|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
3-311 |
6.79e-159 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 480.72 E-value: 6.79e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLkdpalsssfEMKyA--------QRLLQEAVDNLIQNGKSG-VVpeKDARGRLLK 73
Cdd:PRK00566 248 GRFATSDLNDLYRRVINRNNRLKRLL---------ELG-ApeiivrneKRMLQEAVDALFDNGRRGrPV--TGPNNRPLK 315
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 74 SLSDILKGKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLI-RTN 152
Cdd:PRK00566 316 SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVeRED 395
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 153 PLlVSQLLREIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLM 232
Cdd:PRK00566 396 PE-VWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLM 474
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 233 LARNNLLSPATGEPLILPSQDMVLGCYYLTTncaEKwsKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGH--LE 310
Cdd:PRK00566 475 LSSNNILSPANGKPIIVPSQDMVLGLYYLTR---ER--EGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSKklVE 549
|
.
gi 41179068 311 T 311
Cdd:PRK00566 550 T 550
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
3-263 |
8.99e-148 |
|
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 437.34 E-value: 8.99e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPALSSSfeMKYAQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILKGK 82
Cdd:cd01609 163 GRFATSDLNDLYRRVINRNNRLKKLLELGAPEII--VRNEKRMLQEAVDALIDNGRRGK-PVTGANNRPLKSLSDMLKGK 239
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 83 QGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLLRE 162
Cdd:cd01609 240 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEE 319
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 163 IMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPA 242
Cdd:cd01609 320 VIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 399
|
250 260
....*....|....*....|.
gi 41179068 243 TGEPLILPSQDMVLGCYYLTT 263
Cdd:cd01609 400 SGKPIVTPSQDMVLGLYYLTK 420
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
3-315 |
3.44e-146 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 447.68 E-value: 3.44e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKF--LKDPALSSSFEmkyaQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILK 80
Cdd:COG0086 248 GRFATSDLNDLYRRVINRNNRLKRLleLKAPDIIVRNE----KRMLQEAVDALFDNGRRGR-AVTGANKRPLKSLSDMLK 322
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 81 GKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLL 160
Cdd:COG0086 323 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDIL 402
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 161 REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLS 240
Cdd:COG0086 403 EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILS 482
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41179068 241 PATGEPLILPSQDMVLGCYYLTtncaeKWSKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGHLETANNI 315
Cdd:COG0086 483 PANGKPIIVPSQDMVLGLYYLT-----REREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGEQVGKI 552
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
3-311 |
1.17e-142 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 437.94 E-value: 1.17e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPAlsSSFEMKYAQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILKGK 82
Cdd:TIGR02386 240 GRFATSDLNDLYRRVINRNNRLKRLLELGA--PEIIVRNEKRMLQEAVDALFDNGRRGK-PVVGKNNRPLKSLSDMLKGK 316
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 83 QGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLLRE 162
Cdd:TIGR02386 317 QGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLED 396
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 163 IMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPA 242
Cdd:TIGR02386 397 VIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPK 476
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 243 TGEPLILPSQDMVLGCYYLTTncaEKwsKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGH-LET 311
Cdd:TIGR02386 477 DGKPIVTPSQDMVLGLYYLTT---EK--PGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTSGEiLET 541
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
3-259 |
2.41e-114 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 338.72 E-value: 2.41e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPALSSSfeMKYAQRLLQEAVDNLIQNGksGVVPEKDARGRLLKSLSDILKGK 82
Cdd:smart00663 24 GRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSII--IRNEKRLLQEAVDTLIDNE--GLPRANQKSGRPLKSLSQRLKGK 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 83 QGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLAD-----------TYLSAKKLIRT 151
Cdd:smart00663 100 EGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKlvrngpngakyIIRGKKTNLKL 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 152 NPLLVSQ--------LLREIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFE 223
Cdd:smart00663 180 AKKSKIAnhlkigdiVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLE 259
|
250 260 270
....*....|....*....|....*....|....*.
