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Conserved domains on  [gi|125843259|ref|XP_690811|]
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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

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List of domain hits

Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
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 125843259   37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653     1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653    80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653   159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653   199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653   236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653   314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653   382 --------------------------------------------------------------------------GRIERP 387
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653   388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653   417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653   497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653   573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653   652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653   732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
                        1050      1060      1070      1080      1090
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 125843259 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 125843259   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 125843259   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 125843259   37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653     1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653    80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653   159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653   199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653   236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653   314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653   382 --------------------------------------------------------------------------GRIERP 387
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653   388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653   417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653   497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653   573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653   652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653   732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
                        1050      1060      1070      1080      1090
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 125843259 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 125843259   24 KWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDAdPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLR 103
Cdd:PRK08565    1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  104 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLS 183
Cdd:PRK08565   80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  184 KNRIIVDQDRKG---TVGASVTSSTHEKKSRTNM-IVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEEHV 259
Cdd:PRK08565  160 PNRVLVDKGEAGssiTHTAKVISSRAGYRAQVTVeRRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  260 MAAFAPSLEECQKAQIfTQTQALRYIGNKVrrqrMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVRRV 339
Cdd:PRK08565  240 QQELLPSLEQASSIAA-TVEDALDYIGKRV----AIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  340 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAAQFDVVkhMRQDQITNGMVNAIST 418
Cdd:PRK08565  315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  419 GNWSlkrfkMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:PRK08565  393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  499 ITTDMEDGPIIKLAFNLGVEDVNLLCGEElsYPTVFLVFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTD- 577
Cdd:PRK08565  468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  578 -RCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGYRTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEI 656
Cdd:PRK08565  546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNA 736
Cdd:PRK08565  626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  737 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGE 816
Cdd:PRK08565  706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  817 KVENKQVLVNKSMPTVTQTPLEGSAQPGQPQyREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSS 896
Cdd:PRK08565  786 EVKGGDVLIGKTSPPRFLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFAS 864
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  897 RHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRY 976
Cdd:PRK08565  865 RHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKL 944
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  977 GYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1056
Cdd:PRK08565  945 GYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHG 1024
                        1050      1060      1070      1080      1090      1100      1110
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 125843259 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 125843259   536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:TIGR03670    1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:TIGR03670   81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:TIGR03670  161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   776 LRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGEKVENKQVLVNK-SMPTVTQTPLEGSAQPgqPQYREVPVS 854
Cdd:TIGR03670  241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVT--ERRRDTSVT 318
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   855 YKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSR 934
Cdd:TIGR03670  319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   935 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1014
Cdd:TIGR03670  399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  1015 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1088
Cdd:TIGR03670  479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
                          570       580       590
                   ....*....|....*....|....*....|....*...
gi 125843259  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 125843259   29 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITsDADPMWYLKYLNIYVGMPdveesfnvtrPVSPHECRLRDMTYS 108
Cdd:COG0085     8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  109 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpmefsklnecpldpgGYFIVKGQEKVILIQEQLSKNRI 187
Cdd:COG0085    77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  188 IVDQDRKG---TVGASVTSSTH-----EKKSRTNMIVKQGRfylkhntlSEDAPIAIIFKAMGVESDQEIVQMIGtEEHV 259
Cdd:COG0085   133 FVEEEDKSgkdLYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFG-DDPI 203
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  260 MAAFAPSLEecqKAQIFTQTQALRYIGNKVRRqrmwGGPKKtkMEEARELLASTI-------LTHV-----------PVK 321
Cdd:COG0085   204 QEYILATLE---KDNTKTQEEALLEIYRKLRP----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVP 274
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  322 EFNFRAKCIYLAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELK-----KIADQIIPKQraa 395
Cdd:COG0085   275 PEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRermttQDVEAITPQS--- 351
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  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 125843259  471 SQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngnilgvirdhq 550
