08565  852 DLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF-- 929

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  742 seENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQ 821
Cdd:PRK08565  930 --YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRARE 1007

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  822 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekppPSWSAMRNRKYNCTLCSRSDTIDTVSV 901
Cdd:PRK08565 1008 GGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH----------IAWYDRRKNKYVCPIHGDKGNISPVEV 1077

                         890       900
                  ....*....|....*....|..
gi 544346191  902 PYVFRYFVAELAAMNIKVKLDV 923
Cdd:PRK08565 1078 SYAFKLLLQELMSMGISPRLKL 1099
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 345-923 4.68e-147

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: 448.32  E-value: 4.68e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  345 VLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGK 419
Cdd:TIGR03670   1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  420 EELigtmEQIFMNVAIFEDEVFAGVT------------------------THQELFPHSLLSVIANFIPFSDHNQSPRNM 475
Cdd:TIGR03670  71 EHV----EKLKEGELTWDDLVKQGVIeyldaeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  476 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 555
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  556 GFAHGS---VYKSEFID----LSEKIKQGDSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYL 618
Cdd:TIGR03670 227 GLARSTffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELR 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  619 NLNTGE------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMP 692
Cdd:TIGR03670 304 EFGLVTerrrdtSVTV--RHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMP 378

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  693 FTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGI 772
Cdd:TIGR03670 379 FTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGI 454

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  773 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 852
Cdd:TIGR03670 455 TGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346191  853 RSVAHVCVKCGSLlspllekpppSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 923
Cdd:TIGR03670 535 KYVVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 344-923 2.22e-131

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 407.81  E-value: 2.22e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 344 PVLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN------ 414
Cdd:PRK07225   6 KVYVNGKLIGTHDD--PEELVEEIR--EARRSGEISEEVNVSYKEETNE------VIINTDAGRARRPlivVENgepllt 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 415 -----------------LALGKEELIGTMEQIFMNVAIFEDEVFAGvTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 477
Cdd:PRK07225  76 eehieklkngeltfddlVKQGVIEYLDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 478 CQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGF 557
Cdd:PRK07225 155 AGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGL 234

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 558 AHGSVYKSefIDLSEKIKQGDSSLVFGIKPGDPR------VLQKLDDDGLPFIGAKLQYGD--------PyySYLNLNTG 623
Cdd:PRK07225 235 GRSHFFRT--YEGEERRYPGGQEDRFEIPDKDVRgyrgeeAYRHLDEDGLVNPETEVKEGDvligktspP--RFLEEPDD 310

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 624 E----------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPF 693
Cdd:PRK07225 311 FgispekrretSVTM--RSGEEGIVDTVILTETEEGS---RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPF 385

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 694 TESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENSalEYFGEMLKAAGYNFYGTERLYSGIS 773
Cdd:PRK07225 386 TESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAF--SGEDE--EDLREALEKLGFEHTGKEVMYDGIT 461

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 774 GLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDR 853
Cdd:PRK07225 462 GEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDK 541

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544346191 854 SVAHVCVKCGSLlspllekpppswsAMRNRKYN---CTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 923
Cdd:PRK07225 542 VEIYVCAKCGMI-------------AIYDKKRNrkyCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 446-921 1.98e-104

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: 347.48  E-value: 1.98e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  446 THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLV 511
Cdd:COG0085   511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIV 582

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  512 R--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----K 573
Cdd:COG0085   583 RvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearD 653

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  574 IKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSK---- 633
Cdd:COG0085   654 TKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrd 726

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  634 --------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPD 701
Cdd:COG0085   727 tslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVD 806

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  702 ILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEAD 780
Cdd:COG0085   807 IVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNP 881

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  781 IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCV 860
Cdd:COG0085   882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346191  861 kcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAELAAMNIKVKL 921
Cdd:COG0085   962 ---------YE---------AIVK--------GENIPEPGIPESFKVLLKELQSLGLDVEV 996
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 526-852 5.28e-50

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: 191.80  E-value: 5.28e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   526 IGTNAIVAVISYTGYDMEDAMIVNkaswERGF---AHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 602
Cdd:TIGR02013  673 LGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   603 FIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSKEncVVDN--------------IKVCSNDTGS--- 650
Cdd:TIGR02013  749 RIGAEVKAGDilvgkvtpkgeteltPEEKLLRAIFGE------KARD--VRDTslrvppgvegtvidVKVFSREQGDelp 820

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   651 -GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKS 726
Cdd:TIGR02013  821 pGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKR 900

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   727 AALHGLCHdATPfIFseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGA 806
Cdd:TIGR02013  901 LGRKGVPI-ATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGP 976

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 544346191   807 RDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 852
Cdd:TIGR02013  977 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 247-852 5.01e-44

