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Conserved domains on  [gi|17136446|ref|NP_476708|]
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RNA polymerase I subunit B [Drosophila melanogaster]

Protein Classification

DNA-directed RNA polymerase I subunit RPA2( domain architecture ID 10090013)

DNA-directed RNA polymerase I subunit RPA2 is the second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors

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. ...
 35-1125 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: 933.91  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   35 LGGPHVDSFDEMLTVGLDNSAKHMIPNHWlSPAGEKISMKVESIWIAKPKVPQDVIdvrTREIYPTDSRQLHVSYSGMCS 114
Cdd:cd00653    1 LVKQQIDSFNYFLNVGLQEIVKSIPPITD-TDDDGRLKLKFGDIYLGKPKVEEGGV---TRKLTPNECRLRDLTYSAPLY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  115 VRLGWSVNG-VQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRMLIMTRRNHPI--- 190
Cdd:cd00653   77 VDIRLTVNDkGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIved 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  191 -CVKRSSWKDRGQNFSDLGmlvQTVREDESSLSNVVHYlnngtakfmfshvkrlsyvpvclilkCLMDYTDEEiynrlvq 269
Cdd:cd00653  157 sKGKRIYTKTSIPSYSPYR---GSWLEVKSDKKKDRIY--------------------------VRIDLKRQE------- 200

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  270 gyesdqyyvscvqamlrevqnenvythaQCKSFIGNlfrarfpevpewqpdddvtdfilrervmihldtyedKFQLIVFM 349
Cdd:cd00653  201 ----------------------------EALKYIGK------------------------------------RFEDLIYM 216

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  350 IQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSPDALvtsavMTQCMRQAGGVGRA 429
Cdd:cd00653  217 IRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL-----TPQLLINSKPITSG 291

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  430 IESFLATGNIASRTGLglMQNSGLVIMAENINRMRYMSHFRAIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCG 509
Cdd:cd00653  292 IKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCG 369

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  510 LLNHLTLTCEISmrpdpklvkaipkhlidmgmmplsnrrylgeklyvvfldgkhlghihqseaekivdelrygkifgtlp 589
Cdd:cd00653  370 LVKNLALMARIS-------------------------------------------------------------------- 381

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  590 qmmeigfipfkkngqfpglyiatgpARMMRPVWNLKwkrveyigtleqlymeiaidakemypDFTTHLELAKTHFMSNLA 669
Cdd:cd00653  382 -------------------------GRIERPYRIVE--------------------------KEVTHIEISPSQILSVAA 410

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  670 NLIPMPDYNQSPRNMYQCQMGKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGY 749
Cdd:cd00653  411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  750 DMEDAMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFAR-----HPHMPE-LIKHLDTDGLPHPGSKLSYGSPLYCYFD- 822
Cdd:cd00653  491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEitrgdIPNVSEeKLKNLDEDGIIRPGARVEPGDILVGKITp 570

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  823 -------------GEVATYKVVKMDEKEDCIVESIRQLGSFDLSP-KKMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888
Cdd:cd00653  571 kgetestpifgekARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGgNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  889 PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENTAIDYFGKMleagGYNYYGTE 968
Cdd:cd00653  651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEA----GLNYYGKE 726

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  969 RLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDR 1048
Cdd:cd00653  727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806

                       1050      1060      1070      1080      1090      1100      1110
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17136446 1049 LFHNSDKTHTLVCHKCGSILAplqrivkrnetgglssqPDTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFK 1125
Cdd:cd00653  807 LTIKSDDVVARVCVKCGIILS-----------------ANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 564-619 1.91e-19

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: 82.92  E-value: 1.91e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17136446    564 LGHIHQSEAEKIVDELRYGKIFGT--LPQMMEIGFIPFKKNGQFPGLYIATGPARMMR 619
Cdd:pfam06883    1 IGYVSPKLAKRIADTLRYLKVEGEhgVPLTLEIGYVPPSNGGQYPGLYLFTSPARMMR 58
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 35-1125 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: 933.91  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   35 LGGPHVDSFDEMLTVGLDNSAKHMIPNHWlSPAGEKISMKVESIWIAKPKVPQDVIdvrTREIYPTDSRQLHVSYSGMCS 114
Cdd:cd00653    1 LVKQQIDSFNYFLNVGLQEIVKSIPPITD-TDDDGRLKLKFGDIYLGKPKVEEGGV---TRKLTPNECRLRDLTYSAPLY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  115 VRLGWSVNG-VQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRMLIMTRRNHPI--- 190
Cdd:cd00653   77 VDIRLTVNDkGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIved 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  191 -CVKRSSWKDRGQNFSDLGmlvQTVREDESSLSNVVHYlnngtakfmfshvkrlsyvpvclilkCLMDYTDEEiynrlvq 269
Cdd:cd00653  157 sKGKRIYTKTSIPSYSPYR---GSWLEVKSDKKKDRIY--------------------------VRIDLKRQE------- 200

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  270 gyesdqyyvscvqamlrevqnenvythaQCKSFIGNlfrarfpevpewqpdddvtdfilrervmihldtyedKFQLIVFM 349
Cdd:cd00653  201 ----------------------------EALKYIGK------------------------------------RFEDLIYM 216

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  350 IQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSPDALvtsavMTQCMRQAGGVGRA 429
Cdd:cd00653  217 IRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL-----TPQLLINSKPITSG 291

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  430 IESFLATGNIASRTGLglMQNSGLVIMAENINRMRYMSHFRAIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCG 509
Cdd:cd00653  292 IKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCG 369

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  510 LLNHLTLTCEISmrpdpklvkaipkhlidmgmmplsnrrylgeklyvvfldgkhlghihqseaekivdelrygkifgtlp 589
Cdd:cd00653  370 LVKNLALMARIS-------------------------------------------------------------------- 381