Cdd:COG0085   413 SHYGRMCPIETPEGPNIGLIGSLALYARV--------------------------------------------------- 441
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  551 klvytfrlmrragfiNEFvsistnltdrcvyissdgGRLCRPYIIVKNGKpaVKNKhieelsqgyrtfedflheslVEYL 630
Cdd:COG0085   442 ---------------NEY------------------GFIETPYRKVENGK--VTDE--------------------IEYL 466
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  631 DVNEENDCNIAL-----------------------YEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMG 687
Cdd:COG0085   467 TADEEENYYIAQanapldedgnfleervlvryrgeEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQ 546
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  688 KQAMG-----------TIGYNQRNRIDTlmyllAYPQRPMVKT----KTIELI------DFEKLPAGQNATVAVMSYSGY 746
Cdd:COG0085   547 RQAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGY 621
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  747 DIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYtnqtfdkvmgpMLDAE--TR-KP-----IWRHsiLDADGICSPGEKV 818
Cdd:COG0085   622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDT-----------KLGPEeiTRdIPnvseeALRN--LDEDGIIRIGAEV 688
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  819 ENKQVLVNKsmptVT------QTPLEG--SAQPGQPQyRE-------VPVSYKGatdsYIEKVMISSNAEDAFL------ 877
Cdd:COG0085   689 KGGDILVGK----VTpkgeteLTPEERllRAIFGEKA-REvrdtslrVPHGEKG----KVIDVKVFSREEGDELppgvnk 759
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  878 -VKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFH 956
Cdd:COG0085   760 lVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV 839
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  957 YGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGR 1036
Cdd:COG0085   840 ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGK 919
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1037 SRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQS 1116
Cdd:COG0085   920 AQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQS 989
                        1210
                  ....*....|
gi 125843259 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 125843259   665 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYS 744
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   745 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLRRYTNQTFDKVMGPMldaeTRKPIWRHSILDADGICSPGEKVENKQVL 824
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   825 VNKSMPTVTQTPLEGSAQPGQPQYREVPVSYKGATDSYIEKVMI-SSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:pfam00562  155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLIRYGYNYQ 981
Cdd:pfam00562  235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 125843259   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 125843259   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 125843259   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 125843259   37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653     1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653    80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653   159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653   199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653   236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653   314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653   382 --------------------------------------------------------------------------GRIERP 387
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653   388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653   417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653   497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653   573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653   652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653   732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
                        1050      1060      1070      1080      1090
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 125843259 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 125843259   24 KWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDAdPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLR 103
Cdd:PRK08565    1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  104 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLS 183
Cdd:PRK08565   80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  184 KNRIIVDQDRKG---TVGASVTSSTHEKKSRTNM-IVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEEHV 259
Cdd:PRK08565  160 PNRVLVDKGEAGssiTHTAKVISSRAGYRAQVTVeRRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  260 MAAFAPSLEECQKAQIfTQTQALRYIGNKVrrqrMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVRRV 339
Cdd:PRK08565  240 QQELLPSLEQASSIAA-TVEDALDYIGKRV----AIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  340 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAAQFDVVkhMRQDQITNGMVNAIST 418
Cdd:PRK08565  315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  419 GNWSlkrfkMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:PRK08565  393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  499 ITTDMEDGPIIKLAFNLGVEDVNLLCGEElsYPTVFLVFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTD- 577
Cdd:PRK08565  468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  578 -RCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGYRTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEI 656
Cdd:PRK08565  546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNA 736
Cdd:PRK08565  626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  737 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGE 816
Cdd:PRK08565  706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  817 KVENKQVLVNKSMPTVTQTPLEGSAQPGQPQyREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSS 896
Cdd:PRK08565  786 EVKGGDVLIGKTSPPRFLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFAS 864
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  897 RHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRY 976
Cdd:PRK08565  865 RHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKL 944
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  977 GYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1056
Cdd:PRK08565  945 GYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHG 1024
                        1050      1060      1070      1080      1090      1100      1110
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 125843259 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 125843259   536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:TIGR03670    1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:TIGR03670   81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:TIGR03670  161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   776 LRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGEKVENKQVLVNK-SMPTVTQTPLEGSAQPgqPQYREVPVS 854
Cdd:TIGR03670  241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVT--ERRRDTSVT 318
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   855 YKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSR 934
Cdd:TIGR03670  319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   935 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1014
Cdd:TIGR03670  399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  1015 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1088
Cdd:TIGR03670  479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
                          570       580       590
                   ....*....|....*....|....*....|....*...