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 172.97  E-value: 5.01e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  247 DKLNFIRYLSH-FRCVHRGAD-FAKMRTTT-VRRLLPESWGFLCPVHTPDGEPCGLMNHLTaVCEVVTQFvytasipall 323
Cdd:CHL00207  371 DQTNPLSELTHkRRISILGPGgLDKDRISFaVRDIHPSHYGRICPIETPEGPNCGLIGSLA-TNARINKF---------- 439

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  324 cNLGVTPidgaphrsyseCYPVLldgvmVGWVDKDLAPGI--ADSLRHFKVLrekrippwmevvlipmtgkpslyPGlfl 401
Cdd:CHL00207  440 -GFIETP-----------FYKVI-----NGKVKKFGNPIYltADSEDLYRIA-----------------------PN--- 476

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  402 fttpcrlvrpvqNLALGKEELIgtmeqIFMNVAIFEDEVFAGVTTHQELF----PHSLLSVIANFIPFSDHNQSPRnmyq 477
Cdd:CHL00207  477 ------------DINLNKNNYF-----KKNIIPVRYKQEFKTVNPSKVDFiaisPIQVFSIAESLIPFLEHNDANR---- 535

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  478 CQMGK--QTMGFPLL---------------------------------------TYQDRSDNKL-YRLQ----------T 505
Cdd:CHL00207  536 ALMGSnmQRQAVPLLypekpivgtgyekqialdsgmtiisltegivvsvsaykiIIQDDNNRYIhYYLQkyqrsnqntcI 615

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  506 PQSPLVRPS--------MYDYYDMDN--YPIGTNAIVAVISYTGYDMEDAMIVNKAswergFAHGSVYKSEFIDLSEKI- 574
Cdd:CHL00207  616 NYRPIVWVGekinigqiLADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILINKR-----LVYEDLFTSIHIEKYEIEl 690

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  575 ---KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGD-------PYYSYLNLNTGESFVMYYKSKENCVVDN---- 640
Cdd:CHL00207  691 rqtKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDilvgkitPKGESDQLPEGKLLRAIFGEKAKDVKDTslrm 770

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  641 ----------IKVCSNDTGSGKFKCVCITMRV----PRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNP 706
Cdd:CHL00207  771 pnggygrvikVEIFSRSKGDELKFGYYLKIRVfiaqIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNP 850

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  707 HGFPSRMTIGMLIESMAGKSAalHGLCHDATPFIFSEENSALE---YFGEMLKAAG--------YNFY--GTERLYSGIS 773
Cdd:CHL00207  851 LGVPSRMNVGQLFECLLGLAG--DNLNKRFKILPFDEMYGSEYsriLINNKLNQASiknneywlFNSYhpGKMVLRDGRT 928

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544346191  774 GLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 852
Cdd:CHL00207  929 GYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD 1007
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 667-843 1.68e-36

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 149.10  E-value: 1.68e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  667 TIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKsaalhGL-CHDATPfIF- 741
Cdd:PRK00405  881 QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAAK-----GLgIKFATP-VFd 954

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  742 --SEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRN 819
Cdd:PRK00405  955 gaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029

                         170       180
                  ....*....|....*....|....
gi 544346191  820 VQGGIRFGEMERDALLAHGTSFLL 843
Cdd:PRK00405 1030 QFGGQRFGEMEVWALEAYGAAYTL 1053
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 244-308 6.31e-32

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: 118.40  E-value: 6.31e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544346191  244 VVADKLNFIRYLSHFRCVH--RGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCE 308
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
rpoB CHL00001
RNA polymerase beta subunit
 527-852 1.51e-31

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 133.49  E-value: 1.51e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  527 GTNAIVAVISYTGYDMEDAMIVNkaswERgFAHGSVYKSEFIDLSE----KIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 602
Cdd:CHL00001  652 GKNVLVAYMPWEGYNFEDAVLIS----ER-LVYEDIYTSFHIRKYEiqthVTSQGPERITKEIPHLEAHLLRNLDKNGIV 726

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  603 FIGAKLQYGD-------PYYSYLNLNTGESFVMY-------YKSKENC----------VVDNIKVCSNDTGSGKFKCVCI 658
Cdd:CHL00001  727 MLGSWVETGDilvgkltPQEAEESSYAPEGRLLRaifgiqvSTSKETClklpiggrgrVIDVRWIQKKGGSSYNPETIHV 806

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  659 TMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATP 738
Cdd:CHL00001  807 YILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAP 886

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  739 F--IFSEENSALEYFGEMLKA---AGY------NFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGAR 807
Cdd:CHL00001  887 FdeRYEQEASRKLVFSELYEAskqTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPY 966

