|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-180 |
6.06e-159 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 452.82 E-value: 6.06e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 1 VYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIR 80
Cdd:CHL00018 352 PYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIR 431
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 81 EKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARL 160
Cdd:CHL00018 432 EKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARL 511
|
170 180
....*....|....*....|
gi 224987389 161 LMFSHMNLLSPAIGDPISVP 180
Cdd:CHL00018 512 LMFSHMNLLSPAIGDPISVP 531
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
1-180 |
2.65e-131 |
|
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: 382.25 E-value: 2.65e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 1 VYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIR 80
Cdd:cd01609 228 PLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIE 307
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 81 EKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARL 160
Cdd:cd01609 308 RKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARV 387
|
170 180
....*....|....*....|
gi 224987389 161 LMFSHMNLLSPAIGDPISVP 180
Cdd:cd01609 388 LMLSSNNILSPASGKPIVTP 407
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
3-180 |
1.46e-107 |
|
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: 332.12 E-value: 1.46e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:COG0086 315 KSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVERE 394
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:COG0086 395 EPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLM 474
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:COG0086 475 LSTNNILSPANGKPIIVP 492
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
3-180 |
8.96e-105 |
|
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: 324.31 E-value: 8.96e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:TIGR02386 307 KSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQE 386
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:TIGR02386 387 DPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALM 466
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:TIGR02386 467 LASNNILNPKDGKPIVTP 484
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
2-180 |
4.54e-100 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 290.19 E-value: 4.54e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 2 YKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHL------------- 68
Cdd:smart00663 89 LKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLrklvrngpngaky 168
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 69 -----APNIGVAK-SQIREKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGD 142
Cdd:smart00663 169 iirgkKTNLKLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGD 248
|
170 180 190
....*....|....*....|....*....|....*...
gi 224987389 143 QMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVP 180
Cdd:smart00663 249 EMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGP 286
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
22-162 |
1.40e-47 |
|
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: 152.46 E-value: 1.40e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 22 GKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHL------APNI-GVAKSQIREKGPIV-------- 86
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqlvenGPNVyPGANYIIRINGARRdlryqkrr 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 87 --------WEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 158
Cdd:pfam00623 81 ldkeleigDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....
gi 224987389 159 RLLM 162
Cdd:pfam00623 161 EELM 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-180 |
6.06e-159 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 452.82 E-value: 6.06e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 1 VYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIR 80
Cdd:CHL00018 352 PYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIR 431
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 81 EKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARL 160
Cdd:CHL00018 432 EKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARL 511
|
170 180
....*....|....*....|
gi 224987389 161 LMFSHMNLLSPAIGDPISVP 180
Cdd:CHL00018 512 LMFSHMNLLSPAIGDPISVP 531
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
1-180 |
2.65e-131 |
|
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: 382.25 E-value: 2.65e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 1 VYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIR 80
Cdd:cd01609 228 PLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIE 307
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 81 EKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARL 160
Cdd:cd01609 308 RKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARV 387
|
170 180
....*....|....*....|
gi 224987389 161 LMFSHMNLLSPAIGDPISVP 180
Cdd:cd01609 388 LMLSSNNILSPASGKPIVTP 407
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
3-180 |
1.18e-119 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 364.39 E-value: 1.18e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:PRK00566 315 KSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVERE 394
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:PRK00566 395 DPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLM 474
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:PRK00566 475 LSSNNILSPANGKPIIVP 492
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
3-180 |
1.16e-107 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 320.54 E-value: 1.16e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:PRK02625 333 KSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRA 412
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:PRK02625 413 DPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLM 492
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:PRK02625 493 LASNNILSPATGEPIVTP 510
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
3-180 |
1.46e-107 |
|
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: 332.12 E-value: 1.46e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:COG0086 315 KSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVERE 394
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:COG0086 395 EPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLM 474
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:COG0086 475 LSTNNILSPANGKPIIVP 492
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
3-180 |
8.96e-105 |
|
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: 324.31 E-value: 8.96e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:TIGR02386 307 KSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQE 386
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:TIGR02386 387 DPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALM 466
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:TIGR02386 467 LASNNILNPKDGKPIVTP 484
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
2-180 |
4.54e-100 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 290.19 E-value: 4.54e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 2 YKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHL------------- 68
Cdd:smart00663 89 LKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLrklvrngpngaky 168
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 69 -----APNIGVAK-SQIREKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGD 142
Cdd:smart00663 169 iirgkKTNLKLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGD 248
|
170 180 190
....*....|....*....|....*....|....*...
gi 224987389 143 QMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVP 180
Cdd:smart00663 249 EMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGP 286
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
3-180 |
5.75e-90 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 286.77 E-value: 5.75e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:PRK14906 403 KSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRG 482
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:PRK14906 483 ASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLM 562
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:PRK14906 563 LSSNNIKSPAHGRPLTVP 580
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
3-180 |
4.46e-84 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 270.34 E-value: 4.46e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:PRK14844 1758 KSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAE 1837
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:PRK14844 1838 KPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLM 1917
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:PRK14844 1918 MSTNNVLSPSNGRPIIVP 1935
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
3-180 |
1.82e-77 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 251.38 E-value: 1.82e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHLAPNIGVAKSQIREK 82
Cdd:PRK09603 1714 KSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQK 1793
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 GPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:PRK09603 1794 SNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLM 1873
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:PRK09603 1874 LSSMNILLPASGKAVAIP 1891
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
3-180 |
5.56e-64 |
|
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: 204.97 E-value: 5.56e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELfqtfvirglirqhlapnigvaksqirek 82
Cdd:cd00399 138 RSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL---------------------------- 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 83 gpivweilqevmRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 162
Cdd:cd00399 190 ------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELM 257
|
170
....*....|....*...
gi 224987389 163 FSHMNLLSPAIGDPISVP 180
Cdd:cd00399 258 LVPNNILSPQNGEPLIGL 275
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
22-162 |
1.40e-47 |
|
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: 152.46 E-value: 1.40e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 22 GKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHL------APNI-GVAKSQIREKGPIV-------- 86
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqlvenGPNVyPGANYIIRINGARRdlryqkrr 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 87 --------WEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 158
Cdd:pfam00623 81 ldkeleigDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....
gi 224987389 159 RLLM 162
Cdd:pfam00623 161 EELM 164
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
3-177 |
9.48e-44 |
|
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: 154.33 E-value: 9.48e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IELFQTFVIRG------- 62
Cdd:cd02582 294 KTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAkeltvpervtewnIEKMRKLVLNGpdkwpga 373
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 63 --LIRqhlaPN------IGVAKSQIREKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKG 134
Cdd:cd02582 374 nyVIR----PDgrrirlRYVNREELAERLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPP 449
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 224987389 135 FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPI 177
Cdd:cd02582 450 YNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPI 492
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
11-177 |
5.18e-41 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 146.54 E-value: 5.18e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 11 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IELFQTFVIRG---------LIRqhl 68
Cdd:PRK08566 306 GKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAkeltvpervtewnIEELREYVLNGpekhpganyVIR--- 382
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 69 aPN---IGVA---KSQIREKGPIVWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGD 142
Cdd:PRK08566 383 -PDgrrIKLTdknKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGD 461
|
170 180 190
....*....|....*....|....*....|....*
gi 224987389 143 QMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPI 177
Cdd:PRK08566 462 EMNLHVPQTEEARAEARILMLVQEHILSPRYGGPI 496
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
3-177 |
1.04e-36 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 134.38 E-value: 1.04e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 3 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IELFQTFVIRGlirqhla 69
Cdd:PRK14977 308 KSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAmkltipeivnennIEKMKELVING------- 380
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 70 PNIGVAKSQIREKG--PIVWEILQE----------------------VMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAI 125
Cdd:PRK14977 381 PDEFPGANAIRKGDgtKIRLDFLEDkgkdalreaaeqleigdiverhLADGDIVIFNRQPSLHKLSILAHRVKVLPGATF 460
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 224987389 126 CLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPI 177
Cdd:PRK14977 461 RLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPI 512
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
11-177 |
9.45e-35 |
|
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: 128.82 E-value: 9.45e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 11 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IELFQTFVIRG---------LI---- 64
Cdd:cd02583 275 GKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAkiltypervtrynIEKLRKLVLNGpdvhpganfVIkrdg 354
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 65 ----------RQHLAPNIgvaksqirEKGPIVweiLQEVMRGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKG 134
Cdd:cd02583 355 gkkkflkygnRRKIAREL--------KIGDIV---ERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTP 423
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 224987389 135 FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPI 177
Cdd:cd02583 424 YNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPL 466
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
2-171 |
4.20e-30 |
|
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: 115.33 E-value: 4.20e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 2 YKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIEL-FQTFV-------IRGLIRQHLAPNIG 73
Cdd:cd02733 216 LKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFPEIVtpfnidrLQELVRNGPNEYPG 295
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 74 vAKSQIREKGPIV---------WEILQE---VMR----GHPVLLNRAPTLHRLGIQAFqpilvegRAICLHPL------- 130
Cdd:cd02733 296 -AKYIIRDDGERIdlrylkkasDLHLQYgyiVERhlqdGDVVLFNRQPSLHKMSMMGH-------RVKVLPYStfrlnls 367
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 224987389 131 VCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSP 171
Cdd:cd02733 368 VTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSP 408
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
8-177 |
1.64e-27 |
|
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: 108.04 E-value: 1.64e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 8 VIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELfqTF---------------VIRG---------- 62
Cdd:cd01435 233 LLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKL--TFpepvtpfnveelrqaVINGpdvypganai 310
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 63 ---------LIRQHLAPNIGVAKSQIRE--------KGPIVWEILQEvmrGHPVLLNRAPTLHRLGIQAFQ-PILVEGRA 124
Cdd:cd01435 311 ededgrlilLSALSEERRKALAKLLLLLssaklllnGPKKVYRHLLD---GDVVLLNRQPTLHKPSIMAHKvRVLPGEKT 387
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 224987389 125 ICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPI 177
Cdd:cd01435 388 LRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPL 440
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
16-162 |
3.91e-21 |
|
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: 89.77 E-value: 3.91e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 16 FRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIEL-------------FQTFVIRGLI---RQHLAPN---IGVAK 76
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLtvservsswnrerLQEYCDLTLLlkgVIGVRRNgrlVGVRS 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224987389 77 SQIREKGPIVWEILQEvmrGHPVLLNRAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQ 155
Cdd:cd10506 286 HNTLQIGDVIHRPLVD---GDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQAR 362
|
....*..
gi 224987389 156 AEARLLM 162
Cdd:cd10506 363 AELEELV 369
|
|
| |
