NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1207136539|ref|XP_021323450|]
View 

DNA-directed RNA polymerase III subunit RPC2 [Danio rerio]

Protein Classification

DNA-directed RNA polymerase III subunit RPC2( domain architecture ID 10090006)

DNA-directed RNA polymerase III subunit RPC2 is the second largest core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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. ...
37-1124 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: 1228.59  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653      1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653     80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653    159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653    199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653    236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653    314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653    382 --------------------------------------------------------------------------GRIERP 387
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653    388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653    417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653    497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653    573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653    652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653    732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
                         1050      1060      1070      1080      1090
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207136539 1070 DAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1124
Cdd:cd00653    812 DDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
536-597 1.00e-29

RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.


:

Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 112.46  E-value: 1.00e-29
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207136539  536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 597
Cdd:pfam04566    1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
618-658 3.86e-10

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.


:

Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 56.39  E-value: 3.86e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1207136539  618 FEDFLHESLVEYLDVNEENDCNIALY------------EHMISKDTTHLEIEP 658
Cdd:pfam04567    1 WSDLLREGVIEYLDAEEEETSMIAMTpedleessreerEGPYAHTYTHCEIHP 53
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
37-1124 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: 1228.59  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653      1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653     80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653    159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653    199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653    236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653    314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653    382 --------------------------------------------------------------------------GRIERP 387
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653    388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653    417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653    497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653    573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653    652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653    732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
                         1050      1060      1070      1080      1090
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207136539 1070 DAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1124
Cdd:cd00653    812 DDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
24-1126 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 1083.45  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   24 KWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDAdPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLR 103
Cdd:PRK08565     1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  104 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLS 183
Cdd:PRK08565    80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  184 KNRIIVDQDRKG---TVGASVTSSTHEKKSRTNM-IVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEEHV 259
Cdd:PRK08565   160 PNRVLVDKGEAGssiTHTAKVISSRAGYRAQVTVeRRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  260 MAAFAPSLEECQKAQIfTQTQALRYIGNKVrrqrMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVRRV 339
Cdd:PRK08565   240 QQELLPSLEQASSIAA-TVEDALDYIGKRV----AIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  340 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAAQFDVVkhMRQDQITNGMVNAIST 418
Cdd:PRK08565   315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  419 GNWSlkrfkMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:PRK08565   393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  499 ITTDMEDGPIIKLAFNLGVEDVNLLCGEElsYPTVFLVFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTD- 577
Cdd:PRK08565   468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  578 -RCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGYRTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEI 656
Cdd:PRK08565   546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNA 736
Cdd:PRK08565   626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  737 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGE 816
Cdd:PRK08565   706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  817 KVENKQVLVNKSMPTVTQTPLEGSAQPGQPQyREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSS 896
Cdd:PRK08565   786 EVKGGDVLIGKTSPPRFLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFAS 864
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  897 RHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRY 976
Cdd:PRK08565   865 RHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKL 944
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  977 GYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1056
Cdd:PRK08565   945 GYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHG 1024
                         1050      1060      1070      1080      1090      1100      1110
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1207136539 1057 ASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:PRK08565  1025 AAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
536-1126 0e+00

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 709.49  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:TIGR03670    1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:TIGR03670   81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:TIGR03670  161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  776 LRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGEKVENKQVLVNK-SMPTVTQTPLEGSAQPgqPQYREVPVS 854
Cdd:TIGR03670  241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVT--ERRRDTSVT 318
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  855 YKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSR 934
Cdd:TIGR03670  319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  935 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1014
Cdd:TIGR03670  399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539 1015 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1088
Cdd:TIGR03670  479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
                          570       580       590
                   ....*....|....*....|....*....|....*...
gi 1207136539 1089 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:TIGR03670  559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
29-1126 0e+00

