|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-184 |
5.72e-158 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 450.51 E-value: 5.72e-158
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:CHL00018 332 VDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVI 411
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:CHL00018 412 RGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 491
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:CHL00018 492 GDQMAVHVPLSLEAQAEARLLMFS 515
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
1-184 |
9.04e-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: 381.10 E-value: 9.04e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:cd01609 208 VDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVI 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:cd01609 288 RELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD 367
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:cd01609 368 GDQMAVHVPLSLEAQAEARVLMLS 391
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-184 |
8.86e-108 |
|
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: 332.90 E-value: 8.86e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:COG0086 293 VDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIY 372
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:COG0086 373 RKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD 452
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:COG0086 453 GDQMAVHVPLSLEAQLEARLLMLS 476
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
1-184 |
5.66e-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: 325.08 E-value: 5.66e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:TIGR02386 285 VDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFII 364
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:TIGR02386 365 KRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFD 444
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:TIGR02386 445 GDQMAVHVPLSPEAQAEARALMLA 468
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
1-184 |
1.77e-96 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 281.33 E-value: 1.77e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDN-GIRGQPPRGGqnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFV 79
Cdd:smart00663 69 VDTLIDNeGLPRANQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEI 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 80 IRGLIRQDV------------------ASNTGIAKR-KIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILV 140
Cdd:smart00663 147 VTPLNIDKLrklvrngpngakyiirgkKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVL 226
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 1015494653 141 EGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:smart00663 227 EGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLV 270
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
42-182 |
3.20e-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: 151.69 E-value: 3.20e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 42 GKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELF-------------QTFVIRG--------LIRQDVASNTGIA--KRK 98
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTfpeivtpynikrlRQLVENGpnvypganYIIRINGARRDLRyqKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 99 IREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 178
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....
gi 1015494653 179 RLLM 182
Cdd:pfam00623 161 EELM 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-184 |
5.72e-158 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 450.51 E-value: 5.72e-158
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:CHL00018 332 VDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVI 411
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:CHL00018 412 RGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 491
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:CHL00018 492 GDQMAVHVPLSLEAQAEARLLMFS 515
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
1-184 |
9.04e-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: 381.10 E-value: 9.04e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:cd01609 208 VDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVI 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:cd01609 288 RELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD 367
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:cd01609 368 GDQMAVHVPLSLEAQAEARVLMLS 391
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1-184 |
3.75e-118 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 360.54 E-value: 3.75e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:PRK00566 293 VDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIM 372
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:PRK00566 373 KKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD 452
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:PRK00566 453 GDQMAVHVPLSLEAQAEARVLMLS 476
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-184 |
8.86e-108 |
|
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: 332.90 E-value: 8.86e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:COG0086 293 VDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIY 372
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:COG0086 373 RKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD 452
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:COG0086 453 GDQMAVHVPLSLEAQLEARLLMLS 476
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
1-184 |
4.48e-107 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 319.39 E-value: 4.48e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:PRK02625 311 VDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVI 390
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:PRK02625 391 HRLIRQGIVNNIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFD 470
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:PRK02625 471 GDQMAVHVPLSLEAQAEARLLMLA 494
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
1-184 |
5.66e-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: 325.08 E-value: 5.66e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:TIGR02386 285 VDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFII 364
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:TIGR02386 365 KRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFD 444
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:TIGR02386 445 GDQMAVHVPLSPEAQAEARALMLA 468
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
1-184 |
1.77e-96 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 281.33 E-value: 1.77e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDN-GIRGQPPRGGqnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFV 79
Cdd:smart00663 69 VDTLIDNeGLPRANQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEI 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 80 IRGLIRQDV------------------ASNTGIAKR-KIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILV 140
Cdd:smart00663 147 VTPLNIDKLrklvrngpngakyiirgkKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVL 226
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 1015494653 141 EGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:smart00663 227 EGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLV 270
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
1-184 |
1.03e-91 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 291.78 E-value: 1.03e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:PRK14906 381 VDSLFDNGRRGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVM 460
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:PRK14906 461 KRLVELEYAANIKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFD 540
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:PRK14906 541 GDQMAVHVPLSTQAQAEARVLMLS 564
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-184 |
6.75e-79 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 255.70 E-value: 6.75e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQ-PPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFV 79
Cdd:PRK14844 1735 VDSLFDNSRRNAlVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFV 1814
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 80 IRGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADF 159
Cdd:PRK14844 1815 YSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADF 1894
|
170 180
....*....|....*....|....*
gi 1015494653 160 DGDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:PRK14844 1895 DGDQMAVHVPISLEAQLEARVLMMS 1919
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-184 |
3.28e-76 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 247.91 E-value: 3.28e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELFQTFVI 80
Cdd:PRK09603 1692 VDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLL 1771
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 RGLIRQDVASNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:PRK09603 1772 SKLEERGYATTLKQAKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFD 1851
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:PRK09603 1852 GDQMAVHVPLSQEAIAECKVLMLS 1875
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
1-184 |
5.67e-66 |
|
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: 210.37 E-value: 5.67e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELfqtfvi 80
Cdd:cd00399 116 VDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL------ 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 81 rglirqdvasntgiakrkirekepivweilqevmQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 160
Cdd:cd00399 190 ----------------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFD 235
|
170 180
....*....|....*....|....