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  590 qmmeigfipfkkngqfpglyiatgpARMMRPVWNLKwkrveyigtleqlymeiaidakemypDFTTHLELAKTHFMSNLA 669
Cdd:cd00653  382 -------------------------GRIERPYRIVE--------------------------KEVTHIEISPSQILSVAA 410

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  670 NLIPMPDYNQSPRNMYQCQMGKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGY 749
Cdd:cd00653  411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  750 DMEDAMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFAR-----HPHMPE-LIKHLDTDGLPHPGSKLSYGSPLYCYFD- 822
Cdd:cd00653  491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEitrgdIPNVSEeKLKNLDEDGIIRPGARVEPGDILVGKITp 570

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  823 -------------GEVATYKVVKMDEKEDCIVESIRQLGSFDLSP-KKMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888
Cdd:cd00653  571 kgetestpifgekARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGgNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  889 PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENTAIDYFGKMleagGYNYYGTE 968
Cdd:cd00653  651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEA----GLNYYGKE 726

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  969 RLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDR 1048
Cdd:cd00653  727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806

                       1050      1060      1070      1080      1090      1100      1110
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17136446 1049 LFHNSDKTHTLVCHKCGSILAplqrivkrnetgglssqPDTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFK 1125
Cdd:cd00653  807 LTIKSDDVVARVCVKCGIILS-----------------ANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 39-1129 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 568.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    39 HVDSFDEMLTVGLdnsaKHMIPNH-WLSPAGEKISMKVESIWIAKPKVPQdvIDVRTREIYPTDSRQLHVSYSGMCSVRL 117
Cdd:PRK08565   18 HLDSYNDFIERGL----QEIVDEFgEIKTEIPGLKIVLGKIRVGEPEIKE--ADGSERPITPMEARLRNLTYAAPLYLTM 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   118 GWSVNGVQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRMLIMTRRNHPIcVKRSsw 197
Cdd:PRK08565   92 IPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVL-VDKG-- 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   198 kDRGQNFSDLGMLVQTVREDESSLsnVVHYLNNGTAKFMFSHVKrlSYVPVCLILKCLMDYTDEEIYnrlvqgyesdqYY 277
Cdd:PRK08565  169 -EAGSSITHTAKVISSRAGYRAQV--TVERRKDGTIYVSFPAVP--GKIPFVILMRALGLETDRDIV-----------YA 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   278 VSCVQamlrEVQNENVYTHAQCKS----------FIGNLFRARfpevpewQPDDD---VTDFILRERVMIHLDTYED--- 341
Cdd:PRK08565  233 VSLDP----EIQQELLPSLEQASSiaatvedaldYIGKRVAIG-------QPREYrieRAEQILDKYLLPHLGTSPEdri 301

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   342 -KFQLIVFMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSP-----DALVTSAV 415
Cdd:PRK08565  302 kKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGrkldlRAIVRPDI 381

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   416 MTQCMRQAggvgraiesfLATGN-IASRTGLglmqnsglvimAENINRMRYMS---HFRAI----HRG-SYFttmrttEA 486
Cdd:PRK08565  382 ITERIRHA----------LATGNwVGGRTGV-----------SQLLDRTNYLStlsHLRRVvsplSRGqPHF------EA 434

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   487 RQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRPDPKLVKAIpkhLIDMGMMPL-SNRRYLGEKLYVVFLDGKHLG 565
Cdd:PRK08565  435 RDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEI---LYELGVVPVeEAREEEYISWSRVYLNGRLIG 511

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   566 HIHQSE--AEKIVDELRYGKIFGtlpqmmEIGFIpFKKNGQFPGLYIATGPARMMRPVW-----NLKWKR---------- 628
Cdd:PRK08565  512 YHPDGEelAEKIRELRRSGKISD------EVNVA-YIETGEINEVYVNCDSGRVRRPLIvvengKPKLTRehveklkkge 584

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   629 -----------VEYIGTLEQLYMEIAIDAKEMYPDfTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTP 697
Cdd:PRK08565  585 ltfddlvkmgvIEYLDAEEEENAYVALDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLY 663

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   698 CLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFAYGSIYKT--- 774
Cdd:PRK08565  664 AANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTyet 743

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   775 -----------KFLTLDKK-SSYFArhphmPELIKHLDTDGLPHPGSKLSYG-------SPlyCYFDGEVATYKVVKMDE 835
Cdd:PRK08565  744 eerkypggqedKIEIPEPNvRGYRG-----EEYYRKLDEDGIVSPEVEVKGGdvligktSP--PRFLEELEELSLGLQER 816

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   836 KEDCIVESIRQLGSFDL-----SPK--KMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIPDIVFNP 908
Cdd:PRK08565  817 RDTSVTVRHGEKGIVDTvliteSPEgnKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINP 896

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   909 HGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFrfseENTAIDYFGKMLEAGGYNYYGTERLYSGVDGREMTADIFFGVV 988
Cdd:PRK08565  897 HAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVV 972

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   989 HYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSIl 1068
Cdd:PRK08565  973 YYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHI- 1051

                        1130      1140      1150      1160      1170      1180
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17136446  1069 APLQRivKRNETgglssqpdTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNEI 1129
Cdd:PRK08565 1052 AWYDR--RKNKY--------VCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGDK 1102
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 34-428 4.66e-160

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: 480.34  E-value: 4.66e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446     34 NLGGPHVDSFDEMLtvglDNSAKHMIPNHWLSPA----------GEKISMKVESIWIAKPKVPQDVIDvrTREIYPTDSR 103
Cdd:pfam04563    1 GLVRQQLDSFNEFV----DNDLQKIIDENALIESefeiqhpgenGDKLSLKFGQIRLGKPMFDETDGS--TREIYPQECR 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    104 QLHVSYSGMCSVRLGWSV-NGVQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRMLI 182
Cdd:pfam04563   75 LRNLTYSAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    183 MTRRNHPICVKRSSWKDRGQNFSDLGMLVQTVREDESSLSNVVHYLNNGTAKFMFSHVKRLsyVPVCLILKCLMDYTDEE 262
Cdd:pfam04563  155 HRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLEYLSNGTIYFKFPYIKKE--IPIVIILRALGFTSDRE 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    263 IYNRLVqGYESDQYYVSCVQAMLREVQNENVYTHAQCKSFIGNLFRARFPEVPEWQPDDDVTDFILRERVMIHLDTYE-- 340
Cdd:pfam04563  233 IFELIC-YDVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKYAEEILQKEVLPHLGTYEld 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    341 --DKFQLIVFMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSPDalvtsAVMTQ 418
Cdd:pfam04563  312 etKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPD-----DLMLQ 386