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: 603.25  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   29 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITsDADPMWYLKYLNIYVGMPdveesfnvtrPVSPHECRLRDMTYS 108
Cdd:COG0085      8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  109 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpmefsklnecpldpgGYFIVKGQEKVILIQEQLSKNRI 187
Cdd:COG0085     77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  188 IVDQDRKG---TVGASVTSSTH-----EKKSRTNMIVKQGRfylkhntlSEDAPIAIIFKAMGVESDQEIVQMIGtEEHV 259
Cdd:COG0085    133 FVEEEDKSgkdLYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFG-DDPI 203
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  260 MAAFAPSLEecqKAQIFTQTQALRYIGNKVRRqrmwGGPKKtkMEEARELLASTI-------LTHV-----------PVK 321
Cdd:COG0085    204 QEYILATLE---KDNTKTQEEALLEIYRKLRP----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVP 274
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  322 EFNFRAKCIYLAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELK-----KIADQIIPKQraa 395
Cdd:COG0085    275 PEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRermttQDVEAITPQS--- 351
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  396 qfdVVkhmRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSF---ISALGM--MTRISSQFEktrkVsgpRSLQP 470
Cdd:COG0085    352 ---LI---NIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHP 412
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  471 SQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngnilgvirdhq 550
Cdd:COG0085    413 SHYGRMCPIETPEGPNIGLIGSLALYARV--------------------------------------------------- 441
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  551 klvytfrlmrragfiNEFvsistnltdrcvyissdgGRLCRPYIIVKNGKpaVKNKhieelsqgyrtfedflheslVEYL 630
Cdd:COG0085    442 ---------------NEY------------------GFIETPYRKVENGK--VTDE--------------------IEYL 466
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  631 DVNEENDCNIAL-----------------------YEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMG 687
Cdd:COG0085    467 TADEEENYYIAQanapldedgnfleervlvryrgeEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQ 546
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  688 KQAMG-----------TIGYNQRNRIDTlmyllAYPQRPMVKT----KTIELI------DFEKLPAGQNATVAVMSYSGY 746
Cdd:COG0085    547 RQAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGY 621
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  747 DIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYtnqtfdkvmgpMLDAE--TR-KP-----IWRHsiLDADGICSPGEKV 818
Cdd:COG0085    622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDT-----------KLGPEeiTRdIPnvseeALRN--LDEDGIIRIGAEV 688
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  819 ENKQVLVNKsmptVT------QTPLEG--SAQPGQPQyRE-------VPVSYKGatdsYIEKVMISSNAEDAFL------ 877
Cdd:COG0085    689 KGGDILVGK----VTpkgeteLTPEERllRAIFGEKA-REvrdtslrVPHGEKG----KVIDVKVFSREEGDELppgvnk 759
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  878 -VKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFH 956
Cdd:COG0085    760 lVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV 839
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  957 YGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGR 1036
Cdd:COG0085    840 ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGK 919
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539 1037 SRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQS 1116
Cdd:COG0085    920 AQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQS 989
                         1210
                   ....*....|
gi 1207136539 1117 MNIIPRLKLA 1126
Cdd:COG0085    990 LGLDVEVLSE 999
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
665-1038 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: 562.15  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  665 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYS 744
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  745 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLRRYTNQTFDKVMGPMldaeTRKPIWRHSILDADGICSPGEKVENKQVL 824
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  825 VNKSMPTVTQTPLEGSAQPGQPQYREVPVSYKGATDSYIEKVMI-SSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:pfam00562  155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLIRYGYNYQ 981
Cdd:pfam00562  235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1207136539  982 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1038
Cdd:pfam00562  315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
536-597 1.00e-29

RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 112.46  E-value: 1.00e-29
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207136539  536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 597
Cdd:pfam04566    1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
618-658 3.86e-10

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 56.39  E-value: 3.86e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1207136539  618 FEDFLHESLVEYLDVNEENDCNIALY------------EHMISKDTTHLEIEP 658
Cdd:pfam04567    1 WSDLLREGVIEYLDAEEEETSMIAMTpedleessreerEGPYAHTYTHCEIHP 53
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
37-1124 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: 1228.59  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653      1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653     80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653    159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653    199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653    236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653    314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653    382 --------------------------------------------------------------------------GRIERP 387
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653    388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653    417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653    497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653    573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653    652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653    732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
                         1050      1060      1070      1080      1090
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207136539 1070 DAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1124
Cdd:cd00653    812 DDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
24-1126 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 1083.45  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   24 KWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDAdPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLR 103
Cdd:PRK08565     1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  104 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLS 183
Cdd:PRK08565    80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  184 KNRIIVDQDRKG---TVGASVTSSTHEKKSRTNM-IVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEEHV 259
Cdd:PRK08565   160 PNRVLVDKGEAGssiTHTAKVISSRAGYRAQVTVeRRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  260 MAAFAPSLEECQKAQIfTQTQALRYIGNKVrrqrMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVRRV 339
Cdd:PRK08565   240 QQELLPSLEQASSIAA-TVEDALDYIGKRV----AIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  340 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAAQFDVVkhMRQDQITNGMVNAIST 418
Cdd:PRK08565   315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  419 GNWSlkrfkMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:PRK08565   393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  499 ITTDMEDGPIIKLAFNLGVEDVNLLCGEElsYPTVFLVFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTD- 577
Cdd:PRK08565   468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  578 -RCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGYRTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEI 656
Cdd:PRK08565   546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNA 736
Cdd:PRK08565   626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  737 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGE 816
Cdd:PRK08565   706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  817 KVENKQVLVNKSMPTVTQTPLEGSAQPGQPQyREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSS 896
Cdd:PRK08565   786 EVKGGDVLIGKTSPPRFLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFAS 864
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  897 RHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRY 976
Cdd:PRK08565   865 RHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKL 944
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  977 GYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1056
Cdd:PRK08565   945 GYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHG 1024
                         1050      1060      1070      1080      1090      1100      1110
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1207136539 1057 ASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:PRK08565  1025 AAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
536-1126 0e+00