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 544346191  808 DRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 852
Cdd:CHL00001  967 ALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
650-852 3.30e-28

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 123.11  E-value: 3.30e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  650 SGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE---SMAGK- 725
Cdd:PRK09603 1072 NGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlGLVGKe 1151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  726 ----------------------------------------------SAALHGLCHD-------ATPfIFseENSALEYFG 752
Cdd:PRK09603 1152 fgkqiasmledktkdfakelrakmleianainekdpltihalencsDEELLEYAKDwskgvkmAIP-VF--EGISQEKFY 1228

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  753 EMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERD 832
Cdd:PRK09603 1229 KLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308

                         250       260
                  ....*....|....*....|
gi 544346191  833 ALLAHGTSFLLHDRLFNCSD 852
Cdd:PRK09603 1309 ALEAYGAAHTLKEMLTIKSD 1328
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 352-410 8.68e-24

RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.


Pssm-ID: 462028  Cd Length: 58  Bit Score: 94.86  E-value: 8.68e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 544346191  352 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 410
Cdd:pfam06883   1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 9-205 9.08e-24

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: 104.77  E-value: 9.08e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191    9 SAVNMnLHYLENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQ 88
Cdd:pfam04563 192 SWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-ELICYDVNDQQLQEELLPSLEEGFKIRIQTQEQ 267

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   89 VLNYLGECFRVKLNV-PDWYPNEQAAEFLFNQCICIHLK----SNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 163
Cdd:pfam04563 268 ALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRL 347

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 544346191  164 LTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQK-----TSVSMNTDNL 205
Cdd:pfam04563 348 RLAGPLLASLFRVLFKKLVRDVRERLQKVLGSpddlmLQLLVNAKPI 394
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 822-924 3.90e-22

RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.


Pssm-ID: 461355 [Multi-domain]  Cd Length: 87  Bit Score: 91.11  E-value: 3.90e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  822 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGsllspllekpppswsAMRNRKYnCTLCSRSDTIDTVSV 901
Cdd:pfam04560   1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCG---------------LYAAYNK-CPICKGETDISPGYI 64

                          90       100
                  ....*....|....*....|...
gi 544346191  902 PYVFRYFVAELAAMNIKVKLDVV 924
Cdd:pfam04560  65 PESFKLLFQELQSLGIDPRLLLE 87
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
669-852 1.75e-20

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 98.16  E-value: 1.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  669 GDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAG--------------------KSAA 728
Cdd:PRK14844 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgekvgnildeinkiKSAF 1163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  729 LHGL--------------------------------------------------------CHDATPFIFS---------- 742
Cdd:PRK14844 1164 CKGIrslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnsCKSAYSNLRNflievyscgs 1243

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  743 -----------EENSALEY----------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 789
Cdd:PRK14844 1244 nvsicnnirdiSDNNLIEFarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544346191  790 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 852
Cdd:PRK14844 1324 KLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 31-333 1.13e-11

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 68.05  E-value: 1.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191  31 KELFFLPLgfaLKALVSFSDyqifQELIKGKEDDsflRNSVSQMLRIVMEEGCSTQKQVLNYLGEcfRVKLNVPDWYPNE 110
Cdd:PRK09606 215 GSIPFVIL---MRALGLETD----EEIVEAVSDD---PEIVKFMLENLEEAEVDTQEEALEYIGK--RVAPGQTKEYRIK 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 111 QAaEFLFNQCICIHLKSNTEKF----YMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFlmflkEKLegwlvsIK 186
Cdd:PRK09606 283 RA-EYVIDRYLLPHLGVEPEVRrakaHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLM-----EDL------FR 350

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 187 IAF-----DKKAQKTSVSM-NTDNLMRIFTMGIDLTKPFEYLFATGNLRS-KTGLGLLqdsglcvvADKLNFIRYLSHFR 259
Cdd:PRK09606 351 VAFnrlarDVKYQLERANMrNRELSIKTAVRSDVLTERLEHAMATGNWVGgRTGVSQL--------LDRTDYMATLSHLR 422

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191 260 CV---------HRGAdfakmrtttvRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPaLLCNLGVTP 330
Cdd:PRK09606 423 RVvsplsrsqpHFEA----------RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKE-ILKELGVEP 491


                 ...
gi 544346191 331 IDG 333
Cdd:PRK09606 492 ERG 494
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 16-164 7.29e-09

RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).


Pssm-ID: 398318 [Multi-domain]  Cd Length: 185  Bit Score: 56.20  E-value: 7.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346191   16 HYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQIFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYL 93
Cdd:pfam04561  32 LKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDREILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYI 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544346191   94 GECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 164
Cdd:pfam04561 107 GKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
 
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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