gi 41179068 224 ARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGCY 259
Cdd:smart00663 260 ARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
92-234 |
2.70e-46 |
|
RNA polymerase Rpb1, 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). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498 Cd Length: 166 Bit Score: 158.62 E-value: 2.70e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 92 GKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLI----------------------KRILNEKLADTYLSAKKLI 149
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVtpynikrlrqlvengpnvypgaNYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 150 RTNPLLVSQLL-REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEA 228
Cdd:pfam00623 81 LDKELEIGDIVeRHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 41179068 229 WKLMLA 234
Cdd:pfam00623 161 EELMLV 166
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
3-311 |
6.79e-159 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 480.72 E-value: 6.79e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLkdpalsssfEMKyA--------QRLLQEAVDNLIQNGKSG-VVpeKDARGRLLK 73
Cdd:PRK00566 248 GRFATSDLNDLYRRVINRNNRLKRLL---------ELG-ApeiivrneKRMLQEAVDALFDNGRRGrPV--TGPNNRPLK 315
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 74 SLSDILKGKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLI-RTN 152
Cdd:PRK00566 316 SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVeRED 395
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 153 PLlVSQLLREIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLM 232
Cdd:PRK00566 396 PE-VWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLM 474
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 233 LARNNLLSPATGEPLILPSQDMVLGCYYLTTncaEKwsKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGH--LE 310
Cdd:PRK00566 475 LSSNNILSPANGKPIIVPSQDMVLGLYYLTR---ER--EGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSKklVE 549
|
.
gi 41179068 311 T 311
Cdd:PRK00566 550 T 550
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
2-454 |
6.96e-159 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 465.92 E-value: 6.96e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 2 SGQFTISDLNRLYQRIIYRNERLKKFLKDPALSSSFEMKYAQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILKG 81
Cdd:CHL00018 284 GGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGELVMCQKKLLQEAVDALLDNGIRGQ-PMRDGHNKPYKSFSDVIEG 362
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 82 KQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLLR 161
Cdd:CHL00018 363 KEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQ 442
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 162 EIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSP 241
Cdd:CHL00018 443 EVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSP 522
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 242 ATGEPLILPSQDMVLGCYYLTT--------NCAEKWSKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGHLETAN 313
Cdd:CHL00018 523 AIGDPISVPSQDMLLGLYVLTIgnrrgiyaNRYNPCNRKNSTKEPYFSNSYDALGAYRQKRINLDSPLWLRWRLDQRIIA 602
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 314 NIEQPLEIRiplnqkyfYSQKGSYTalagrpwqlllredayssngliaeanagnlpqinvaegevnknildlrylnlnym 393
Cdd:CHL00018 603 SREVPIEVQ--------YESLGTYH------------------------------------------------------- 619
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41179068 394 EIYSKthnllnvnhstlvaqrGQIKDNIHLpQLTTQIIRTTPGKILFNIIVKNAIEKRPKL 454
Cdd:CHL00018 620 EIYEH----------------YLIVKSRKK-EILSIYIRTTVGRILFNREIEEAIQGFSRA 663
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
3-263 |
8.99e-148 |
|
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 437.34 E-value: 8.99e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPALSSSfeMKYAQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILKGK 82
Cdd:cd01609 163 GRFATSDLNDLYRRVINRNNRLKKLLELGAPEII--VRNEKRMLQEAVDALIDNGRRGK-PVTGANNRPLKSLSDMLKGK 239
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 83 QGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLLRE 162
Cdd:cd01609 240 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEE 319
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 163 IMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPA 242
Cdd:cd01609 320 VIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 399
|
250 260
....*....|....*....|.