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 709.49  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:TIGR03670    1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:TIGR03670   81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:TIGR03670  161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  776 LRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGEKVENKQVLVNK-SMPTVTQTPLEGSAQPgqPQYREVPVS 854
Cdd:TIGR03670  241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVT--ERRRDTSVT 318
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  855 YKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSR 934
Cdd:TIGR03670  319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  935 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1014
Cdd:TIGR03670  399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539 1015 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1088
Cdd:TIGR03670  479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
                          570       580       590
                   ....*....|....*....|....*....|....*...
gi 1207136539 1089 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:TIGR03670  559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
536-1125 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 704.03  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:PRK07225     7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:PRK07225    87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:PRK07225   167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  776 LRRYTNQTFDKVMGPmlDAETR----KPIWRHsiLDADGICSPGEKVENKQVLVNKSMPtvtqtP--LEGSAQPGQP--Q 847
Cdd:PRK07225   247 ERRYPGGQEDRFEIP--DKDVRgyrgEEAYRH--LDEDGLVNPETEVKEGDVLIGKTSP-----PrfLEEPDDFGISpeK 317
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  848 YREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMN 927
Cdd:PRK07225   318 RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIIN 397
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  928 PHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQ 1007
Cdd:PRK07225   398 PHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQ 477
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539 1008 KLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY-- 1085
Cdd:PRK07225   478 KLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIyd 557
                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....
gi 1207136539 1086 ----SGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKL 1125
Cdd:PRK07225   558 kkrnRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
29-1126 0e+00

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: 603.25  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   29 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITsDADPMWYLKYLNIYVGMPdveesfnvtrPVSPHECRLRDMTYS 108
Cdd:COG0085      8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  109 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpmefsklnecpldpgGYFIVKGQEKVILIQEQLSKNRI 187
Cdd:COG0085     77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  188 IVDQDRKG---TVGASVTSSTH-----EKKSRTNMIVKQGRfylkhntlSEDAPIAIIFKAMGVESDQEIVQMIGtEEHV 259
Cdd:COG0085    133 FVEEEDKSgkdLYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFG-DDPI 203
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  260 MAAFAPSLEecqKAQIFTQTQALRYIGNKVRRqrmwGGPKKtkMEEARELLASTI-------LTHV-----------PVK 321
Cdd:COG0085    204 QEYILATLE---KDNTKTQEEALLEIYRKLRP----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVP 274
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  322 EFNFRAKCIYLAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELK-----KIADQIIPKQraa 395
Cdd:COG0085    275 PEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRermttQDVEAITPQS--- 351
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  396 qfdVVkhmRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSF---ISALGM--MTRISSQFEktrkVsgpRSLQP 470
Cdd:COG0085    352 ---LI---NIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHP 412
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  471 SQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngnilgvirdhq 550
Cdd:COG0085    413 SHYGRMCPIETPEGPNIGLIGSLALYARV--------------------------------------------------- 441
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  551 klvytfrlmrragfiNEFvsistnltdrcvyissdgGRLCRPYIIVKNGKpaVKNKhieelsqgyrtfedflheslVEYL 630
Cdd:COG0085    442 ---------------NEY------------------GFIETPYRKVENGK--VTDE--------------------IEYL 466
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  631 DVNEENDCNIAL-----------------------YEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMG 687
Cdd:COG0085    467 TADEEENYYIAQanapldedgnfleervlvryrgeEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQ 546
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  688 KQAMG-----------TIGYNQRNRIDTlmyllAYPQRPMVKT----KTIELI------DFEKLPAGQNATVAVMSYSGY 746
Cdd:COG0085    547 RQAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGY 621
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  747 DIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYtnqtfdkvmgpMLDAE--TR-KP-----IWRHsiLDADGICSPGEKV 818
Cdd:COG0085    622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDT-----------KLGPEeiTRdIPnvseeALRN--LDEDGIIRIGAEV 688
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  819 ENKQVLVNKsmptVT------QTPLEG--SAQPGQPQyRE-------VPVSYKGatdsYIEKVMISSNAEDAFL------ 877
Cdd:COG0085    689 KGGDILVGK----VTpkgeteLTPEERllRAIFGEKA-REvrdtslrVPHGEKG----KVIDVKVFSREEGDELppgvnk 759
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  878 -VKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFH 956
Cdd:COG0085    760 lVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV 839
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  957 YGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGR 1036
Cdd:COG0085    840 ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGK 919
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539 1037 SRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQS 1116
Cdd:COG0085    920 AQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQS 989
                         1210
                   ....*....|
gi 1207136539 1117 MNIIPRLKLA 1126
Cdd:COG0085    990 LGLDVEVLSE 999
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
665-1038 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: 562.15  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  665 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYS 744
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  745 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLRRYTNQTFDKVMGPMldaeTRKPIWRHSILDADGICSPGEKVENKQVL 824
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  825 VNKSMPTVTQTPLEGSAQPGQPQYREVPVSYKGATDSYIEKVMI-SSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:pfam00562  155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLIRYGYNYQ 981
Cdd:pfam00562  235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1207136539  982 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1038
Cdd:pfam00562  315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
22-520 3.80e-113