                          410
                   ....*....|
gi 17136446    419 CMRQAGGVGR 428
Cdd:pfam04563  387 LLVNAKPITS 396
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 557-1128 1.10e-137

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: 429.45  E-value: 1.10e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    557 VFLDGKHLGHIhqSEAEKIVDELRYGKIFGTLPQMMEIGFIpfKKNGQfpgLYIATGPARMMRP---VWN---------- 623
Cdd:TIGR03670    1 VYLNGRLIGYH--DDPEELVEEVRKLRRSGKLSQEVNVAYY--EETNE---VYINCDAGRIRRPlivVENgkpkltrehv 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    624 -------LKWKR------VEYIGTLEQLYMEIAIDAKEMYPDFTtHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMG 690
Cdd:TIGR03670   74 eklkegeLTWDDlvkqgvIEYLDAEEEENAYIALDPEELTPEHT-HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMA 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    691 KQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFAYGS 770
Cdd:TIGR03670  153 KQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARST 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    771 IYKT--------------KFlTLDKKSSYFARHPhmpELIKHLDTDGLPHPGSKLSYG-------SPlyCYFDGEVATYK 829
Cdd:TIGR03670  233 FFRTyeaeerrypggqedRF-EIPEPDVRGYRGE---EAYKHLDEDGIVYPEVEVKGGdvligktSP--PRFLEELREFG 306

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    830 VVKMDEKEDCIVESIRQLGSFD-------LSPKKMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIP 902
Cdd:TIGR03670  307 LVTERRRDTSVTVRHGEKGIVDkviitetEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVP 386

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    903 DIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFrfseENTAIDYFGKMLEAGGYNYYGTERLYSGVDGREMTAD 982
Cdd:TIGR03670  387 DLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF----EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAE 462

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    983 IFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCH 1062
Cdd:TIGR03670  463 IFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCE 542

                          570       580       590       600       610       620
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17136446   1063 KCGSIlAPLQRivKRNETgglssqpdTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNE 1128
Cdd:TIGR03670  543 NCGHI-AWEDK--RKGTA--------YCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 485-1128 2.13e-86

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: 301.64  E-value: 2.13e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  485 EARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEIS-----MRPdpklvkaipkhlidmgmmplsnrrylgeklYVVFL 559
Cdd:COG0085  406 EVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNeygfiETP------------------------------YRKVE 455

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  560 DGKHLGHIHQSEAEkivDELRYgkifgtlpqmmeigfipfkkngqfpglYIATGPARMmrpvwNLKWKRVEyigtlEQLY 639
Cdd:COG0085  456 NGKVTDEIEYLTAD---EEENY---------------------------YIAQANAPL-----DEDGNFLE-----ERVL 495

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  640 MEIAIDAKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPCLNWPKqaanKLYRLQT----- 714
Cdd:COG0085  496 VRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----LHYPLQKfqrsn 571

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  715 PGT-----PLFRP---VHYDNIQLD-------DFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFaYGSI-------- 771
Cdd:COG0085  572 QGTcinqrPIVRVgdrVEKGDVLADgpatdngELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV-LTSIhieeyeie 650

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  772 -YKTKF----LTLDKkssyfarhP-HMPELIKHLDTDGLPHPGSKLSYG-------SP------------LYCYFdGEVA 826
Cdd:COG0085  651 aRDTKLgpeeITRDI--------PnVSEEALRNLDEDGIIRIGAEVKGGdilvgkvTPkgeteltpeerlLRAIF-GEKA 721

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  827 TY--------------KV--VKMDEKEDcivesirqlGSfDLSPK--KMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888
Cdd:COG0085  722 REvrdtslrvphgekgKVidVKVFSREE---------GD-ELPPGvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRIL 791

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  889 PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFR-FSEENTAidyfgKMLEAGGYNYYGT 967
Cdd:COG0085  792 PQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEEIR-----ELLEKAGLPPDGK 866

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  968 ERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQD 1047
Cdd:COG0085  867 EVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 946

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446 1048 RLFHNSDKThtlvchkCGSIlAPLQRIVKrnetgglssqpdtcrlcGDNssVSMIEIPFSFKYLVTELSSVNINARFKLN 1127
Cdd:COG0085  947 RLTIKSDDV-------CGRV-KVYEAIVK-----------------GEN--IPEPGIPESFKVLLKELQSLGLDVEVLSE 999


                 .
gi 17136446 1128 E 1128
Cdd:COG0085 1000 D 1000
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 564-619 1.91e-19

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: 82.92  E-value: 1.91e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17136446    564 LGHIHQSEAEKIVDELRYGKIFGT--LPQMMEIGFIPFKKNGQFPGLYIATGPARMMR 619
Cdd:pfam06883    1 IGYVSPKLAKRIADTLRYLKVEGEhgVPLTLEIGYVPPSNGGQYPGLYLFTSPARMMR 58
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 35-1125 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: 933.91  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   35 LGGPHVDSFDEMLTVGLDNSAKHMIPNHWlSPAGEKISMKVESIWIAKPKVPQDVIdvrTREIYPTDSRQLHVSYSGMCS 114
Cdd:cd00653    1 LVKQQIDSFNYFLNVGLQEIVKSIPPITD-TDDDGRLKLKFGDIYLGKPKVEEGGV---TRKLTPNECRLRDLTYSAPLY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  115 VRLGWSVNG-VQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRMLIMTRRNHPI--- 190
Cdd:cd00653   77 VDIRLTVNDkGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIved 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  191 -CVKRSSWKDRGQNFSDLGmlvQTVREDESSLSNVVHYlnngtakfmfshvkrlsyvpvclilkCLMDYTDEEiynrlvq 269
Cdd:cd00653  157 sKGKRIYTKTSIPSYSPYR---GSWLEVKSDKKKDRIY--------------------------VRIDLKRQE------- 200