gi 41179068 243 TGEPLILPSQDMVLGCYYLTT 263
Cdd:cd01609 400 SGKPIVTPSQDMVLGLYYLTK 420
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
3-315 |
3.44e-146 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 447.68 E-value: 3.44e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKF--LKDPALSSSFEmkyaQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILK 80
Cdd:COG0086 248 GRFATSDLNDLYRRVINRNNRLKRLleLKAPDIIVRNE----KRMLQEAVDALFDNGRRGR-AVTGANKRPLKSLSDMLK 322
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 81 GKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLL 160
Cdd:COG0086 323 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDIL 402
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 161 REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLS 240
Cdd:COG0086 403 EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILS 482
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41179068 241 PATGEPLILPSQDMVLGCYYLTtncaeKWSKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGHLETANNI 315
Cdd:COG0086 483 PANGKPIIVPSQDMVLGLYYLT-----REREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGEQVGKI 552
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
3-311 |
1.17e-142 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 437.94 E-value: 1.17e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPAlsSSFEMKYAQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILKGK 82
Cdd:TIGR02386 240 GRFATSDLNDLYRRVINRNNRLKRLLELGA--PEIIVRNEKRMLQEAVDALFDNGRRGK-PVVGKNNRPLKSLSDMLKGK 316
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 83 QGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLLRE 162
Cdd:TIGR02386 317 QGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLED 396
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 163 IMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPA 242
Cdd:TIGR02386 397 VIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPK 476
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 243 TGEPLILPSQDMVLGCYYLTTncaEKwsKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGH-LET 311
Cdd:TIGR02386 477 DGKPIVTPSQDMVLGLYYLTT---EK--PGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTSGEiLET 541
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
3-321 |
1.06e-139 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 415.69 E-value: 1.06e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKdpALSSSFEMKYAQRLLQEAVDNLIQNGKSG--VVpekDARGRLLKSLSDILK 80
Cdd:PRK02625 266 GRFATSDLNDLYRRVINRNNRLARLQE--ILAPEIIVRNEKRMLQEAVDALIDNGRRGrtVV---GANNRPLKSLSDIIE 340
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 81 GKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLL 160
Cdd:PRK02625 341 GKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADPEVWQVL 420
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 161 REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLS 240
Cdd:PRK02625 421 EEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILS 500
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 241 PATGEPLILPSQDMVLGCYYLTtncAEKwSKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQGHLETANNIEQPLE 320
Cdd:PRK02625 501 PATGEPIVTPSQDMVLGCYYLT---AEN-PGAQKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFNGEVEDDDEDTEPLK 576
|
.
gi 41179068 321 I 321
Cdd:PRK02625 577 T 577
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
3-259 |
2.41e-114 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 338.72 E-value: 2.41e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPALSSSfeMKYAQRLLQEAVDNLIQNGksGVVPEKDARGRLLKSLSDILKGK 82
Cdd:smart00663 24 GRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSII--IRNEKRLLQEAVDTLIDNE--GLPRANQKSGRPLKSLSQRLKGK 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 83 QGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLAD-----------TYLSAKKLIRT 151
Cdd:smart00663 100 EGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKlvrngpngakyIIRGKKTNLKL 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 152 NPLLVSQ--------LLREIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFE 223
Cdd:smart00663 180 AKKSKIAnhlkigdiVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLE 259
|
250 260 270
....*....|....*....|....*....|....*.