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 360.80  E-value: 3.80e-113
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   22 EEKWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDADPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECR 101
Cdd:PRK09606     3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEAR 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  102 LRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQ 181
Cdd:PRK09606    83 LRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLED 162
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  182 LSKNRIIVDQDRKG---TVGASVTSSTHEKKSR-TNMIVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEE 257
Cdd:PRK09606   163 LAPNKILVEKDERYgdrIEVAKVFSQRRGYRALvTVERNRDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDP 242
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  258 HVMAAFAPSLEEcqkAQIFTQTQALRYIGNKVRRqrmwGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVR 337
Cdd:PRK09606   243 EIVKFMLENLEE---AEVDTQEEALEYIGKRVAP----GQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAE 315
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  338 RVI-LAQGDNKVDDRDYYGNKRLELAGQLLsllfEDLFK-KFNSELKKIADQIipkQRAA----QFDVVKHMRQDQITNG 411
Cdd:PRK09606   316 ACFeLALGRREEDDKDHYANKRLKLAGDLM----EDLFRvAFNRLARDVKYQL---ERANmrnrELSIKTAVRSDVLTER 388
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  412 MVNAISTGNWslkrfKMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVK 491
Cdd:PRK09606   389 LEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVK 463
                          490       500
                   ....*....|....*....|....*....
gi 1207136539  492 NLALMTHITTDMEDGPIIKLAFNLGVEDV 520
Cdd:PRK09606   464 NFAQMVEISTGEDEEEVKEILKELGVEPE 492
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
36-410 1.56e-112

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: 355.53  E-value: 1.56e-112
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   36 GLVKQHIDSFNYFINVEIKKIMKANEKITSDADP--------MWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLRDMTY 107
Cdd:pfam04563    1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIqhpgengdKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  108 SAPITVDIEYTR-GSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNR 186
Cdd:pfam04563   81 SAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  187 IIVDQDR---KGTVGASVTSSTHE-----KKSRTNMI--VKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTE 256
Cdd:pfam04563  161 PIVFKKAdpkKRGSVASVRSSAEIsvrpdSTSWVNVLeyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYD 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  257 EH---VMAAFAPSLEECQKAQIFTQTQALRYIGNKVRRQRMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLA 333
Cdd:pfam04563  241 VNdqqLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYFIG 320
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207136539  334 VMVRRVIL-AQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAaqFDVVKHMRQDQITN 410
Cdd:pfam04563  321 YMIRRLLLlALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDD--LMLQLLVNAKPITS 396
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
29-1117 4.54e-68