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  270 gyesdqyyvscvqamlrevqnenvythaQCKSFIGNlfrarfpevpewqpdddvtdfilrervmihldtyedKFQLIVFM 349
Cdd:cd00653  201 ----------------------------EALKYIGK------------------------------------RFEDLIYM 216

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  350 IQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSPDALvtsavMTQCMRQAGGVGRA 429
Cdd:cd00653  217 IRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL-----TPQLLINSKPITSG 291

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  430 IESFLATGNIASRTGLglMQNSGLVIMAENINRMRYMSHFRAIHRGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCG 509
Cdd:cd00653  292 IKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCG 369

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  510 LLNHLTLTCEISmrpdpklvkaipkhlidmgmmplsnrrylgeklyvvfldgkhlghihqseaekivdelrygkifgtlp 589
Cdd:cd00653  370 LVKNLALMARIS-------------------------------------------------------------------- 381

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  590 qmmeigfipfkkngqfpglyiatgpARMMRPVWNLKwkrveyigtleqlymeiaidakemypDFTTHLELAKTHFMSNLA 669
Cdd:cd00653  382 -------------------------GRIERPYRIVE--------------------------KEVTHIEISPSQILSVAA 410

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  670 NLIPMPDYNQSPRNMYQCQMGKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGY 749
Cdd:cd00653  411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  750 DMEDAMIINKAAYERGFAYGSIYKTKFLTLDKKSSYFAR-----HPHMPE-LIKHLDTDGLPHPGSKLSYGSPLYCYFD- 822
Cdd:cd00653  491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEitrgdIPNVSEeKLKNLDEDGIIRPGARVEPGDILVGKITp 570

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  823 -------------GEVATYKVVKMDEKEDCIVESIRQLGSFDLSP-KKMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888
Cdd:cd00653  571 kgetestpifgekARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGgNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  889 PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEENTAIDYFGKMleagGYNYYGTE 968
Cdd:cd00653  651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEA----GLNYYGKE 726

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  969 RLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDR 1048
Cdd:cd00653  727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806

                       1050      1060      1070      1080      1090      1100      1110
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17136446 1049 LFHNSDKTHTLVCHKCGSILAplqrivkrnetgglssqPDTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFK 1125
Cdd:cd00653  807 LTIKSDDVVARVCVKCGIILS-----------------ANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 39-1129 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 568.82  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    39 HVDSFDEMLTVGLdnsaKHMIPNH-WLSPAGEKISMKVESIWIAKPKVPQdvIDVRTREIYPTDSRQLHVSYSGMCSVRL 117
Cdd:PRK08565   18 HLDSYNDFIERGL----QEIVDEFgEIKTEIPGLKIVLGKIRVGEPEIKE--ADGSERPITPMEARLRNLTYAAPLYLTM 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   118 GWSVNGVQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRMLIMTRRNHPIcVKRSsw 197
Cdd:PRK08565   92 IPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVL-VDKG-- 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   198 kDRGQNFSDLGMLVQTVREDESSLsnVVHYLNNGTAKFMFSHVKrlSYVPVCLILKCLMDYTDEEIYnrlvqgyesdqYY 277
Cdd:PRK08565  169 -EAGSSITHTAKVISSRAGYRAQV--TVERRKDGTIYVSFPAVP--GKIPFVILMRALGLETDRDIV-----------YA 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   278 VSCVQamlrEVQNENVYTHAQCKS----------FIGNLFRARfpevpewQPDDD---VTDFILRERVMIHLDTYED--- 341
Cdd:PRK08565  233 VSLDP----EIQQELLPSLEQASSiaatvedaldYIGKRVAIG-------QPREYrieRAEQILDKYLLPHLGTSPEdri 301

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   342 -KFQLIVFMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSP-----DALVTSAV 415
Cdd:PRK08565  302 kKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGrkldlRAIVRPDI 381

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   416 MTQCMRQAggvgraiesfLATGN-IASRTGLglmqnsglvimAENINRMRYMS---HFRAI----HRG-SYFttmrttEA 486
Cdd:PRK08565  382 ITERIRHA----------LATGNwVGGRTGV-----------SQLLDRTNYLStlsHLRRVvsplSRGqPHF------EA 434

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   487 RQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRPDPKLVKAIpkhLIDMGMMPL-SNRRYLGEKLYVVFLDGKHLG 565
Cdd:PRK08565  435 RDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEI---LYELGVVPVeEAREEEYISWSRVYLNGRLIG 511

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   566 HIHQSE--AEKIVDELRYGKIFGtlpqmmEIGFIpFKKNGQFPGLYIATGPARMMRPVW-----NLKWKR---------- 628
Cdd:PRK08565  512 YHPDGEelAEKIRELRRSGKISD------EVNVA-YIETGEINEVYVNCDSGRVRRPLIvvengKPKLTRehveklkkge 584

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   629 -----------VEYIGTLEQLYMEIAIDAKEMYPDfTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTP 697
Cdd:PRK08565  585 ltfddlvkmgvIEYLDAEEEENAYVALDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLY 663

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   698 CLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFAYGSIYKT--- 774
Cdd:PRK08565  664 AANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTyet 743

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   775 -----------KFLTLDKK-SSYFArhphmPELIKHLDTDGLPHPGSKLSYG-------SPlyCYFDGEVATYKVVKMDE 835
Cdd:PRK08565  744 eerkypggqedKIEIPEPNvRGYRG-----EEYYRKLDEDGIVSPEVEVKGGdvligktSP--PRFLEELEELSLGLQER 816