gi 1015494653 161 GDQMAVHVPLSLEAQAEARLLMFS 184
Cdd:cd00399 236 GDEMNLHVPQSEEARAEARELMLV 259
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
42-182 |
3.20e-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: 151.69 E-value: 3.20e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 42 GKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELF-------------QTFVIRG--------LIRQDVASNTGIA--KRK 98
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTfpeivtpynikrlRQLVENGpnvypganYIIRINGARRDLRyqKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 99 IREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 178
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....
gi 1015494653 179 RLLM 182
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 ... |
1-182 |
9.52e-45 |
|
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: 157.41 E-value: 9.52e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPP---RGGqnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIA------ 71
Cdd:cd02582 271 VTTYFDNEIPGIPParhRSG--RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAkeltvp 348
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 72 -------IELFQTFVIRG---------LIRQDVA--SNTGIAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQ 133
Cdd:cd02582 349 ervtewnIEKMRKLVLNGpdkwpganyVIRPDGRriRLRYVNREELAERLEPGWIVERHLIDGDIVLFNRQPSLHRMSIM 428
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 1015494653 134 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 182
Cdd:cd02582 429 AHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELM 477
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
1-182 |
8.29e-43 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 151.93 E-value: 8.29e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPP---RGGqnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIA------ 71
Cdd:PRK08566 275 VTTYFDNEIPGIPParhRSG--RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAkeltvp 352
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 72 -------IELFQTFVIRG---------LIRQDvasntgiaKRKIR----------EKEPIVWEILQEVMQGHPVLLNRAP 125
Cdd:PRK08566 353 ervtewnIEELREYVLNGpekhpganyVIRPD--------GRRIKltdknkeelaEKLEPGWIVERHLIDGDIVLFNRQP 424
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 1015494653 126 TLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 182
Cdd:PRK08566 425 SLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILM 481
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
1-182 |
3.20e-36 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 133.23 E-value: 3.20e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPP--RGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIA------- 71
Cdd:PRK14977 284 TSTFFDNATAGIPQahHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAmkltipe 363
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 72 ------IELFQTFVIRG----------------LIRQDVASNTG-IAKRKIREKEPIVWEILQEVMQGHPVLLNRAPTLH 128
Cdd:PRK14977 364 ivnennIEKMKELVINGpdefpganairkgdgtKIRLDFLEDKGkDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLH 443
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1015494653 129 RLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 182
Cdd:PRK14977 444 KLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELM 497
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
11-182 |
1.61e-33 |
|
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: 125.35 E-value: 1.61e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 11 GQPPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIA-------------IELFQT 77
Cdd:cd02583 255 GLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAkiltypervtrynIEKLRK 334
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 78 FVIRG---------LIRQDV--ASNTGIAKRKIREKEPIVWEILQ-EVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAI 145
Cdd:cd02583 335 LVLNGpdvhpganfVIKRDGgkKKFLKYGNRRKIARELKIGDIVErHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTF 414
|
170 180 190
....*....|....*....|....*....|....*..
gi 1015494653 146 CLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 182
Cdd:cd02583 415 RFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELM 451
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
1-182 |
5.04e-33 |
|
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: 123.80 E-value: 5.04e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIRGQPP---RGGqnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIEL-FQ 76
Cdd:cd02733 194 VATYMDNEIPGLPQatqKSG--RPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFP 271
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 77 TFV-------IRGLIRQDVASNTGiAKRKIRE-----------KEPIVweILQE-------VMQGHPVLLNRAPTLHRLG 131
Cdd:cd02733 272 EIVtpfnidrLQELVRNGPNEYPG-AKYIIRDdgeridlrylkKASDL--HLQYgyiverhLQDGDVVLFNRQPSLHKMS 348
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 1015494653 132 IQAFqpilvegRAICLHPL-------VCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 182
Cdd:cd02733 349 MMGH-------RVKVLPYStfrlnlsVTTPYNADFDGDEMNLHVPQSLETRAELKELM 399
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
1-182 |
8.46e-28 |
|
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: 108.81 E-value: 8.46e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 1 VDTLLDNGIrgqpPRGGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIELfqTF-- 78
Cdd:cd01435 210 VNELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKL--TFpe 283
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 79 -------------VIRG-------------------LIRQDVASNTGIAKRKIREKEP--------IVWEILQEvmqGHP 118
Cdd:cd01435 284 pvtpfnveelrqaVINGpdvypganaiededgrlilLSALSEERRKALAKLLLLLSSAklllngpkKVYRHLLD---GDV 360
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1015494653 119 VLLNRAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 182
Cdd:cd01435 361 VLLNRQPTLHKPSIMAHKvRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIA 425
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
36-182 |
7.17e-22 |
|
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: 91.70 E-value: 7.17e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 36 FRETLLGKRVDYSGRSVIVVGPLLSLHQCGLPREIAIEL-------------FQTFVIRGLI---RQDVASNTGIAKRKI 99
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLtvservsswnrerLQEYCDLTLLlkgVIGVRRNGRLVGVRS 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1015494653 100 REKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 178
Cdd:cd10506 286 HNTLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAEL 365
|
....
gi 1015494653 179 RLLM 182
Cdd:cd10506 366 EELV 369
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-40 |
5.35e-08 |
|
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: 51.14 E-value: 5.35e-08
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 1015494653 1 VDTLLDNGIRGQPP-RGGQNKVYKSFSDVIEGKEGRFRETL 40
Cdd:pfam04997 280 VATLFDNEIPGLPPaLQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| |