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: 249.19  E-value: 4.54e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   29 PAFLKVKGLVKQHIDSFNYFINVE----------IKKIMKANEKITSDADPMwYLKYLNIYVGMPDVeesfnvtrpvSPH 98
Cdd:TIGR02013   12 PEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPIEDYTGNI-ELEYLSYRLGEPKY----------SVE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   99 ECRLRDMTYSAPITVDIEYT----RGSQRIIRNALPIGRMPIMlrssncvlTGKtpmefsklnecpldpgGYFIVKGQEK 174
Cdd:TIGR02013   81 ECKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLM--------TDR----------------GTFIINGAER 136
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  175 VILIQEQLSKNrIIVDQDrkgtvgasVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDA-----------PIAIIFKAMGV 243
Cdd:TIGR02013  137 VVVSQLHRSPG-VFFSSE--------KDTTKSGKVLFSARIIPYRGSWLEFETDKKDVlyvridrkrklPATVLLRALGY 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  244 ESDQEIVQMIGTEEHVMAAFapsleecQKAQIFTQTQALRYIGNKVRRqrmwGGPkkTKMEEARELLASTI-------LT 316
Cdd:TIGR02013  208 TIDTLILNRLGSGEYIRNTL-------RKDPTNSEEEALVEIYRKLRP----GEP--PTVEAARSLLENLFfdpkrydLG 274
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  317 HVPVKEFNFRAK-------CIY-----LAVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKI 384
Cdd:TIGR02013  275 RVGRYKLNKKLGldvpesiGVLtkediIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQ-------NQFRVGLARM 347
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  385 ADQIipKQRAAQFDVVKHMRQDQITNGMVNAIST---GNWSLKRFkMDRqgvTQVLSRLSF---ISALGM--MTRISSQF 456
Cdd:TIGR02013  348 ERIV--RERMSTQDTDTLTPQDLINAKPISAAIKeffGSSQLSQF-MDQ---TNPLAELTHkrrLSALGPggLTRERAGF 421
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  457 EKtrkvsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLAlmthittdmedgpiiklafnlgvedvnllcgeelsyptvflv 536
Cdd:TIGR02013  422 EV-------RDVHPTHYGRICPIETPEGPNIGLINSLS------------------------------------------ 452
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  537 flngnilgvirdhqklVYTFrlmrragfINEFVSISTnltdrcvyissdggrlcrPYIIVKNGKPAVknkhieelsqgyr 616
Cdd:TIGR02013  453 ----------------TYAR--------VNEYGFIET------------------PYRKVKDGKVVV------------- 477
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  617 tfedflhESLVEYLDVNEENDCNIA-------------------LYEHMIS----KDTTHLEIEPFTLLGVCAGLIPYPH 673
Cdd:TIGR02013  478 -------TDEIDYLTADEEDNYVIAqanapldengrfvedlvvaRYRGEITlvspDQVDYMDVSPKQVVSVAASLIPFLE 550
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  674 HNQSPRNTYQCAMGKQAM-------------------------------GTIGYNQRNRI---------DTLMYLLAYP- 712
Cdd:TIGR02013  551 HDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRl 630
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  713 -------------QRPMV----KTKTIELI------DFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVY 769
Cdd:TIGR02013  631 lkyqrsnqdtcinQRPIVsvgdRVEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISE---------RLVK 701
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  770 KNAKCT--LRRYTNQTFDKVMGPmlDAETR------KPIWRHsiLDADGICSPGEKVENKQVLVNKSMPT--VTQTPLEG 839
Cdd:TIGR02013  702 DDVFTSihIEEYEVEARDTKLGP--EEITRdipnvsEEALRN--LDENGIVRIGAEVKAGDILVGKVTPKgeTELTPEEK 777
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  840 --SAQPGQpQYREV-------PVSYKGAtdsyIEKVMISSNAEDAFL-------VKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:TIGR02013  778 llRAIFGE-KARDVrdtslrvPPGVEGT----VIDVKVFSREQGDELppgvnklVKVYIAQKRKIQVGDKMAGRHGNKGV 852
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRF--HYGTA-FGGSKVKDVCEDLIRYGYNY 980
Cdd:TIGR02013  853 VSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKgvPIATPvFDGASEEEIKEYLEKAGLPR 932
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  981 QGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASML 1060
Cdd:TIGR02013  933 DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1012
                         1210      1220      1230      1240      1250      1260
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1207136539 1061 LLERLMISSD-------AFEVDVCGQcgllgysgwchycksscHVSSLRIPYACKLLFQELQSM 1117
Cdd:TIGR02013 1013 LQEMLTVKSDdvvgrtkAYEAIVKGE-----------------NVPEPGIPESFNVLIKELQSL 1059
rpoB CHL00207
RNA polymerase beta subunit; Provisional
33-1130 1.46e-59