gi 41179068 224 ARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGCY 259
Cdd:smart00663 260 ARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
3-317 |
1.16e-108 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 352.25 E-value: 1.16e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLK--DPALSSSFEmkyaQRLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILK 80
Cdd:PRK14906 336 GRFATSDLNDLYRRVINRNNRLKRLLDlgAPEIIVNNE----KRMLQEAVDSLFDNGRRGR-PVTGPGNRPLKSLADMLK 410
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 81 GKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLL 160
Cdd:PRK14906 411 GKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASYVWDVL 490
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 161 REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLS 240
Cdd:PRK14906 491 EEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKS 570
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41179068 241 PATGEPLILPSQDMVLGCYYLTTNcaekwSKLKKGSGMYFHNIHEVLKAYNQHL-IHLHAVIWVNIQGHLETANNIEQ 317
Cdd:PRK14906 571 PAHGRPLTVPTQDMIIGVYYLTTE-----RDGFEGEGRTFADFDDALNAYDARAdLDLQAKIVVRLSRDMTVRGSYGD 643
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
3-301 |
1.62e-99 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 328.42 E-value: 1.62e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPAlsSSFEMKYAQRLLQEAVDNLIQNGKSGVVPeKDARGRLLKSLSDILKGK 82
Cdd:PRK09603 1647 GKFAVSDVNELYRRVINRNQRLKRLMELGA--PEIIVRNEKRMLQEAVDVLFDNGRSTNAV-KGANKRPLKSLSEIIKGK 1723
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 83 QGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLLRE 162
Cdd:PRK09603 1724 QGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSNEVWECLQE 1803
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 163 IMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPA 242
Cdd:PRK09603 1804 ITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPA 1883
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 41179068 243 TGEPLILPSQDMVLGCYYLTTncaEKwsKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVI 301
Cdd:PRK09603 1884 SGKAVAIPSQDMVLGLYYLSL---EK--SGVKGEHKLFSSVNEIITAIDTKELDIHAKI 1937
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
2-316 |
2.39e-96 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 319.26 E-value: 2.39e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 2 SGQFTISDLNRLYQRIIYRNERLKKFLK-DPAlssSFEMKYAQRLLQEAVDNLIQNGKSGVVPEKDARGRLLKSLSDILK 80
Cdd:PRK14844 1689 SGRPAVSDLNHHYRTIINRNNRLRKLLSlNPP---EIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKKSISDMLK 1765
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 81 GKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKLADTYLSAKKLIRTNPLLVSQLL 160
Cdd:PRK14844 1766 GKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDML 1845
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 161 REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLS 240
Cdd:PRK14844 1846 EEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41179068 241 PATGEPLILPSQDMVLGCYYLTTNcaekwsKLKKGSGMYFHNIHEVLKAYNQHLIHLHAVIWVNIQgHLETANNIE 316
Cdd:PRK14844 1926 PSNGRPIIVPSKDIVLGIYYLTLQ------EPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRME-YINSSGETH 1994
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
44-262 |
9.15e-80 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 257.75 E-value: 9.15e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 44 RLLQEAVDNLIQNGKSGVvPEKDARGRLLKSLSDILKGKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALv 123
Cdd:cd00399 110 RLLQEHVDTYLDNGIAGQ-PQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIAL- 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 124 lyspflikrILNEKladtylsakklirtnpllvsqllreimkscPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCP 203
Cdd:cd00399 188 ---------TLDGD------------------------------PVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCS 228
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 41179068 204 AFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGCYYLT 262
Cdd:cd00399 229 PYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLT 287
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
17-262 |
7.87e-54 |
|
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 194.00 E-value: 7.87e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 17 IIYRNERLKKFLKDPALSSSFEMKYaqRLLQEAVDNLIQNGKSGVVPEKDARGRLLKSLSDILKGKQGRFRQYLLGKRVD 96
Cdd:cd02582 240 IIRINQRLKENIEAGAPQLIIEDLW--DLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVN 317
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 97 YSGRSVIVVGPRLRLHECGIPKEMALVL-----YSPFLIKR----ILNEKlaDTYLSAKKLIR----------TNPLLVS 157
Cdd:cd02582 318 FSARTVISPDPNLSINEVGVPEDIAKELtvperVTEWNIEKmrklVLNGP--DKWPGANYVIRpdgrrirlryVNREELA 395
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 158 QLL-------REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWK 230
Cdd:cd02582 396 ERLepgwiveRHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARE 475
|
250 260 270
....*....|....*....|....*....|..
gi 41179068 231 LMLARNNLLSPATGEPLILPSQDMVLGCYYLT 262
Cdd:cd02582 476 LMLVQEHILSPRYGGPIIGGIQDYISGAYLLT 507
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
45-264 |
1.06e-47 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 176.58 E-value: 1.06e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 45 LLQEAVDNLIQNGKSGVVPEKDARGRLLKSLSDILKGKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVL 124
Cdd:PRK08566 270 LLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKEL 349
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 125 -----YSPFLIKR----ILNEklADTYLSAKKLIRTN-----------PLLVSQLL------REIMKSCPVLLNRAPTLH 178
Cdd:PRK08566 350 tvperVTEWNIEElreyVLNG--PEKHPGANYVIRPDgrrikltdknkEELAEKLEpgwiveRHLIDGDIVLFNRQPSLH 427
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 179 RLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGC 258
Cdd:PRK08566 428 RMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGA 507
|
....*.
gi 41179068 259 YYLTTN 264
Cdd:PRK08566 508 YLLTRK 513
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
92-234 |
2.70e-46 |
|
RNA polymerase Rpb1, 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). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498 Cd Length: 166 Bit Score: 158.62 E-value: 2.70e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 92 GKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLI----------------------KRILNEKLADTYLSAKKLI 149
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVtpynikrlrqlvengpnvypgaNYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 150 RTNPLLVSQLL-REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFEARAEA 228
Cdd:pfam00623 81 LDKELEIGDIVeRHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 41179068 229 WKLMLA 234
Cdd:pfam00623 161 EELMLV 166
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
9-262 |
2.86e-45 |
|
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 169.27 E-value: 2.86e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 9 DLNRLYQRIIYRNERLKKFLKDPAlsSSFEMKYAQRLLQEAVDNLIqNGKSGVVPEKDARGRLLKSLSDILKGKQGRFRQ 88
Cdd:cd02583 206 DLTVKLSEIIFLNDVIKKHLEKGA--KTQKIMEDWDFLQLQCALYI-NSELPGLPLSMQPKKPIRGFCQRLKGKQGRFRG 282
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 89 YLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSP---------FLIKRILNE----------KLADTylSAKKLI 149
Cdd:cd02583 283 NLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPervtrynieKLRKLVLNGpdvhpganfvIKRDG--GKKKFL 360
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 150 R-TNPLLVSQLL-------REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPIT 221
Cdd:cd02583 361 KyGNRRKIARELkigdiveRHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQT 440
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 41179068 222 FEARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGCYYLT 262
Cdd:cd02583 441 EEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLT 481
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
2-262 |
2.52e-43 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 164.43 E-value: 2.52e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 2 SGQFTISDLNRLYQRIIYRNERLKKFLKDPALSSSFEMKYaqRLLQEAVDNLIQNGKSGV-VPEKDARGRLLKSLSDILK 80
Cdd:PRK14977 238 TGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEV--DHLQYHTSTFFDNATAGIpQAHHKGSGRPLKSLFQRLK 315
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 81 GKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKL-------ADTYLSAKKLIRTNP 153
Cdd:PRK14977 316 GKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMkelvingPDEFPGANAIRKGDG 395
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 154 LLVS---------QLLREIMKSCP--------------VLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFD 210
Cdd:PRK14977 396 TKIRldfledkgkDALREAAEQLEigdiverhladgdiVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFD 475
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|..
gi 41179068 211 GDQMAVHVPITFEARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGCYYLT 262
Cdd:PRK14977 476 GDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLIT 527
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
9-262 |
4.39e-41 |
|
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 156.93 E-value: 4.39e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 9 DLNRLYQRIIYRNERLKKFLKDPAlSSSFEMKYAQrLLQEAVDNLIQNGKSGVVPEKDARGRLLKSLSDILKGKQGRFRQ 88
Cdd:cd02733 155 DLTHKLADIIKANNQLKRQEQNGA-PAHIIEEDEQ-LLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRG 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 89 YLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVL-----YSPFLIKRIlnEKLA----DTYLSAKKLIRTN------- 152
Cdd:cd02733 233 NLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtfpeiVTPFNIDRL--QELVrngpNEYPGAKYIIRDDgeridlr 310
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 153 --PLLVSQLL-------REIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAILLHPLVCPAFNADFDGDQMAVHVPITFE 223
Cdd:cd02733 311 ylKKASDLHLqygyiveRHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLE 390
|
250 260 270
....*....|....*....|....*....|....*....
gi 41179068 224 ARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGCYYLT 262
Cdd:cd02733 391 TRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLT 429
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
11-262 |
1.05e-32 |
|
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain] Cd Length: 779 Bit Score: 132.31 E-value: 1.05e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 11 NRLYQRIIYRNERLKKFLKDPALSSSFEMKYAQRL-------------LQEAVDNLIQNGKSGVVPEKDARGrllksLSD 77
Cdd:cd01435 158 NVLLSKILKDNQQIRDLLASMRQAESQSKLDLISGktnseklinawlqLQSAVNELFDSTKAPKSGKKSPPG-----IKQ 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 78 ILKGKQGRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSP-------------------------FLI-- 130
Cdd:cd01435 233 LLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPepvtpfnveelrqavingpdvypgaNAIed 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 131 ---KRILNEKLADTYLSAKKLIRTNPLLVSQLLREIMKSC-------PVLLNRAPTLHRLGFQAFQPK-LVDGKAILLHP 199
Cdd:cd01435 313 edgRLILLSALSEERRKALAKLLLLLSSAKLLLNGPKKVYrhlldgdVVLLNRQPTLHKPSIMAHKVRvLPGEKTLRLHY 392
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41179068 200 LVCPAFNADFDGDQMAVHVPITFEARAEAWKLMLARNNLLSPATGEP---LIlpsQDMVLGCYYLT 262
Cdd:cd01435 393 ANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPlrgLI---QDHVVSGVLLT 455
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
66-262 |
1.73e-23 |
|
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain] Cd Length: 744 Bit Score: 104.02 E-value: 1.73e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 66 DARGRLLKSLSDILKGKQgRFRQYLLGKRVDYSGRSVIVVGPRLRLHECGIPKEMALVLYSPFLIKRILNEKL---ADTY 142
Cdd:cd10506 187 DFIGTANESAASKKSGLK-WMKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERLqeyCDLT 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 143 LSAKK--LIRTNPLLVSQ-----------LLREIMKSCPVLLNRAPTLHRLGFQAFQPKLVDGKAIL-LHPLVCPAFNAD 208
Cdd:cd10506 266 LLLKGviGVRRNGRLVGVrshntlqigdvIHRPLVDGDVVLVNRPPSIHQHSLIALSVKVLPTNSVVsINPLCCSPFRGD 345
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 41179068 209 FDGDQMAVHVPITFEARAEAWKLMLARNNLLSPATGEPLILPSQDMVLGCYYLT 262
Cdd:cd10506 346 FDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMT 399
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
3-90 |
4.78e-17 |
|
RNA polymerase Rpb1, domain 1; 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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595 Cd Length: 320 Bit Score: 81.95 E-value: 4.78e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41179068 3 GQFTISDLNRLYQRIIYRNERLKKFLKDPALSSSFEMkyAQRLLQEAVDNLIQNGKSGVVPEKDARGRLLKSLSDILKGK 82
Cdd:pfam04997 235 GRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIRE--EWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGK 312
|
....*...
gi 41179068 83 QGRFRQYL 90
Cdd:pfam04997 313 EGRFRGNL 320
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
237-305 |
2.80e-10 |
|
RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 58.79 E-value: 2.80e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41179068 237 NLLSPATGEPLILPSQDMVLGCYYLTTNCAekwsklkkgsgmyFHNIHEVLKAYNQHLIHLHAVIWVNI 305
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDT-------------FFDREEVMQLLMYGIVLPHPAILKPI 56
|
|
| |