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   836 KEDCIVESIRQLGSFDL-----SPK--KMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIPDIVFNP 908
Cdd:PRK08565  817 RDTSVTVRHGEKGIVDTvliteSPEgnKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINP 896

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   909 HGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFrfseENTAIDYFGKMLEAGGYNYYGTERLYSGVDGREMTADIFFGVV 988
Cdd:PRK08565  897 HAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVV 972

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   989 HYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSIl 1068
Cdd:PRK08565  973 YYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHI- 1051

                        1130      1140      1150      1160      1170      1180
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17136446  1069 APLQRivKRNETgglssqpdTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNEI 1129
Cdd:PRK08565 1052 AWYDR--RKNKY--------VCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGDK 1102
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 34-428 4.66e-160

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: 480.34  E-value: 4.66e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446     34 NLGGPHVDSFDEMLtvglDNSAKHMIPNHWLSPA----------GEKISMKVESIWIAKPKVPQDVIDvrTREIYPTDSR 103
Cdd:pfam04563    1 GLVRQQLDSFNEFV----DNDLQKIIDENALIESefeiqhpgenGDKLSLKFGQIRLGKPMFDETDGS--TREIYPQECR 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    104 QLHVSYSGMCSVRLGWSV-NGVQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRMLI 182
Cdd:pfam04563   75 LRNLTYSAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    183 MTRRNHPICVKRSSWKDRGQNFSDLGMLVQTVREDESSLSNVVHYLNNGTAKFMFSHVKRLsyVPVCLILKCLMDYTDEE 262
Cdd:pfam04563  155 HRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLEYLSNGTIYFKFPYIKKE--IPIVIILRALGFTSDRE 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    263 IYNRLVqGYESDQYYVSCVQAMLREVQNENVYTHAQCKSFIGNLFRARFPEVPEWQPDDDVTDFILRERVMIHLDTYE-- 340
Cdd:pfam04563  233 IFELIC-YDVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKYAEEILQKEVLPHLGTYEld 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    341 --DKFQLIVFMIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQKYLSERVESWVSQVRRCLQKKLTSPDalvtsAVMTQ 418
Cdd:pfam04563  312 etKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPD-----DLMLQ 386

                          410
                   ....*....|
gi 17136446    419 CMRQAGGVGR 428
Cdd:pfam04563  387 LLVNAKPITS 396
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 668-1022 2.96e-146

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: 443.51  E-value: 2.96e-146
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    668 LANLIPMPDYNQSPRNMYQCQMGKQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYT 747
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    748 GYDMEDAMIINKAAYERGFAYGSIYKTKFL---TLDKKSSYFARHPHMPEL-IKHLDTDGLPHPGSKLSYGSPLYCY--- 820
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEArktKLGPIEEITRDIPNVSEEaLKKLDEDGIVRVGAEVKPGDILVGKvgp 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    821 ---------FDGEVA---TYKVVKMDEKEDCIVESIRQlgsFDLSPK--KMVAITLRVPRPATIGDKFASRAGQKGICSQ 886
Cdd:pfam00562  161 teltkllraIFGEKArdvKDTSLKVPPGEEGVVDDVIV---FELPPGgiKMVKVYIRQKRKPEVGDKFASRHGQKGVVSR 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    887 KYPAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSeeNTAIDYFGKMLEAGGYNYYG 966
Cdd:pfam00562  238 ILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGA--STEVEDIGELLEKAGYNYYG 315

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 17136446    967 TERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKR 1022
Cdd:pfam00562  316 KEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 557-1128 1.10e-137

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: 429.45  E-value: 1.10e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    557 VFLDGKHLGHIhqSEAEKIVDELRYGKIFGTLPQMMEIGFIpfKKNGQfpgLYIATGPARMMRP---VWN---------- 623
Cdd:TIGR03670    1 VYLNGRLIGYH--DDPEELVEEVRKLRRSGKLSQEVNVAYY--EETNE---VYINCDAGRIRRPlivVENgkpkltrehv 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    624 -------LKWKR------VEYIGTLEQLYMEIAIDAKEMYPDFTtHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMG 690
Cdd:TIGR03670   74 eklkegeLTWDDlvkqgvIEYLDAEEEENAYIALDPEELTPEHT-HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMA 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    691 KQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFAYGS 770
Cdd:TIGR03670  153 KQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARST 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    771 IYKT--------------KFlTLDKKSSYFARHPhmpELIKHLDTDGLPHPGSKLSYG-------SPlyCYFDGEVATYK 829
Cdd:TIGR03670  233 FFRTyeaeerrypggqedRF-EIPEPDVRGYRGE---EAYKHLDEDGIVYPEVEVKGGdvligktSP--PRFLEELREFG 306

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    830 VVKMDEKEDCIVESIRQLGSFD-------LSPKKMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIP 902
Cdd:TIGR03670  307 LVTERRRDTSVTVRHGEKGIVDkviitetEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVP 386

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    903 DIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFrfseENTAIDYFGKMLEAGGYNYYGTERLYSGVDGREMTAD 982
Cdd:TIGR03670  387 DLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF----EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAE 462

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    983 IFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCH 1062
Cdd:TIGR03670  463 IFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCE 542

                          570       580       590       600       610       620
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17136446   1063 KCGSIlAPLQRivKRNETgglssqpdTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKLNE 1128
Cdd:TIGR03670  543 NCGHI-AWEDK--RKGTA--------YCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 557-1126 2.86e-131

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 412.82  E-value: 2.86e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   557 VFLDGKHLGHiHQsEAEKIVDELRYGKIFGTLPQMMEIGFIPFKKNgqfpgLYIATGPARMMRP---VWN---------- 623
Cdd:PRK07225    7 VYVNGKLIGT-HD-DPEELVEEIREARRSGEISEEVNVSYKEETNE-----VIINTDAGRARRPlivVENgepllteehi 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   624 -------LKWK------RVEYIGTLEQLYMEIAIDAKEMYPDfTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMG 690
Cdd:PRK07225   80 eklkngeLTFDdlvkqgVIEYLDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   691 KQTMGTPCLNWPKQAANKLYRLQTPGTPLFRPVHYDNIQLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFAYGS 770
Cdd:PRK07225  159 KQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSH 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   771 IYKT--------------KFLTLDKKssyfARHPHMPELIKHLDTDGLPHPGSKLSYG-------SP---LYCYFDGEVA 826
Cdd:PRK07225  239 FFRTyegeerrypggqedRFEIPDKD----VRGYRGEEAYRHLDEDGLVNPETEVKEGdvligktSPprfLEEPDDFGIS 314

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   827 TYK----VVKMDEKEDCIVESIRQLGSFDLSpkKMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIP 902
Cdd:PRK07225  315 PEKrretSVTMRSGEEGIVDTVILTETEEGS--RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVP 392

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   903 DIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFRFSEEntaiDYFGKMLEAGGYNYYGTERLYSGVDGREMTAD 982
Cdd:PRK07225  393 DLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDE----EDLREALEKLGFEHTGKEVMYDGITGEKIEAE 468

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   983 IFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCH 1062
Cdd:PRK07225  469 IFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCA 548

                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17136446  1063 KCGSIlAPLQRivKRNETgglssqpdTCRLCGDNSSVSMIEIPFSFKYLVTELSSVNINARFKL 1126
Cdd:PRK07225  549 KCGMI-AIYDK--KRNRK--------YCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 485-1128 2.13e-86

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: 301.64  E-value: 2.13e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  485 EARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEIS-----MRPdpklvkaipkhlidmgmmplsnrrylgeklYVVFL 559
Cdd:COG0085  406 EVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNeygfiETP------------------------------YRKVE 455

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  560 DGKHLGHIHQSEAEkivDELRYgkifgtlpqmmeigfipfkkngqfpglYIATGPARMmrpvwNLKWKRVEyigtlEQLY 639
Cdd:COG0085  456 NGKVTDEIEYLTAD---EEENY---------------------------YIAQANAPL-----DEDGNFLE-----ERVL 495

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  640 MEIAIDAKEMYPDFTTHLELAKTHFMSNLANLIPMPDYNQSPRNMYQCQMGKQTMGTPCLNWPKqaanKLYRLQT----- 714
Cdd:COG0085  496 VRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----LHYPLQKfqrsn 571

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  715 PGT-----PLFRP---VHYDNIQLD-------DFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGFaYGSI-------- 771
Cdd:COG0085  572 QGTcinqrPIVRVgdrVEKGDVLADgpatdngELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV-LTSIhieeyeie 650

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  772 -YKTKF----LTLDKkssyfarhP-HMPELIKHLDTDGLPHPGSKLSYG-------SP------------LYCYFdGEVA 826
Cdd:COG0085  651 aRDTKLgpeeITRDI--------PnVSEEALRNLDEDGIIRIGAEVKGGdilvgkvTPkgeteltpeerlLRAIF-GEKA 721

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  827 TY--------------KV--VKMDEKEDcivesirqlGSfDLSPK--KMVAITLRVPRPATIGDKFASRAGQKGICSQKY 888
Cdd:COG0085  722 REvrdtslrvphgekgKVidVKVFSREE---------GD-ELPPGvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRIL 791

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  889 PAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVYDATPFR-FSEENTAidyfgKMLEAGGYNYYGT 967
Cdd:COG0085  792 PQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEEIR-----ELLEKAGLPPDGK 866

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  968 ERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQD 1047
Cdd:COG0085  867 EVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 946

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446 1048 RLFHNSDKThtlvchkCGSIlAPLQRIVKrnetgglssqpdtcrlcGDNssVSMIEIPFSFKYLVTELSSVNINARFKLN 1127
Cdd:COG0085  947 RLTIKSDDV-------CGRV-KVYEAIVK-----------------GEN--IPEPGIPESFKVLLKELQSLGLDVEVLSE 999


                 .
gi 17136446 1128 E 1128
Cdd:COG0085 1000 D 1000
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 185-375 1.08e-47

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: 168.29  E-value: 1.08e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    185 RRNHPICVKRSSWKDRgqnfsdlgmlVQTVREDESSLSNVVHYLNNGTAKFMFSHVKRLSYVPVCLILKCLMDYTDEEIY 264
Cdd:pfam04561    1 RSNGIYVEKELDKNGI----------IATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREIL 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    265 NRLVqgyESDQYYVSCVQAMLREVQNENVYTHAQCKSFIGNLFRARFPEVPEWQPDDDVTDFILRE-RVMIHLDTYED-- 341
Cdd:pfam04561   71 DRLC---YDFNDPQMLELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREILYSRDPKyNLNKHLGLNEPfe 147

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 17136446    342 ----KFQLIVFMIQKLFQCAQGKYKVENVDSAMMQEVL 375
Cdd:pfam04561  148 nerlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 729-1123 6.12e-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: 160.98  E-value: 6.12e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    729 QLDDFAMGTNAIVAVISYTGYDMEDAMIINkaayERGF---AYGSIYKTKFLTL--DKK--SSYFARH-PHMPE-LIKHL 799
Cdd:TIGR02013  667 DLGELALGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEYEVEarDTKlgPEEITRDiPNVSEeALRNL 742

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    800 DTDGLPHPGSKLSYG-------SP------------LYCYFdGEVATY---KVVKMDEKEDCIVESIRQL---GSFDLSP 854
Cdd:TIGR02013  743 DENGIVRIGAEVKAGdilvgkvTPkgeteltpeeklLRAIF-GEKARDvrdTSLRVPPGVEGTVIDVKVFsreQGDELPP 821

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    855 --KKMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIET---MAGKGA 929
Cdd:TIGR02013  822 gvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKRL 901

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    930 AIHGnVYDATPFRFSEENTAIDyfgKMLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAV 1009
Cdd:TIGR02013  902 GRKG-VPIATPVFDGASEEEIK---EYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPY 977

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   1010 EARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHtlvchkcGSILApLQRIVKrnetgglssqpdt 1089
Cdd:TIGR02013  978 SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVV-------GRTKA-YEAIVK------------- 1036

                          410       420       430
                   ....*....|....*....|....*....|....
gi 17136446   1090 crlcGDNSSVSmiEIPFSFKYLVTELSSVNINAR 1123
Cdd:TIGR02013 1037 ----GENVPEP--GIPESFNVLIKELQSLGLDIE 1064
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 732-1121 5.29e-35

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 145.23  E-value: 5.29e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   732 DFAMGTNAIVAVISYTGYDMEDAMIINK-AAYERGFAYGSI--YKTKFLTLDKKSSYFARHphMPEL----IKHLDTDGL 804
Cdd:CHL00207  643 ELALGQNVLVAYMPWEGYNFEDAILINKrLVYEDLFTSIHIekYEIELRQTKLGSEEITRN--IPNVseysLKNLDENGI 720

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   805 PHPGSKLSYGSPL-------------------YCYFdGEVATY---KVVKMDEKEDCIVESIRQLG--SFDLSPKkMVAI 860
Cdd:CHL00207  721 ISIGSKVLAGDILvgkitpkgesdqlpegkllRAIF-GEKAKDvkdTSLRMPNGGYGRVIKVEIFSrsKGDELKF-GYYL 798

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   861 TLRV----PRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHGNVY 936
Cdd:CHL00207  799 KIRVfiaqIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRF 878

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   937 DATPFrfSEENTAidYFGKML-------------EAGGYNYY--GTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKW 1001
Cdd:CHL00207  879 KILPF--DEMYGS--EYSRILinnklnqasiknnEYWLFNSYhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKI 954

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  1002 QVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSD----KTHTlvchkcgsilapLQRIVKR 1077
Cdd:CHL00207  955 HARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDdmqgRNET------------LNAIVKG 1022

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....
gi 17136446  1078 NetgglssqpdtcrlcgdnsSVSMIEIPFSFKYLVTELSSVNIN 1121
Cdd:CHL00207 1023 Q-------------------PIPKPGTPESFKVLMRELQSLGLD 1047
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 455-519 1.73e-31

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: 117.63  E-value: 1.73e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17136446    455 IMAENINRMRYMSHFRAIH--RGSYFTTMRTTEARQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCE 519
Cdd:pfam04565    1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
rpoB CHL00001
RNA polymerase beta subunit
 734-1121 2.34e-31

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 133.49  E-value: 2.34e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   734 AMGTNAIVAVISYTGYDMEDAMIIN-KAAYERgfAYGSIYKTKFLTLDKKSS----YFARH-PHM-PELIKHLDTDGLPH 806
Cdd:CHL00001  650 ALGKNVLVAYMPWEGYNFEDAVLISeRLVYED--IYTSFHIRKYEIQTHVTSqgpeRITKEiPHLeAHLLRNLDKNGIVM 727

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   807 PGS----------KL-------SYGSP----LYCYFDGEVATYKvvkmdekEDCI------------VESIRQLGSFDLS 853
Cdd:CHL00001  728 LGSwvetgdilvgKLtpqeaeeSSYAPegrlLRAIFGIQVSTSK-------ETCLklpiggrgrvidVRWIQKKGGSSYN 800

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   854 PKkMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAGKGAAIHG 933
Cdd:CHL00001  801 PE-TIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLN 879

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   934 NVYDATPF--RFSEENTAIDYFGKMLEAG---GY------NYYGTERLYsgvDGRemTADIF-----FGVVHYQRLRHMV 997
Cdd:CHL00001  880 RHYRIAPFdeRYEQEASRKLVFSELYEASkqtANpwvfepEYPGKSRLF---DGR--TGDPFeqpvtIGKAYILKLIHQV 954

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   998 FDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDktHtlvchkcgsilaplqrIVKR 1077
Cdd:CHL00001  955 DDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD--H----------------IRAR 1016

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 17136446  1078 NE------TGGLSSQPDTcrlcgdnssvsmieIPFSFKYLVTELSSVNIN 1121
Cdd:CHL00001 1017 QEvlgaiiTGGTIPKPED--------------APESFRLLVRELRSLALE 1052
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 38-544 1.61e-29

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 124.29  E-value: 1.61e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446    38 PHVDSFDEMLTVGLDNSAKHMIPNHWLSPAGEKIsmKVESIWIAKPKVPQdvIDVRTREIYPTDSRQLHVSYSGMCSVRL 117
Cdd:PRK09606   21 HHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYV--ELGKIRVGKPVVKE--ADGSEREIYPMEARLRNLTYSAPLYLEM 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   118 GWSVNGVQKTPINMDLGEVPIMLRSKACNLGQATPEEMVKHGEHDSEWGGIFVIRGNEKIVRML-------IMTRRNHpi 190
Cdd:PRK09606   97 SPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLedlapnkILVEKDE-- 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   191 cvKRSSWKDRGQNFSdlgmlvqtVREDESSLSnVVHYLNNGTAKFMFSHVKRlsYVPVCLILKCLMDYTDEEIYNRLvqg 270
Cdd:PRK09606  175 --RYGDRIEVAKVFS--------QRRGYRALV-TVERNRDGLLEVSFPSVPG--SIPFVILMRALGLETDEEIVEAV--- 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   271 yeSDQYYVscVQAMLREVQNENVYTHAQCKSFIGNLFRARFPEVPEWQPDDDVTDFILrervMIHLDTYEDKFQLIVF-- 348
Cdd:PRK09606  239 --SDDPEI--VKFMLENLEEAEVDTQEEALEYIGKRVAPGQTKEYRIKRAEYVIDRYL----LPHLGVEPEVRRAKAHyl 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   349 --MIQKLFQCAQGKYKVENVDSAMMQEVLLPGHLYQ--------------KYLSErveswvsqvRRCLQKKLTSPDALVT 412
Cdd:PRK09606  311 grMAEACFELALGRREEDDKDHYANKRLKLAGDLMEdlfrvafnrlardvKYQLE---------RANMRNRELSIKTAVR 381

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   413 SAVMTQCMRQAggvgraiesfLATGN-IASRTGLglmqnSGLVimaENINRMRYMSHFR----AIHRGS-YFttmrttEA 486
Cdd:PRK09606  382 SDVLTERLEHA----------MATGNwVGGRTGV-----SQLL---DRTDYMATLSHLRrvvsPLSRSQpHF------EA 437

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 17136446   487 RQLLPDAWGFICPVHTPDGTPCGLLNHLTLTCEISMRPDPKLVKAIpkhLIDMGMMPL 544
Cdd:PRK09606  438 RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEI---LKELGVEPE 492
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 851-1121 4.64e-27

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 119.44  E-value: 4.64e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   851 DLSP--KKMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIET---MA 925
Cdd:PRK00405  861 ELPPgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWA 940

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   926 GKGAAIHGnvydATPFrF---SEENtaidyFGKMLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQ 1002
Cdd:PRK00405  941 AKGLGIKF----ATPV-FdgaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIH 1010

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  1003 VRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSD------KThtlvchkcgsilapLQRIVK 1076
Cdd:PRK00405 1011 ARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvvgrtKV--------------YEAIVK 1076

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 17136446  1077 rnetgglssqpdtcrlcGDNssvsMIE--IPFSFKYLVTELSSVNIN 1121
Cdd:PRK00405 1077 -----------------GEN----IPEpgIPESFNVLVKELQSLGLD 1102
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 1024-1126 7.50e-26

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: 102.28  E-value: 7.50e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   1024 GGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVCHKCGSILAplqrivkrnetgglssqPDTCRLCGDNSSVSMIE 1103
Cdd:pfam04560    1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAA-----------------YNKCPICKGETDISPGY 63

                           90       100
                   ....*....|....*....|...
gi 17136446   1104 IPFSFKYLVTELSSVNINARFKL 1126
Cdd:pfam04560   64 IPESFKLLFQELQSLGIDPRLLL 86
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
856-1056 5.88e-24

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 110.01  E-value: 5.88e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   856 KMVAITLRVPRPATIGDKFASRAGQKGICSQKYPAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIET---MAGK--GAA 930
Cdd:PRK09603 1076 KKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMhlgLVGKefGKQ 1155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   931 IHG------------------------NVYDATPFRFSE-------------------------ENTAIDYFGKMLEAGG 961
Cdd:PRK09603 1156 IASmledktkdfakelrakmleianaiNEKDPLTIHALEncsdeelleyakdwskgvkmaipvfEGISQEKFYKLFELAK 1235

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   962 YNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRSTGAVEARTHQPIKGRKRGGGVRFGEMERDALISHGA 1041
Cdd:PRK09603 1236 IAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGA 1315

                         250
                  ....*....|....*
gi 17136446  1042 AFLLQDRLFHNSDKT 1056
Cdd:PRK09603 1316 AHTLKEMLTIKSDDI 1330
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 564-619 1.91e-19

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: 82.92  E-value: 1.91e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 17136446    564 LGHIHQSEAEKIVDELRYGKIFGT--LPQMMEIGFIPFKKNGQFPGLYIATGPARMMR 619
Cdd:pfam06883    1 IGYVSPKLAKRIADTLRYLKVEGEhgVPLTLEIGYVPPSNGGQYPGLYLFTSPARMMR 58
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
729-1129 2.03e-17

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 88.53  E-value: 2.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   729 QLDDFAMGTNAIVAVISYTGYDMEDAMIINKAAYERGfAYGSIYKTKFLTLDKKSSyfarhpHMPELIKHLDTDglphpg 808
Cdd:PRK14844  972 EINDFEKERDYIINVTSEYFYDELKKLLINSGSQDRE-KFDSIEREQWWGIGLKNQ------SISEQVKSLKKD------ 1038

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   809 sklsygsplycyFDGEVaTYKVVKMDEKedciVESIRQlgSFDLsPKKM---VAITLRVPRPATIGDKFASRAGQKGICS 885
Cdd:PRK14844 1039 ------------FDEKV-SHAIAQFKRK----VEKLHE--GYDL-PQGVsmsVKVFIAVKHSLQPGDKMAGRHGNKGVIS 1098

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   886 QKYPAEDLPFTESGLIPDIVFNPHGFPSRMTIAMMIETMAG----KGAAIHGNVYDA----------------------- 938
Cdd:PRK14844 1099 RVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackKLGEKVGNILDEinkiksafckgirslnddnftkf 1178

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   939 ------------------------TP----------------------------------------------FRFSEENT 948
Cdd:PRK14844 1179 aaayldnkkienidddeitasvlnTPnknalndelnelvenylnscksaysnlrnflievyscgsnvsicnnIRDISDNN 1258

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446   949 AIDY----------------------FGKMLEAGGYNYYGTERLYSGVDGREMTADIFFGVVHYQRLRHMVFDKWQVRST 1006
Cdd:PRK14844 1259 LIEFarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSV 1338

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17136446  1007 GAVEARTHQPIKGRKRGGGVRFGEMERDALISHGAAFLLQDRLFHNSDKTHTLVchkcgsilAPLQRIVKrnetgglssq 1086
Cdd:PRK14844 1339 GPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRV--------KIYESIIK---------- 1400

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|...
gi 17136446  1087 PDTCRLCGdnssvsmieIPFSFKYLVTELSSVNINARFKLNEI 1129
Cdd:PRK14844 1401 GDSNFECG---------IPESFNVMIKELRSLCLNVDLKQNDV 1434
 
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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