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 223.04  E-value: 1.46e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539   33 KVKGLVKQHIDSFNYFINVEIKKIMKANEKITsdaDPMWYLKYLNIYvgmpdveESFNVTRP-VSPHECRLRDMTYSAPI 111
Cdd:CHL00207     6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFG-------KNYKLKYPkYNLLSAKSYDSNYSIQI 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  112 TVDIEYTRGSQRIIRNA-LPIGRMPIMLRSSNCVLTGktpMEFSKLNECPLDPGGYFivkgqEKVIliqeqlsknriivd 190
Cdd:CHL00207    76 YLPLKFINLKTNKIKFInYLIGNLPKMTQRGTFIING---LERVIVSQIIRSPGIYF-----KKEI-------------- 133
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  191 qDRKGTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEdAPIAIIFKAMGVeSDQEIVQmigteeHVMAAFAPSLEEC 270
Cdd:CHL00207   134 -KKNSNKIYSATLIPNRGSWIKFELDKNKEIWIRIDKNRK-KPLIIFLKALGL-TDQDIYS------RLTKSEFLKKLKP 204
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  271 QKAQI--FTQTQALRYIGNKVRRQRMWGGPKKTKMEEAR----------ELLASTILTHVPVKEFNFRAKCIY---LAVM 335
Cdd:CHL00207   205 ILLNSnsYTNEEILLEIYKNLSPIEPATVNDANQNLFSRffdpknydlgKVGRYKINNKLNLNIPERVRNLTYediLSII 284
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  336 VRRVILAQGDNKVDDRDYYGNKRLELAGQLLsllfedlFKKFNSELKKIaDQIIPKQraaqfdVVKHmRQDQITNGMVNA 415
Cdd:CHL00207   285 DKLINLKINKGNFDDIDHLKNRRVRSVGELL-------QNQFRIGLKRL-ERILRNR------MTIC-DIDSLSKFNLIN 349
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  416 ISTGNWSLKRFKMDRQgVTQVLSRLSFISALGMMTRIS----SQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLvk 491
Cdd:CHL00207   350 PKPLIALIREFFGSSQ-LSQYMDQTNPLSELTHKRRISilgpGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGL-- 426
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  492 nlalmthittdmedgpIIKLAFNLGVEDVNLLcgeelsyPTVFLVFLNGNILgvirDHQKLVYTfrlmrrAGFINEFVSI 571
Cdd:CHL00207   427 ----------------IGSLATNARINKFGFI-------ETPFYKVINGKVK----KFGNPIYL------TADSEDLYRI 473
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  572 STNltdrcvyissdggrlcrPYIIVKNGkpAVKNKHIEelsqgyrtfedflheslveyldVNEENDCNIALYEH--MISk 649
Cdd:CHL00207   474 APN-----------------DINLNKNN--YFKKNIIP----------------------VRYKQEFKTVNPSKvdFIA- 511
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  650 dtthleIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLM-------------- 706
Cdd:CHL00207   512 ------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisltegivvsvs 585
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  707 ----------------YLLAYP---------QRPMV----KTKTIEL------IDFEKLPAGQNATVAVMSYSGYDIEDA 751
Cdd:CHL00207   586 aykiiiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMPWEGYNFEDA 665
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  752 LVLNKAsldrgfgrcLVYKNAkctlrrYTNQTFDKV-----MGPMLDAETRKPIWRHSI-----LDADGICSPGEKVENK 821
Cdd:CHL00207   666 ILINKR---------LVYEDL------FTSIHIEKYeielrQTKLGSEEITRNIPNVSEyslknLDENGIISIGSKVLAG 730
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  822 QVLVNK--SMPTVTQTPLE-------GSAQPGqpqYREVPVSYKGATDSYIEKVMI---SSNAEDAFLVKILLR----QT 885
Cdd:CHL00207   731 DILVGKitPKGESDQLPEGkllraifGEKAKD---VKDTSLRMPNGGYGRVIKVEIfsrSKGDELKFGYYLKIRvfiaQI 807
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  886 RRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAG-VLDGRF---HYGTAF 961
Cdd:CHL00207   808 RKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdNLNKRFkilPFDEMY 887
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  962 GGSKVKDVCEDLIR-----------YGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTR 1030
Cdd:CHL00207   888 GSEYSRILINNKLNqasiknneywlFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQ 967
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539 1031 QPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGLLGYsgwchYCKSSCHVSSLrIPYACKLL 1110
Cdd:CHL00207   968 QPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD----DMQGRNETLNA-----IVKGQPIPKPG-TPESFKVL 1037
                         1210      1220
                   ....*....|....*....|.
gi 1207136539 1111 FQELQSMNI-IPRLKLARYNE 1130
Cdd:CHL00207  1038 MRELQSLGLdIEAYKIENFLE 1058
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
1040-1126 3.42e-46

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: 160.06  E-value: 3.42e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539 1040 GGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1119
Cdd:pfam04560    1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80

                   ....*..
gi 1207136539 1120 IPRLKLA 1126
Cdd:pfam04560   81 DPRLLLE 87
rpoB CHL00001
RNA polymerase beta subunit
733-1070 1.30e-43

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 172.78  E-value: 1.30e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  733 GQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTL--RRY------TNQTFDKVMG--PMLDAEtrkpIWR 802
Cdd:CHL00001   652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFhiRKYeiqthvTSQGPERITKeiPHLEAH----LLR 718
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  803 HsiLDADGICSPGEKVENKQVLVNKSMPtvtQTPLEGSAQP----------GQ-PQYRE----VPVSYKG-ATD-SYIEK 865
Cdd:CHL00001   719 N--LDKNGIVMLGSWVETGDILVGKLTP---QEAEESSYAPegrllraifgIQvSTSKEtclkLPIGGRGrVIDvRWIQK 793
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  866 VMISSNaeDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLA 945
Cdd:CHL00001   794 KGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  946 GKAGVLDGRfHYgtafggsKVKDVCEdliRYG------------Y--------------NYQGKDYVTSGITGEPLEAYI 999
Cdd:CHL00001   872 GLAGDLLNR-HY-------RIAPFDE---RYEqeasrklvfselYeaskqtanpwvfepEYPGKSRLFDGRTGDPFEQPV 940
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207136539 1000 YFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD 1070
Cdd:CHL00001   941 TIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
877-1078 3.02e-40

