|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-169 |
5.05e-145 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 417.00 E-value: 5.05e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 1 IRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHL 80
Cdd:CHL00018 340 IRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHL 419
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 81 ASNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHV 160
Cdd:CHL00018 420 ASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHV 499
|
....*....
gi 1002153229 161 PLSLEAQAE 169
Cdd:CHL00018 500 PLSLEAQAE 508
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
2-169 |
2.70e-117 |
|
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: 345.66 E-value: 2.70e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:cd01609 217 RGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLA 296
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:cd01609 297 PNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVP 376
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:cd01609 377 LSLEAQAE 384
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
2-169 |
4.20e-95 |
|
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: 298.23 E-value: 4.20e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:COG0086 302 RGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLA 381
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:COG0086 382 TTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVP 461
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:COG0086 462 LSLEAQLE 469
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
2-169 |
3.62e-93 |
|
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: 292.72 E-value: 3.62e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:TIGR02386 294 RGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELA 373
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:TIGR02386 374 ANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVP 453
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:TIGR02386 454 LSPEAQAE 461
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
1-169 |
3.81e-89 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 262.07 E-value: 3.81e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 1 IRGQPMRDGhnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHL 80
Cdd:smart00663 78 LPRANQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKL 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 81 ------------------ASNIGVAK-SQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHP 141
Cdd:smart00663 156 rklvrngpngakyiirgkKTNLKLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNP 235
|
170 180
....*....|....*....|....*...
gi 1002153229 142 LVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:smart00663 236 LVCSPYNADFDGDEMNLHVPQSLEARAE 263
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
34-169 |
6.30e-45 |
|
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: 145.52 E-value: 6.30e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 34 GKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHL--ASNIG-----VAKSQIRDKGPII-------- 98
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqLVENGpnvypGANYIIRINGARRdlryqkrr 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002153229 99 --------WEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:pfam00623 81 ldkeleigDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAE 159
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-169 |
5.05e-145 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 417.00 E-value: 5.05e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 1 IRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHL 80
Cdd:CHL00018 340 IRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHL 419
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 81 ASNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHV 160
Cdd:CHL00018 420 ASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHV 499
|
....*....
gi 1002153229 161 PLSLEAQAE 169
Cdd:CHL00018 500 PLSLEAQAE 508
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
2-169 |
2.70e-117 |
|
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: 345.66 E-value: 2.70e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:cd01609 217 RGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLA 296
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:cd01609 297 PNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVP 376
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:cd01609 377 LSLEAQAE 384
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
2-169 |
1.81e-105 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 325.87 E-value: 1.81e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:PRK00566 302 RGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLA 381
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:PRK00566 382 TTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVP 461
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:PRK00566 462 LSLEAQAE 469
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
2-169 |
6.66e-97 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 292.42 E-value: 6.66e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:PRK02625 320 RGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIV 399
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:PRK02625 400 NNIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVP 479
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:PRK02625 480 LSLEAQAE 487
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
2-169 |
4.20e-95 |
|
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: 298.23 E-value: 4.20e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:COG0086 302 RGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLA 381
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:COG0086 382 TTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVP 461
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:COG0086 462 LSLEAQLE 469
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
2-169 |
3.62e-93 |
|
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: 292.72 E-value: 3.62e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:TIGR02386 294 RGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELA 373
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:TIGR02386 374 ANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVP 453
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:TIGR02386 454 LSPEAQAE 461
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
1-169 |
3.81e-89 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 262.07 E-value: 3.81e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 1 IRGQPMRDGhnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHL 80
Cdd:smart00663 78 LPRANQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKL 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 81 ------------------ASNIGVAK-SQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHP 141
Cdd:smart00663 156 rklvrngpngakyiirgkKTNLKLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNP 235
|
170 180
....*....|....*....|....*...
gi 1002153229 142 LVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:smart00663 236 LVCSPYNADFDGDEMNLHVPQSLEARAE 263
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
2-169 |
3.33e-81 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 261.34 E-value: 3.33e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 2 RGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLA 81
Cdd:PRK14906 390 RGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYA 469
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 82 SNIGVAKSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVP 161
Cdd:PRK14906 470 ANIKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVP 549
|
....*...
gi 1002153229 162 LSLEAQAE 169
Cdd:PRK14906 550 LSTQAQAE 557
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-169 |
3.67e-73 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 238.37 E-value: 3.67e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 15 KSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLASNIGVAKSQIRDK 94
Cdd:PRK14844 1758 KSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAE 1837
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002153229 95 GPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:PRK14844 1838 KPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLE 1912
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
9-169 |
1.35e-68 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 225.19 E-value: 1.35e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 9 GHNK-VYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHLASNIGVA 87
Cdd:PRK09603 1707 GANKrPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQA 1786
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 88 KSQIRDKGPIIWEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQ 167
Cdd:PRK09603 1787 KRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAI 1866
|
..
gi 1002153229 168 AE 169
Cdd:PRK09603 1867 AE 1868
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
1-169 |
1.15e-57 |
|
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: 188.03 E-value: 1.15e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 1 IRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELfqafvicslirqhl 80
Cdd:cd00399 124 IAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL-------------- 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 81 asnigvaksqirdkgpiiweilqevmRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHV 160
Cdd:cd00399 190 --------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHV 243
|
....*....
gi 1002153229 161 PLSLEAQAE 169
Cdd:cd00399 244 PQSEEARAE 252
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
34-169 |
6.30e-45 |
|
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: 145.52 E-value: 6.30e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 34 GKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLIRQHL--ASNIG-----VAKSQIRDKGPII-------- 98
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqLVENGpnvypGANYIIRINGARRdlryqkrr 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002153229 99 --------WEILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:pfam00623 81 ldkeleigDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAE 159
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
5-169 |
2.03e-35 |
|
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: 130.06 E-value: 2.03e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 5 PMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICslirqhlASNI 84
Cdd:cd02582 284 PARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVT-------EWNI 356
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 85 GVAKSQIRDkGPIIW----------------------EILQEV----------MRGHPVLLNRAPTLHRLGIQAFQPVLV 132
Cdd:cd02582 357 EKMRKLVLN-GPDKWpganyvirpdgrrirlryvnreELAERLepgwiverhlIDGDIVLFNRQPSLHRMSIMAHRVRVL 435
|
170 180 190
....*....|....*....|....*....|....*..
gi 1002153229 133 EGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:cd02582 436 PGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAE 472
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
23-169 |
1.30e-32 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 122.27 E-value: 1.30e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 23 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQAFVICSLirqhlasNIGVAKSQIRdKGPIIW--- 99
Cdd:PRK08566 306 GKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEW-------NIEELREYVL-NGPEKHpga 377
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 100 ------------------EILQE-------VMR----GHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKGFNAD 150
Cdd:PRK08566 378 nyvirpdgrrikltdknkEELAEklepgwiVERhlidGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNAD 457
|
170
....*....|....*....
gi 1002153229 151 FDGDQMAVHVPLSLEAQAE 169
Cdd:PRK08566 458 FDGDEMNLHVPQTEEARAE 476
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
4-169 |
9.36e-30 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 113.97 E-value: 9.36e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 4 QPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IELFQAF 70
Cdd:PRK14977 297 QAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAmkltipeivnennIEKMKEL 376
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 71 VI--------CSLIRQHLASNIGVAKSQIRDKGPI--IWEILQ-------EVMRGHPVLLNRAPTLHRLGIQAFQPVLVE 133
Cdd:PRK14977 377 VIngpdefpgANAIRKGDGTKIRLDFLEDKGKDALreAAEQLEigdiverHLADGDIVIFNRQPSLHKLSILAHRVKVLP 456
|
170 180 190
....*....|....*....|....*....|....*.
gi 1002153229 134 GRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:PRK14977 457 GATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAE 492
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
1-169 |
5.33e-28 |
|
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: 108.78 E-value: 5.33e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 1 IRGQPM---RDGhnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAI-----ELFQAFVI 72
Cdd:cd02733 202 IPGLPQatqKSG--RPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNI 279
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 73 CSLirQHLASNiGV-----AKSQIRDKGPII---------WEILQE---VMR----GHPVLLNRAPTLHRLGIQAFqpvl 131
Cdd:cd02733 280 DRL--QELVRN-GPneypgAKYIIRDDGERIdlrylkkasDLHLQYgyiVERhlqdGDVVLFNRQPSLHKMSMMGH---- 352
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 1002153229 132 vegRAICLHPL-------VCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:cd02733 353 ---RVKVLPYStfrlnlsVTTPYNADFDGDEMNLHVPQSLETRAE 394
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
23-169 |
2.31e-27 |
|
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: 106.86 E-value: 2.31e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 23 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IELFQAFVI---------CSLI---- 76
Cdd:cd02583 275 GKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAkiltypervtrynIEKLRKLVLngpdvhpgaNFVIkrdg 354
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 77 ----------RQHLASNIgvaksQIRDKgpiiweILQEVMRGHPVLLNRAPTLHRLGIQAFQPVLVEGRAICLHPLVCKG 146
Cdd:cd02583 355 gkkkflkygnRRKIAREL-----KIGDI------VERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTP 423
|
170 180
....*....|....*....|...
gi 1002153229 147 FNADFDGDQMAVHVPLSLEAQAE 169
Cdd:cd02583 424 YNADFDGDEMNLHVPQTEEARAE 446
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
20-169 |
9.77e-22 |
|
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: 90.71 E-value: 9.77e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 20 VIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAI--------------ELFQAFVI-------CSLIRQ 78
Cdd:cd01435 233 LLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKkltfpepvtpfnveELRQAVINgpdvypgANAIED 312
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 79 HLASNIGVAKSQIRDKGPIIWEILQE------------VMR----GHPVLLNRAPTLHRLGIQAFQ-PVLVEGRAICLHP 141
Cdd:cd01435 313 EDGRLILLSALSEERRKALAKLLLLLssaklllngpkkVYRhlldGDVVLLNRQPTLHKPSIMAHKvRVLPGEKTLRLHY 392
|
170 180
....*....|....*....|....*...
gi 1002153229 142 LVCKGFNADFDGDQMAVHVPLSLEAQAE 169
Cdd:cd01435 393 ANCKSYNADFDGDEMNLHFPQSELARAE 420
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
28-169 |
9.46e-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: 88.23 E-value: 9.46e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 28 FRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIEL----------FQAFVICSLIRQHLASNIGVAKSQIRD---- 93
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLtvservsswnRERLQEYCDLTLLLKGVIGVRRNGRLVgvrs 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002153229 94 -----KGPIIWEILQEvmrGHPVLLNRAPTLHRLGIQAFQ-PVLVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQ 167
Cdd:cd10506 286 hntlqIGDVIHRPLVD---GDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQAR 362
|
..
gi 1002153229 168 AE 169
Cdd:cd10506 363 AE 364
|
|
| |