gi 125843259  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 125843259  536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:PRK07225    7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:PRK07225   87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:PRK07225  167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  776 LRRYTNQTFDKVMGPmlDAETR----KPIWRHsiLDADGICSPGEKVENKQVLVNKSMPtvtqtP--LEGSAQPGQP--Q 847
Cdd:PRK07225  247 ERRYPGGQEDRFEIP--DKDVRgyrgEEAYRH--LDEDGLVNPETEVKEGDVLIGKTSP-----PrfLEEPDDFGISpeK 317
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  848 YREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMN 927
Cdd:PRK07225  318 RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIIN 397
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  928 PHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQ 1007
Cdd:PRK07225  398 PHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQ 477
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1008 KLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY-- 1085
Cdd:PRK07225  478 KLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIyd 557
                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....
gi 125843259 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 125843259   29 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITsDADPMWYLKYLNIYVGMPdveesfnvtrPVSPHECRLRDMTYS 108
Cdd:COG0085     8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  109 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpmefsklnecpldpgGYFIVKGQEKVILIQEQLSKNRI 187
Cdd:COG0085    77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  188 IVDQDRKG---TVGASVTSSTH-----EKKSRTNMIVKQGRfylkhntlSEDAPIAIIFKAMGVESDQEIVQMIGtEEHV 259
Cdd:COG0085   133 FVEEEDKSgkdLYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFG-DDPI 203
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  260 MAAFAPSLEecqKAQIFTQTQALRYIGNKVRRqrmwGGPKKtkMEEARELLASTI-------LTHV-----------PVK 321
Cdd:COG0085   204 QEYILATLE---KDNTKTQEEALLEIYRKLRP----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVP 274
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  322 EFNFRAKCIYLAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELK-----KIADQIIPKQraa 395
Cdd:COG0085   275 PEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRermttQDVEAITPQS--- 351
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  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 125843259  471 SQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngnilgvirdhq 550
Cdd:COG0085   413 SHYGRMCPIETPEGPNIGLIGSLALYARV--------------------------------------------------- 441
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  551 klvytfrlmrragfiNEFvsistnltdrcvyissdgGRLCRPYIIVKNGKpaVKNKhieelsqgyrtfedflheslVEYL 630
Cdd:COG0085   442 ---------------NEY------------------GFIETPYRKVENGK--VTDE--------------------IEYL 466
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  631 DVNEENDCNIAL-----------------------YEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMG 687
Cdd:COG0085   467 TADEEENYYIAQanapldedgnfleervlvryrgeEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQ 546
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  688 KQAMG-----------TIGYNQRNRIDTlmyllAYPQRPMVKT----KTIELI------DFEKLPAGQNATVAVMSYSGY 746
Cdd:COG0085   547 RQAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGY 621
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  747 DIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYtnqtfdkvmgpMLDAE--TR-KP-----IWRHsiLDADGICSPGEKV 818
Cdd:COG0085   622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDT-----------KLGPEeiTRdIPnvseeALRN--LDEDGIIRIGAEV 688
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  819 ENKQVLVNKsmptVT------QTPLEG--SAQPGQPQyRE-------VPVSYKGatdsYIEKVMISSNAEDAFL------ 877
Cdd:COG0085   689 KGGDILVGK----VTpkgeteLTPEERllRAIFGEKA-REvrdtslrVPHGEKG----KVIDVKVFSREEGDELppgvnk 759
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  878 -VKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFH 956
Cdd:COG0085   760 lVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV 839
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  957 YGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGR 1036
Cdd:COG0085   840 ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGK 919
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1037 SRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQS 1116
Cdd:COG0085   920 AQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQS 989
                        1210
                  ....*....|
gi 125843259 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 125843259   665 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYS 744
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   745 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLRRYTNQTFDKVMGPMldaeTRKPIWRHSILDADGICSPGEKVENKQVL 824
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   825 VNKSMPTVTQTPLEGSAQPGQPQYREVPVSYKGATDSYIEKVMI-SSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:pfam00562  155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLIRYGYNYQ 981
Cdd:pfam00562  235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 125843259   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 125843259   22 EEKWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDADPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECR 101
Cdd:PRK09606    3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEAR 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  102 LRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQ 181
Cdd:PRK09606   83 LRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLED 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  182 LSKNRIIVDQDRKG---TVGASVTSSTHEKKSR-TNMIVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEE 257
Cdd:PRK09606  163 LAPNKILVEKDERYgdrIEVAKVFSQRRGYRALvTVERNRDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDP 242
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  258 HVMAAFAPSLEEcqkAQIFTQTQALRYIGNKVRRqrmwGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVR 337
Cdd:PRK09606  243 EIVKFMLENLEE---AEVDTQEEALEYIGKRVAP----GQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAE 315
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  338 RVI-LAQGDNKVDDRDYYGNKRLELAGQLLsllfEDLFK-KFNSELKKIADQIipkQRAA----QFDVVKHMRQDQITNG 411
Cdd:PRK09606  316 ACFeLALGRREEDDKDHYANKRLKLAGDLM----EDLFRvAFNRLARDVKYQL---ERANmrnrELSIKTAVRSDVLTER 388
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  412 MVNAISTGNWslkrfKMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVK 491
Cdd:PRK09606  389 LEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVK 463
                         490       500
                  ....*....|....*....|....*....
gi 125843259  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 125843259    36 GLVKQHIDSFNYFINVEIKKIMKANEKITSDADP--------MWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLRDMTY 107
Cdd:pfam04563    1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIqhpgengdKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTY 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   108 SAPITVDIEYTR-GSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNR 186
Cdd:pfam04563   81 SAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   187 IIVDQDR---KGTVGASVTSSTHE-----KKSRTNMI--VKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTE 256
Cdd:pfam04563  161 PIVFKKAdpkKRGSVASVRSSAEIsvrpdSTSWVNVLeyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYD 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   257 EH---VMAAFAPSLEECQKAQIFTQTQALRYIGNKVRRQRMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLA 333
Cdd:pfam04563  241 VNdqqLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYFIG 320
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 125843259   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 125843259    29 PAFLKVKGLVKQHIDSFNYFINVE----------IKKIMKANEKITSDADPMwYLKYLNIYVGMPDVeesfnvtrpvSPH 98
Cdd:TIGR02013   12 PEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPIEDYTGNI-ELEYLSYRLGEPKY----------SVE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259    99 ECRLRDMTYSAPITVDIEYT----RGSQRIIRNALPIGRMPIMlrssncvlTGKtpmefsklnecpldpgGYFIVKGQEK 174
Cdd:TIGR02013   81 ECKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLM--------TDR----------------GTFIINGAER 136
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   175 VILIQEQLSKNrIIVDQDrkgtvgasVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDA-----------PIAIIFKAMGV 243
Cdd:TIGR02013  137 VVVSQLHRSPG-VFFSSE--------KDTTKSGKVLFSARIIPYRGSWLEFETDKKDVlyvridrkrklPATVLLRALGY 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   244 ESDQEIVQMIGTEEHVMAAFapsleecQKAQIFTQTQALRYIGNKVRRqrmwGGPkkTKMEEARELLASTI-------LT 316
Cdd:TIGR02013  208 TIDTLILNRLGSGEYIRNTL-------RKDPTNSEEEALVEIYRKLRP----GEP--PTVEAARSLLENLFfdpkrydLG 274
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   317 HVPVKEFNFRAK-------CIY-----LAVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKI 384
Cdd:TIGR02013  275 RVGRYKLNKKLGldvpesiGVLtkediIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQ-------NQFRVGLARM 347
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   385 ADQIipKQRAAQFDVVKHMRQDQITNGMVNAIST---GNWSLKRFkMDRqgvTQVLSRLSF---ISALGM--MTRISSQF 456
Cdd:TIGR02013  348 ERIV--RERMSTQDTDTLTPQDLINAKPISAAIKeffGSSQLSQF-MDQ---TNPLAELTHkrrLSALGPggLTRERAGF 421
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   457 EKtrkvsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLAlmthittdmedgpiiklafnlgvedvnllcgeelsyptvflv 536
Cdd:TIGR02013  422 EV-------RDVHPTHYGRICPIETPEGPNIGLINSLS------------------------------------------ 452
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   537 flngnilgvirdhqklVYTFrlmrragfINEFVSISTnltdrcvyissdggrlcrPYIIVKNGKPAVknkhieelsqgyr 616
Cdd:TIGR02013  453 ----------------TYAR--------VNEYGFIET------------------PYRKVKDGKVVV------------- 477
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   617 tfedflhESLVEYLDVNEENDCNIA-------------------LYEHMIS----KDTTHLEIEPFTLLGVCAGLIPYPH 673
Cdd:TIGR02013  478 -------TDEIDYLTADEEDNYVIAqanapldengrfvedlvvaRYRGEITlvspDQVDYMDVSPKQVVSVAASLIPFLE 550
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   674 HNQSPRNTYQCAMGKQAM-------------------------------GTIGYNQRNRI---------DTLMYLLAYP- 712
Cdd:TIGR02013  551 HDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRl 630
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   713 -------------QRPMV----KTKTIELI------DFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVY 769
Cdd:TIGR02013  631 lkyqrsnqdtcinQRPIVsvgdRVEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISE---------RLVK 701
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   770 KNAKCT--LRRYTNQTFDKVMGPmlDAETR------KPIWRHsiLDADGICSPGEKVENKQVLVNKSMPT--VTQTPLEG 839
Cdd:TIGR02013  702 DDVFTSihIEEYEVEARDTKLGP--EEITRdipnvsEEALRN--LDENGIVRIGAEVKAGDILVGKVTPKgeTELTPEEK 777
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   840 --SAQPGQpQYREV-------PVSYKGAtdsyIEKVMISSNAEDAFL-------VKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:TIGR02013  778 llRAIFGE-KARDVrdtslrvPPGVEGT----VIDVKVFSREQGDELppgvnklVKVYIAQKRKIQVGDKMAGRHGNKGV 852
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRF--HYGTA-FGGSKVKDVCEDLIRYGYNY 980
Cdd:TIGR02013  853 VSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKgvPIATPvFDGASEEEIKEYLEKAGLPR 932
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   981 QGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASML 1060
Cdd:TIGR02013  933 DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1012
                         1210      1220      1230      1240      1250      1260
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 125843259  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 125843259   33 KVKGLVKQHIDSFNYFINVEIKKIMKANEKITsdaDPMWYLKYLNIYvgmpdveESFNVTRP-VSPHECRLRDMTYSAPI 111
Cdd:CHL00207    6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFG-------KNYKLKYPkYNLLSAKSYDSNYSIQI 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  112 TVDIEYTRGSQRIIRNA-LPIGRMPIMLRSSNCVLTGktpMEFSKLNECPLDPGGYFivkgqEKVIliqeqlsknriivd 190
Cdd:CHL00207   76 YLPLKFINLKTNKIKFInYLIGNLPKMTQRGTFIING---LERVIVSQIIRSPGIYF-----KKEI-------------- 133
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  191 qDRKGTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEdAPIAIIFKAMGVeSDQEIVQmigteeHVMAAFAPSLEEC 270
Cdd:CHL00207  134 -KKNSNKIYSATLIPNRGSWIKFELDKNKEIWIRIDKNRK-KPLIIFLKALGL-TDQDIYS------RLTKSEFLKKLKP 204
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  271 QKAQI--FTQTQALRYIGNKVRRQRMWGGPKKTKMEEAR----------ELLASTILTHVPVKEFNFRAKCIY---LAVM 335
Cdd:CHL00207  205 ILLNSnsYTNEEILLEIYKNLSPIEPATVNDANQNLFSRffdpknydlgKVGRYKINNKLNLNIPERVRNLTYediLSII 284
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  336 VRRVILAQGDNKVDDRDYYGNKRLELAGQLLsllfedlFKKFNSELKKIaDQIIPKQraaqfdVVKHmRQDQITNGMVNA 415
Cdd:CHL00207  285 DKLINLKINKGNFDDIDHLKNRRVRSVGELL-------QNQFRIGLKRL-ERILRNR------MTIC-DIDSLSKFNLIN 349
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  416 ISTGNWSLKRFKMDRQgVTQVLSRLSFISALGMMTRIS----SQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLvk 491
Cdd:CHL00207  350 PKPLIALIREFFGSSQ-LSQYMDQTNPLSELTHKRRISilgpGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGL-- 426
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  492 nlalmthittdmedgpIIKLAFNLGVEDVNLLcgeelsyPTVFLVFLNGNILgvirDHQKLVYTfrlmrrAGFINEFVSI 571
Cdd:CHL00207  427 ----------------IGSLATNARINKFGFI-------ETPFYKVINGKVK----KFGNPIYL------TADSEDLYRI 473
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  572 STNltdrcvyissdggrlcrPYIIVKNGkpAVKNKHIEelsqgyrtfedflheslveyldVNEENDCNIALYEH--MISk 649
Cdd:CHL00207  474 APN-----------------DINLNKNN--YFKKNIIP----------------------VRYKQEFKTVNPSKvdFIA- 511
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  650 dtthleIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLM-------------- 706
Cdd:CHL00207  512 ------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisltegivvsvs 585
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  707 ----------------YLLAYP---------QRPMV----KTKTIEL------IDFEKLPAGQNATVAVMSYSGYDIEDA 751
Cdd:CHL00207  586 aykiiiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMPWEGYNFEDA 665
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  752 LVLNKAsldrgfgrcLVYKNAkctlrrYTNQTFDKV-----MGPMLDAETRKPIWRHSI-----LDADGICSPGEKVENK 821
Cdd:CHL00207  666 ILINKR---------LVYEDL------FTSIHIEKYeielrQTKLGSEEITRNIPNVSEyslknLDENGIISIGSKVLAG 730
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  822 QVLVNK--SMPTVTQTPLE-------GSAQPGqpqYREVPVSYKGATDSYIEKVMI---SSNAEDAFLVKILLR----QT 885
Cdd:CHL00207  731 DILVGKitPKGESDQLPEGkllraifGEKAKD---VKDTSLRMPNGGYGRVIKVEIfsrSKGDELKFGYYLKIRvfiaQI 807
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  886 RRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAG-VLDGRF---HYGTAF 961
Cdd:CHL00207  808 RKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdNLNKRFkilPFDEMY 887
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  962 GGSKVKDVCEDLIR-----------YGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTR 1030
Cdd:CHL00207  888 GSEYSRILINNKLNqasiknneywlFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQ 967
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1031 QPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGLLGYsgwchYCKSSCHVSSLrIPYACKLL 1110
Cdd:CHL00207  968 QPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD----DMQGRNETLNA-----IVKGQPIPKPG-TPESFKVL 1037
                        1210      1220
                  ....*....|....*....|.
gi 125843259 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 125843259  1040 GGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1119
Cdd:pfam04560    1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80

                   ....*..
gi 125843259  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 125843259  733 GQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTL--RRY------TNQTFDKVMG--PMLDAEtrkpIWR 802
Cdd:CHL00001  652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFhiRKYeiqthvTSQGPERITKeiPHLEAH----LLR 718
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  803 HsiLDADGICSPGEKVENKQVLVNKSMPtvtQTPLEGSAQP----------GQ-PQYRE----VPVSYKG-ATD-SYIEK 865
Cdd:CHL00001  719 N--LDKNGIVMLGSWVETGDILVGKLTP---QEAEESSYAPegrllraifgIQvSTSKEtclkLPIGGRGrVIDvRWIQK 793
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  866 VMISSNaeDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLA 945
Cdd:CHL00001  794 KGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  946 GKAGVLDGRfHYgtafggsKVKDVCEdliRYG------------Y--------------NYQGKDYVTSGITGEPLEAYI 999
Cdd:CHL00001  872 GLAGDLLNR-HY-------RIAPFDE---RYEqeasrklvfselYeaskqtanpwvfepEYPGKSRLFDGRTGDPFEQPV 940
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 125843259 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 125843259  877 LVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRfH 956
Cdd:PRK00405  869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-K 947
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  957 YGT-AFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 1035
Cdd:PRK00405  948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 125843259 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 125843259  344 GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKIADQIIPKQRAAQFDVVKHMRQDQITNGMVNAistgnwSL 423
Cdd:PRK09603  450 NQGKIDDRDHLGNRRIRAVGELLA-------NELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITS------TI 516
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  424 KRFKMDRQgVTQVLSRLSFISALGMMTRISSQFE----KTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHI 499
Cdd:PRK09603  517 MEFFMGGQ-LSQFMDQTNPLSEVTHKRRLSALGEgglvKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV 595
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  500 ttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngNILGVIRDHQKLVytfrlmrragfinefvsISTNLTDRC 579
Cdd:PRK09603  596 -----------------------------------------NDLGFIEAPYKKV-----------------VDGKVVGET 617
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  580 VYISS---DGgrlcrpYIIVKNGKPAVKNKHIEElsqgyrtfedflheSLVEyldvnEENDCNIALYEhmiSKDTTHLEI 656
Cdd:PRK09603  618 IYLTAiqeDS------HIIAPASTPIDEEGNILG--------------DLIE-----TRVEGEIVLNE---KSKVTLMDL 669
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM-----------------------GTIGYNQR---NRIDTL-MYLL 709
Cdd:PRK09603  670 SSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswGAIKANRAgvvEKIDSKnIYIL 749
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  710 ----------AYP--------------QRPMVKT-KTIEL---------IDFEKLPAGQNATVAVMSYSGYDIEDALVLN 755
Cdd:PRK09603  750 gegkeeayidAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiiadgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVS 829
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  756 KasldrgfgrCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRK-PIWRH---SILDADGICSPGEKVENKQVLVNKSMPT 831
Cdd:PRK09603  830 E---------RITKDDIFTSTHIYEKEVDARELKHGVEEFTADiPDVKEealAHLDESGIVKVGTYVSAGMILVGKTSPK 900
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  832 --VTQTP--------------------------LEGSA------------------------------------------ 841
Cdd:PRK09603  901 geIKSTPeerllraifgdkaghvvnkslycppsLEGTVidvkvftkkgyekdarvlsayeeekakldmehfdrltmlnre 980
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  842 -------------------------QPGQ--PQY------------------REVPVSYKGATDSYIE-KVMISSNAEDA 875
Cdd:PRK09603  981 ellrvssllsqaileepfshngkdyKEGDqiPKEeiasinrftlaslvkkysKEVQNHYEITKNNFLEqKKVLGEEHEEK 1060
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  876 F---------------LVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKL 940
Cdd:PRK09603 1061 LsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQI 1140
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  941 IEL---LAGK------AGVLDGRFHYGTAFGGSKVKDVC-------------------EDLIRYGYNYQ----------- 981
Cdd:PRK09603 1141 LEMhlgLVGKefgkqiASMLEDKTKDFAKELRAKMLEIAnainekdpltihalencsdEELLEYAKDWSkgvkmaipvfe 1220
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  982 -------------------GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGL 1042
Cdd:PRK09603 1221 gisqekfyklfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQ 1300
                         970       980       990      1000      1010      1020      1030
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 125843259 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 125843259   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 125843259   183 SKNRIIVDQDRKGT-VGASVTSSTHEKKSRTNMIVKQGRFYLKHN-TLSEDAPIAIIFKAMGVESDQEIVQMI-GTEEHV 259
Cdd:pfam04561    1 RSNGIYVEKELDKNgIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLcYDFNDP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259   260 MAAFAPSLEECQKAQIFTQTQALRYIGNKVRRqrmwGGPKKTKMEEARELLAST-----ILTHVPVKE--FNFRAKCIYL 332
Cdd:pfam04561   81 QMLELLKPELEEAENIYTQEEALDYIGKGFAL----RRGEEPRLQRAREILYSRdpkynLNKHLGLNEpfENERLKAQDI 156
                          170       180
                   ....*....|....*....|....*....
gi 125843259   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 125843259  313 TILTHVPVKEfnfrakciylavMVRRVILAQ-GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKIADQIIPK 391
Cdd:PRK14844  439 TVLTHEDIIE------------IVRKIVLLRdGQGSVDDIDHLGNRRVRSVGEFIE-------NQFRTGLLKLERAVVDS 499
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  392 QRAAQFDVVK---HMRQDQITNGMVNAISTGNwsLKRFkMDRQGVTQVLSRLSFISALGM--MTRISSQFEKtrkvsgpR 466
Cdd:PRK14844  500 MSTSSLDKVSpsdFINPKVLTNVLRDFFNSSQ--LSQF-MDQTNPLSEITHKRRLSALGPggLTRERAGFEV-------R 569
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  467 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITT-DMEDGPIIKLAFNLGVEDVNLLCG--EELSYPTVFLVFLNGNil 543
Cdd:PRK14844  570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKyGFIESPYRKVVNRVVTDQIEYLSAidEGLYYIADTSAKLDEN-- 647
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  544 gvirdhQKLVYTFRLMRRAGfinEFVSISTnltDRCVYISsdggrlcrpyiivkngkpaVKNKHIEELSQgyrtfedflh 623
Cdd:PRK14844  648 ------NCFVDDMLYCRYAG---SFVMVSS---DQVSYID-------------------VSPKQVISVAA---------- 686
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  624 eSLVEYLdvnEENDCNIALYEHMISKDTTHL----------EIEPFTLLGVCA-------GLIpyphhNQSPRNTYQC-A 685
Cdd:PRK14844  687 -SLIPFL---ENDDANRALMGSNMQRQAVPLlkptaplvatGMESFVASGSGAvvlakrdGIV-----DSSDSNSIVIrA 757
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  686 MGKQAMGTIGYN-------QRNRIDTLMyllayPQRPMVKTKTI----------ELIDFEKLPAGQNATVAVMSYSGYDI 748
Cdd:PRK14844  758 FDKERVNYLDVDiyhlrkfQRSNHNTCI-----NQKPLVCVGDYvkegdviadgPAINSGELALGQNLLVAFMSWQGYNF 832
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  749 EDALVLNKASLDRGFGRCLVYKNAKCTLRRyTNQTFDKVMG--PMLDAETrkpiWRHsiLDADGICSPGEKVENKQVLVN 826
Cdd:PRK14844  833 EDSIIISSEVVKKDLFTSIHIEEFECVVHD-TPLGSEKITRaiPGVNEEN----LYH--LDDSGIVKIGTRVGPGYILVG 905
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  827 KSMPT----------------------------VTQTPLEGSAQPGQ--------PQYREVPVSYKGATD-----SYI-- 863
Cdd:PRK14844  906 KVTPKpslslppetkllmtifgeksfdcadsslYTSPDVEGTVIDVQvftrrgveENERALLIKQKEINDfekerDYIin 985
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  864 ----------EKVMISSNAED----------------------------------------------------------- 874
Cdd:PRK14844  986 vtseyfydelKKLLINSGSQDrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydlpq 1065
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  875 --AFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAG------ 946
Cdd:PRK14844 1066 gvSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackkl 1145
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  947 ---------------------------------KAGVLDGR--------------------------------------- 954
Cdd:PRK14844 1146 gekvgnildeinkiksafckgirslnddnftkfAAAYLDNKkienidddeitasvlntpnknalndelnelvenylnsck 1225
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  955 -------------FHYGT--------------------------------AFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:PRK14844 1226 saysnlrnflievYSCGSnvsicnnirdisdnnliefarklrdgipvaapVFEGPKDEQIAKLFELAGLDNSGQAVLYDG 1305
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259  990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:PRK14844 1306 CSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKS 1385

                  .
gi 125843259 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 125843259   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 125843259   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.
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