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 162.19  E-value: 3.02e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  877 LVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRfH 956
Cdd:PRK00405   869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-K 947
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  957 YGT-AFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 1035
Cdd:PRK00405   948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1207136539 1036 RSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCG 1078
Cdd:PRK00405  1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVVG 1066
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
344-1117 1.12e-30

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 131.97  E-value: 1.12e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  344 GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKIADQIIPKQRAAQFDVVKHMRQDQITNGMVNAistgnwSL 423
Cdd:PRK09603   450 NQGKIDDRDHLGNRRIRAVGELLA-------NELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITS------TI 516
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  424 KRFKMDRQgVTQVLSRLSFISALGMMTRISSQFE----KTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHI 499
Cdd:PRK09603   517 MEFFMGGQ-LSQFMDQTNPLSEVTHKRRLSALGEgglvKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV 595
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  500 ttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngNILGVIRDHQKLVytfrlmrragfinefvsISTNLTDRC 579
Cdd:PRK09603   596 -----------------------------------------NDLGFIEAPYKKV-----------------VDGKVVGET 617
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  580 VYISS---DGgrlcrpYIIVKNGKPAVKNKHIEElsqgyrtfedflheSLVEyldvnEENDCNIALYEhmiSKDTTHLEI 656
Cdd:PRK09603   618 IYLTAiqeDS------HIIAPASTPIDEEGNILG--------------DLIE-----TRVEGEIVLNE---KSKVTLMDL 669
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM-----------------------GTIGYNQR---NRIDTL-MYLL 709
Cdd:PRK09603   670 SSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswGAIKANRAgvvEKIDSKnIYIL 749
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  710 ----------AYP--------------QRPMVKT-KTIEL---------IDFEKLPAGQNATVAVMSYSGYDIEDALVLN 755
Cdd:PRK09603   750 gegkeeayidAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiiadgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVS 829
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  756 KasldrgfgrCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRK-PIWRH---SILDADGICSPGEKVENKQVLVNKSMPT 831
Cdd:PRK09603   830 E---------RITKDDIFTSTHIYEKEVDARELKHGVEEFTADiPDVKEealAHLDESGIVKVGTYVSAGMILVGKTSPK 900
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  832 --VTQTP--------------------------LEGSA------------------------------------------ 841
Cdd:PRK09603   901 geIKSTPeerllraifgdkaghvvnkslycppsLEGTVidvkvftkkgyekdarvlsayeeekakldmehfdrltmlnre 980
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  842 -------------------------QPGQ--PQY------------------REVPVSYKGATDSYIE-KVMISSNAEDA 875
Cdd:PRK09603   981 ellrvssllsqaileepfshngkdyKEGDqiPKEeiasinrftlaslvkkysKEVQNHYEITKNNFLEqKKVLGEEHEEK 1060
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  876 F---------------LVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKL 940
Cdd:PRK09603  1061 LsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQI 1140
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  941 IEL---LAGK------AGVLDGRFHYGTAFGGSKVKDVC-------------------EDLIRYGYNYQ----------- 981
Cdd:PRK09603  1141 LEMhlgLVGKefgkqiASMLEDKTKDFAKELRAKMLEIAnainekdpltihalencsdEELLEYAKDWSkgvkmaipvfe 1220
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  982 -------------------GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGL 1042
Cdd:PRK09603  1221 gisqekfyklfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQ 1300
                          970       980       990      1000      1010      1020      1030
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207136539 1043 RLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGllGYSGwchyCKSSCHVSSLRIPYACKLLFQELQSM 1117
Cdd:PRK09603  1301 RFGEMEVWALEAYGAAHTLKEMLTIKSD----DIRGREN--AYRA----IAKGEQVGESEIPETFYVLTKELQSL 1365
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
536-597 1.00e-29

RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 112.46  E-value: 1.00e-29
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207136539  536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 597
Cdd:pfam04566    1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
183-360 1.56e-25

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: 104.74  E-value: 1.56e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  183 SKNRIIVDQDRKGT-VGASVTSSTHEKKSRTNMIVKQGRFYLKHN-TLSEDAPIAIIFKAMGVESDQEIVQMI-GTEEHV 259
Cdd:pfam04561    1 RSNGIYVEKELDKNgIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLcYDFNDP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  260 MAAFAPSLEECQKAQIFTQTQALRYIGNKVRRqrmwGGPKKTKMEEARELLAST-----ILTHVPVKE--FNFRAKCIYL 332
Cdd:pfam04561   81 QMLELLKPELEEAENIYTQEEALDYIGKGFAL----RRGEEPRLQRAREILYSRdpkynLNKHLGLNEpfENERLKAQDI 156
                          170       180
                   ....*....|....*....|....*....
gi 1207136539  333 AVMVRRVI-LAQGDNKVDDRDYYGNKRLE 360
Cdd:pfam04561  157 LYMIDRLLnLKLGRRKPDDIDHLGNKRVR 185
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
313-1070 2.76e-22

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 104.32  E-value: 2.76e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  313 TILTHVPVKEfnfrakciylavMVRRVILAQ-GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKIADQIIPK 391
Cdd:PRK14844   439 TVLTHEDIIE------------IVRKIVLLRdGQGSVDDIDHLGNRRVRSVGEFIE-------NQFRTGLLKLERAVVDS 499
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  392 QRAAQFDVVK---HMRQDQITNGMVNAISTGNwsLKRFkMDRQGVTQVLSRLSFISALGM--MTRISSQFEKtrkvsgpR 466
Cdd:PRK14844   500 MSTSSLDKVSpsdFINPKVLTNVLRDFFNSSQ--LSQF-MDQTNPLSEITHKRRLSALGPggLTRERAGFEV-------R 569
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  467 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITT-DMEDGPIIKLAFNLGVEDVNLLCG--EELSYPTVFLVFLNGNil 543
Cdd:PRK14844   570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKyGFIESPYRKVVNRVVTDQIEYLSAidEGLYYIADTSAKLDEN-- 647
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  544 gvirdhQKLVYTFRLMRRAGfinEFVSISTnltDRCVYISsdggrlcrpyiivkngkpaVKNKHIEELSQgyrtfedflh 623
Cdd:PRK14844   648 ------NCFVDDMLYCRYAG---SFVMVSS---DQVSYID-------------------VSPKQVISVAA---------- 686
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  624 eSLVEYLdvnEENDCNIALYEHMISKDTTHL----------EIEPFTLLGVCA-------GLIpyphhNQSPRNTYQC-A 685
Cdd:PRK14844   687 -SLIPFL---ENDDANRALMGSNMQRQAVPLlkptaplvatGMESFVASGSGAvvlakrdGIV-----DSSDSNSIVIrA 757
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  686 MGKQAMGTIGYN-------QRNRIDTLMyllayPQRPMVKTKTI----------ELIDFEKLPAGQNATVAVMSYSGYDI 748
Cdd:PRK14844   758 FDKERVNYLDVDiyhlrkfQRSNHNTCI-----NQKPLVCVGDYvkegdviadgPAINSGELALGQNLLVAFMSWQGYNF 832
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  749 EDALVLNKASLDRGFGRCLVYKNAKCTLRRyTNQTFDKVMG--PMLDAETrkpiWRHsiLDADGICSPGEKVENKQVLVN 826
Cdd:PRK14844   833 EDSIIISSEVVKKDLFTSIHIEEFECVVHD-TPLGSEKITRaiPGVNEEN----LYH--LDDSGIVKIGTRVGPGYILVG 905
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  827 KSMPT----------------------------VTQTPLEGSAQPGQ--------PQYREVPVSYKGATD-----SYI-- 863
Cdd:PRK14844   906 KVTPKpslslppetkllmtifgeksfdcadsslYTSPDVEGTVIDVQvftrrgveENERALLIKQKEINDfekerDYIin 985
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  864 ----------EKVMISSNAED----------------------------------------------------------- 874
Cdd:PRK14844   986 vtseyfydelKKLLINSGSQDrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydlpq 1065
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  875 --AFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAG------ 946
Cdd:PRK14844  1066 gvSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackkl 1145
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  947 ---------------------------------KAGVLDGR--------------------------------------- 954
Cdd:PRK14844  1146 gekvgnildeinkiksafckgirslnddnftkfAAAYLDNKkienidddeitasvlntpnknalndelnelvenylnsck 1225
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  955 -------------FHYGT--------------------------------AFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:PRK14844  1226 saysnlrnflievYSCGSnvsicnnirdisdnnliefarklrdgipvaapVFEGPKDEQIAKLFELAGLDNSGQAVLYDG 1305
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207136539  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:PRK14844  1306 CSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKS 1385

                   .
gi 1207136539 1070 D 1070
Cdd:PRK14844  1386 D 1386
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
435-498 3.99e-21

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: 87.97  E-value: 3.99e-21
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207136539  435 QVLSRLSFISALGMMTRISS---QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:pfam04565    1 QVLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
618-658 3.86e-10

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 56.39  E-value: 3.86e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1207136539  618 FEDFLHESLVEYLDVNEENDCNIALY------------EHMISKDTTHLEIEP 658
Cdd:pfam04567    1 WSDLLREGVIEYLDAEEEETSMIAMTpedleessreerEGPYAHTYTHCEIHP 53
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH