|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
1-375 |
1.22e-137 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 405.67 E-value: 1.22e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDYGQLSYKQLLEGYEWRALEDKLYPQSSSL 80
Cdd:PRK02625 102 RMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSEL 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 FGIQ-VSIGAEAIYTLLNDLDLQAIVEHLREDalkppktIKNSS-PKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIP 158
Cdd:PRK02625 182 EGEEvVGIGAEALKRLLEDLNLEEEAEQLREE-------IANSKgQKRAKLIKRLRVIDNFIATGSRPEWMVLDVIPVIP 254
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 159 PDLRPMVQLDGG******************************************************************** 238
Cdd:PRK02625 255 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKS 334
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 239 *************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKIIQKNES 318
Cdd:PRK02625 335 LSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADP 414
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 1886015742 319 AIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK02625 415 EVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDG 471
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
1-375 |
3.75e-133 |
|
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Pssm-ID: 131440 [Multi-domain] Cd Length: 619 Bit Score: 393.95 E-value: 3.75e-133
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDYGQLSYKQLLEGYEWRALEDKLYPQSSSL 80
Cdd:TIGR02387 95 RMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSEL 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 FGIQ-VSIGAEAIYTLLNDLDLQAIVEHLREDALKppktikNSSPKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIPP 159
Cdd:TIGR02387 175 ENEEvVGIGAEALKQLLADLNLEEVAEQLREEING------SKGQKRAKLIKRLRVIDNFIATSSRPEWMVLDVIPVIPP 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 160 DLRPMVQLDGG********************************************************************* 239
Cdd:TIGR02387 249 DLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSL 328
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 240 ************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKIIQKNESA 319
Cdd:TIGR02387 329 SDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADDE 408
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1886015742 320 IWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:TIGR02387 409 IWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDG 464
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-375 |
8.29e-105 |
|
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: 333.67 E-value: 8.29e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDYGqLSYKQLLEGYEWRALEDKlYPQSssl 80
Cdd:COG0086 91 RMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTP-LEKGQLLTEDEYREILEE-YGDE--- 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 fgIQVSIGAEAIYTLLNDLDLQAIVEHLREDAlkppkTIKNSSPKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIPPD 160
Cdd:COG0086 166 --FVAKMGAEAIKDLLGRIDLEKESEELREEL-----KETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPD 238
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 161 LRPMVQLD------------------------------------------------------------------------ 168
Cdd:COG0086 239 LRPLVPLDggrfatsdlndlyrrvinrnnrlkrllelkapdiivrnekrmlqeavdalfdngrrgravtgankrplksls 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 169 ---------------------GG********************************************************* 227
Cdd:COG0086 319 dmlkgkqgrfrqnllgkrvdySG--------------------------------------------------------- 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 228 ************************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIK 307
Cdd:COG0086 342 ------------------------------------RSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIK 385
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1886015742 308 AAKKIIQKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:COG0086 386 SAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDG 453
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
1-375 |
7.90e-83 |
|
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: 265.15 E-value: 7.90e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFhsyvvidpgdygqlsykqllegyewraledklypqsssl 80
Cdd:cd01609 87 RMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------------- 127
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 fgiqvsigaeaiytllndldlqaivehlredalkppktiknsspkfnkkmkrlrLLENFISTQASPSWMVFSVIPVIPPD 160
Cdd:cd01609 128 ------------------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPD 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 161 LRPMVQLDGG********************************************************************** 240
Cdd:cd01609 154 LRPMVQLDGG---------------------------------------------------------------------- 163
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 241 ***********************R-----------------------------SVI------------------------ 267
Cdd:cd01609 164 -----------------------RfatsdlndlyrrvinrnnrlkkllelgapEIIvrnekrmlqeavdalidngrrgkp 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 268 ----------------------------------------VVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIK 307
Cdd:cd01609 221 vtgannrplkslsdmlkgkqgrfrqnllgkrvdysgrsviVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIK 300
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1886015742 308 AAKKIIQKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:cd01609 301 SAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDG 368
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
264-375 |
5.24e-54 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 180.02 E-value: 5.24e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQPFVINRL------------------IFQGLVNNIKAAKKIIQKNESAI-WAVL 324
Cdd:smart00663 117 RSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrklvrngpngakyIIRGKKTNLKLAKKSKIANHLKIgDIVE 196
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1886015742 325 QEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:smart00663 197 RHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDG 247
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
264-375 |
2.10e-30 |
|
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: 113.94 E-value: 2.10e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIF---QGLVNNIK----AAKKIIQKNESAI---------------- 320
Cdd:pfam00623 9 RTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIkrlRQLVENGPnvypGANYIIRINGARRdlryqkrrldkeleig 88
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 1886015742 321 WAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:pfam00623 89 DIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDG 143
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
1-375 |
1.22e-137 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 405.67 E-value: 1.22e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDYGQLSYKQLLEGYEWRALEDKLYPQSSSL 80
Cdd:PRK02625 102 RMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSEL 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 FGIQ-VSIGAEAIYTLLNDLDLQAIVEHLREDalkppktIKNSS-PKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIP 158
Cdd:PRK02625 182 EGEEvVGIGAEALKRLLEDLNLEEEAEQLREE-------IANSKgQKRAKLIKRLRVIDNFIATGSRPEWMVLDVIPVIP 254
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 159 PDLRPMVQLDGG******************************************************************** 238
Cdd:PRK02625 255 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKS 334
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 239 *************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKIIQKNES 318
Cdd:PRK02625 335 LSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADP 414
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 1886015742 319 AIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK02625 415 EVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDG 471
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
1-375 |
3.75e-133 |
|
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Pssm-ID: 131440 [Multi-domain] Cd Length: 619 Bit Score: 393.95 E-value: 3.75e-133
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDYGQLSYKQLLEGYEWRALEDKLYPQSSSL 80
Cdd:TIGR02387 95 RMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSEL 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 FGIQ-VSIGAEAIYTLLNDLDLQAIVEHLREDALKppktikNSSPKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIPP 159
Cdd:TIGR02387 175 ENEEvVGIGAEALKQLLADLNLEEVAEQLREEING------SKGQKRAKLIKRLRVIDNFIATSSRPEWMVLDVIPVIPP 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 160 DLRPMVQLDGG********************************************************************* 239
Cdd:TIGR02387 249 DLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSL 328
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 240 ************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKIIQKNESA 319
Cdd:TIGR02387 329 SDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADDE 408
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1886015742 320 IWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:TIGR02387 409 IWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDG 464
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1-375 |
1.04e-125 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 389.04 E-value: 1.04e-125
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDyGQLSYKQLLEGYEWRALEDKlYPQSssl 80
Cdd:PRK00566 91 RMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGD-TPLEKKQLLTEEEYREALEE-YGDE--- 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 fgIQVSIGAEAIYTLLNDLDLQAIVEHLREDalkppktIKNSSPKFNKK--MKRLRLLENFISTQASPSWMVFSVIPVIP 158
Cdd:PRK00566 166 --FVAKMGAEAIKELLKNIDLEAEAEELREE-------LKETGSEQKRKkaLKRLKVVEAFRKSGNKPEWMILDVLPVIP 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 159 PDLRPMVQLDGG******************************************************************** 238
Cdd:PRK00566 237 PDLRPLVQLDGG-------------------------------------------------------------------- 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 239 *************************R------------------------------------------------------ 264
Cdd:PRK00566 249 -------------------------Rfatsdlndlyrrvinrnnrlkrllelgapeiivrnekrmlqeavdalfdngrrg 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 265 ---------------------------------------SVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNN 305
Cdd:PRK00566 304 rpvtgpnnrplkslsdmlkgkqgrfrqnllgkrvdysgrSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATT 383
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 306 IKAAKKIIQKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK00566 384 IKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDG 453
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-375 |
9.99e-117 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 353.05 E-value: 9.99e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYF-HSYVVIDPGDYGQLSYKQLLEGY--EWRALEDKLYPQS 77
Cdd:CHL00018 103 RMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCdFSFARPIAKKPTFLRLRGLFEYEiqSWKYSIPLFFSTQ 182
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 78 S--SLFGIQVSIGAEAIYTLLNDLDLQAIVEHLREDALKPPKTIKNSSPKFNKK--------MKRLRLLENFISTQASPS 147
Cdd:CHL00018 183 GfdTFRNREISTGAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKigrrkdflVRRIKLAKHFIRTNIEPE 262
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 148 WMVFSVIPVIPPDLRPMVQLDGG********************************************************* 227
Cdd:CHL00018 263 WMVLCLLPVLPPELRPIIQLDGG--------------------------------------------------------- 285
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 228 ************************************RSVI---------------------------------------- 267
Cdd:CHL00018 286 -------------------------KLMSSDLNELYRRVIyrnntltdllttsrstpgelvmcqkkllqeavdalldngi 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 268 --------------------------------------------VVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLV 303
Cdd:CHL00018 341 rgqpmrdghnkpyksfsdviegkegrfrenllgkrvdysgrsviVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLA 420
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1886015742 304 NNIKAAKKIIQKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:CHL00018 421 SNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDG 492
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
1-375 |
1.53e-107 |
|
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: 340.49 E-value: 1.53e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDYGqLSYKQLLEGYEWRALEDKlypqSSSL 80
Cdd:TIGR02386 83 RMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTK-LDKKEVLDETEYREVLKR----YGDG 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 FgiQVSIGAEAIYTLLNDLDLQAIVEHLREDALKppktiKNSSPKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIPPD 160
Cdd:TIGR02386 158 F--RAGMGAEAIKELLEKIDLDKEIEELKIQLRE-----SKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPE 230
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 161 LRPMVQLDGG********************************************************************** 240
Cdd:TIGR02386 231 LRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLS 310
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 241 ***********************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKIIQKNESAI 320
Cdd:TIGR02386 311 DMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEV 390
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 1886015742 321 WAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:TIGR02386 391 WDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDG 445
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-375 |
8.29e-105 |
|
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: 333.67 E-value: 8.29e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGDYGqLSYKQLLEGYEWRALEDKlYPQSssl 80
Cdd:COG0086 91 RMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTP-LEKGQLLTEDEYREILEE-YGDE--- 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 fgIQVSIGAEAIYTLLNDLDLQAIVEHLREDAlkppkTIKNSSPKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIPPD 160
Cdd:COG0086 166 --FVAKMGAEAIKDLLGRIDLEKESEELREEL-----KETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPD 238
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 161 LRPMVQLD------------------------------------------------------------------------ 168
Cdd:COG0086 239 LRPLVPLDggrfatsdlndlyrrvinrnnrlkrllelkapdiivrnekrmlqeavdalfdngrrgravtgankrplksls 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 169 ---------------------GG********************************************************* 227
Cdd:COG0086 319 dmlkgkqgrfrqnllgkrvdySG--------------------------------------------------------- 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 228 ************************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIK 307
Cdd:COG0086 342 ------------------------------------RSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIK 385
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1886015742 308 AAKKIIQKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:COG0086 386 SAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDG 453
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
1-375 |
7.90e-83 |
|
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: 265.15 E-value: 7.90e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFhsyvvidpgdygqlsykqllegyewraledklypqsssl 80
Cdd:cd01609 87 RMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------------- 127
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 fgiqvsigaeaiytllndldlqaivehlredalkppktiknsspkfnkkmkrlrLLENFISTQASPSWMVFSVIPVIPPD 160
Cdd:cd01609 128 ------------------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPD 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 161 LRPMVQLDGG********************************************************************** 240
Cdd:cd01609 154 LRPMVQLDGG---------------------------------------------------------------------- 163
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 241 ***********************R-----------------------------SVI------------------------ 267
Cdd:cd01609 164 -----------------------RfatsdlndlyrrvinrnnrlkkllelgapEIIvrnekrmlqeavdalidngrrgkp 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 268 ----------------------------------------VVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIK 307
Cdd:cd01609 221 vtgannrplkslsdmlkgkqgrfrqnllgkrvdysgrsviVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIK 300
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1886015742 308 AAKKIIQKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:cd01609 301 SAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDG 368
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
1-375 |
2.77e-78 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 262.12 E-value: 2.77e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVI--------------------------------- 47
Cdd:PRK14906 93 RMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITsvdkeareedaddlrdelaadleeldaerdrli 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 48 -------------------DPGDYGQLSYKQLLEG-------YEWR------ALE-------------DKLYPQSSSLFG 82
Cdd:PRK14906 173 eatrrlsvdyvpeddefvdDIGDDERLTAEEVRAEvadiyeeYNERkalrreAFDafmqiepkqlisdEALYREMRLNYS 252
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 83 IQVS--IGAEAIYTLLNDLDLQAIVEHLREdalkppkTIKNSS-PKFNKKMKRLRLLENFISTQASPSWMVFSVIPVIPP 159
Cdd:PRK14906 253 IYFKggMGAEAVRDLLDAIDLEKEAEELRA-------IIANGKgQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPP 325
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 160 DLRPMVQLDGG********************************************************************* 239
Cdd:PRK14906 326 DLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSL 405
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 240 ************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKIIQKNESA 319
Cdd:PRK14906 406 ADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASY 485
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1886015742 320 IWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK14906 486 VWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDG 541
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-375 |
4.65e-76 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 256.09 E-value: 4.65e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPgdygqlsykqLLEGYE-WRALEDKLYPQSSS 79
Cdd:PRK14844 1532 RMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDP----------LVSPFEkGEIISEKAYNEAKD 1601
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 80 LFGIQVSI---GAEAIYTLLNDLDLQAIVEHLREDALKPPKTIKNsspkfNKKMKRLRLLENFISTQASPSWMVFSVIPV 156
Cdd:PRK14844 1602 SYGIDSFVamqGVEAIRELLTRLDLHEIRKDLRLELESVASEIRR-----KKIIKRLRIVENFIKSGNRPEWMILTTIPI 1676
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 157 IPPDLRPMVQLDGG****************************************************************** 236
Cdd:PRK14844 1677 LPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGY 1756
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 237 ***************************-RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKIIQK 315
Cdd:PRK14844 1757 KKSISDMLKGKQGRFRQNLLGKRVDYSgRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRA 1836
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 316 NESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK14844 1837 EKPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDG 1896
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-375 |
4.31e-73 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 247.53 E-value: 4.31e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKGSTSYIALALNLTVKEVEKIVYFHSYVVIDPGD--YGQLSYKQLLEgyeWRALEDKLYPQSS 78
Cdd:PRK09603 1481 RMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEaaYDNEGTKLVMK---YDILNEEQYQNIS 1557
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 79 SLF---GIQVSIGAEAIYTLLNDLDLQAIVEHLREDalkppktIKNSSPKFNKK--MKRLRLLENFISTQASPSWMVFSV 153
Cdd:PRK09603 1558 RRYedrGFVAQMGGEAIKDLLEEIDLITLLQSLKEE-------VKDTNSDAKKKklIKRLKVVESFLNSGNRPEWMMLTV 1630
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 154 IPVIPPDLRPMVQLDGG*************************************************************** 233
Cdd:PRK09603 1631 LPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANK 1710
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 234 ******************************RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIFQGLVNNIKAAKKII 313
Cdd:PRK09603 1711 RPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMI 1790
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1886015742 314 QKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK09603 1791 EQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDG 1852
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
264-375 |
5.24e-54 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 180.02 E-value: 5.24e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQPFVINRL------------------IFQGLVNNIKAAKKIIQKNESAI-WAVL 324
Cdd:smart00663 117 RSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrklvrngpngakyIIRGKKTNLKLAKKSKIANHLKIgDIVE 196
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1886015742 325 QEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:smart00663 197 RHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDG 247
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
264-375 |
2.10e-30 |
|
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: 113.94 E-value: 2.10e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQPFVINRLIF---QGLVNNIK----AAKKIIQKNESAI---------------- 320
Cdd:pfam00623 9 RTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIkrlRQLVENGPnvypGANYIIRINGARRdlryqkrrldkeleig 88
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 1886015742 321 WAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:pfam00623 89 DIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDG 143
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
264-375 |
4.29e-28 |
|
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: 115.22 E-value: 4.29e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELfqpfvinrlifqglvnnikaakkiiqknesaiwavlqeviSGHPILLNRAPTLHR 343
Cdd:cd00399 165 RSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFNRQPSLHK 204
|
90 100 110
....*....|....*....|....*....|..
gi 1886015742 344 LGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:cd00399 205 LSIMAHRVRVLPGSTFRLNPLVCSPYNADFDG 236
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-170 |
3.01e-22 |
|
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: 95.82 E-value: 3.01e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 1 RMAYIELSAPVTHVWYLKgstsyialalnLTVKEVEKIVYFHSYVVIDPGDYGQLSYKQLLEGYEwraledklypqsssl 80
Cdd:pfam04997 70 HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLE--------------- 123
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 81 fgiQVSIGAEAIYTLLNDLDLQAIVEHLREDALKPPKTIKNSSPKFNKKMK---------------RLRLL--------- 136
Cdd:pfam04997 124 ---NLKMGAKAILELCKKKDLCEHCGGKNGVCGSQQPVSRKEGLKLKAAIKkskeeeekeilnpekVLKIFkrisdedve 200
|
170 180 190
....*....|....*....|....*....|....*
gi 1886015742 137 -ENFISTQASPSWMVFSVIPVIPPDLRPMVQLDGG 170
Cdd:pfam04997 201 iLGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGG 235
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
264-375 |
4.70e-16 |
|
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: 79.98 E-value: 4.70e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQPFVINRlifqglvNNIKAAKK--------------IIQKNESAI--------- 320
Cdd:cd02582 321 RTVISPDPNLSINEVGVPEDIAKELTVPERVTE-------WNIEKMRKlvlngpdkwpganyVIRPDGRRIrlryvnree 393
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1886015742 321 --------WAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:cd02582 394 laerlepgWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDG 456
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
264-375 |
7.88e-14 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 72.97 E-value: 7.88e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQPFVIN--------RLIFQGL-----VNNIKAAK----KIIQKNESAI------ 320
Cdd:PRK08566 325 RTVISPDPNLSINEVGVPEAIAKELTVPERVTewnieelrEYVLNGPekhpgANYVIRPDgrriKLTDKNKEELaeklep 404
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 1886015742 321 -WAVLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK08566 405 gWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDG 460
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
264-375 |
2.01e-11 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 65.82 E-value: 2.01e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQPFVIN--------RLIFQGL-----VNNI------KAAKKIIQKNESAIWAVL 324
Cdd:PRK14977 335 RTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNenniekmkELVINGPdefpgANAIrkgdgtKIRLDFLEDKGKDALREA 414
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90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1886015742 325 QE-----------VISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:PRK14977 415 AEqleigdiverhLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDG 476
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| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
264-375 |
1.24e-09 |
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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: 59.86 E-value: 1.24e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMAL-----ELFQPFVINRLifQGLVNN----IKAAKKIIQKNESAI-------------- 320
Cdd:cd02733 244 RTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRL--QELVRNgpneYPGAKYIIRDDGERIdlrylkkasdlhlq 321
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90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1886015742 321 --WAVLQEVISGHPILLNRAPTLHRLGIQafepilveGRAIKLHPL--------VCPAFNADFDG 375
Cdd:cd02733 322 ygYIVERHLQDGDVVLFNRQPSLHKMSMM--------GHRVKVLPYstfrlnlsVTTPYNADFDG 378
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| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
264-375 |
2.54e-09 |
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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: 58.96 E-value: 2.54e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELF---QPFVINRLIFQGLVNNIKAAKKIIQKNESAIWAV------LQ--EVIS--- 329
Cdd:cd10506 220 RSVVVGDPYLELNEIGIPCEIAERLTvseRVSSWNRERLQEYCDLTLLLKGVIGVRRNGRLVGvrshntLQigDVIHrpl 299
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90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1886015742 330 --GHPILLNRAPTLHRLGIQAFE-PILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:cd10506 300 vdGDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDG 348
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| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
264-375 |
5.81e-09 |
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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: 57.94 E-value: 5.81e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALELFQP-----FVINRLifQGLVNNIKA----AKKIIQKNES----------AIWA-- 322
Cdd:cd02583 294 RTVISPDPNLRIDQVGVPEHVAKILTYPervtrYNIEKL--RKLVLNGPDvhpgANFVIKRDGGkkkflkygnrRKIAre 371
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90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1886015742 323 ------VLQEVISGHPILLNRAPTLHRLGIQAFEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:cd02583 372 lkigdiVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDG 430
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| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
264-375 |
2.50e-08 |
|
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: 55.65 E-value: 2.50e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1886015742 264 RSVIVVGPNLKLHQCGLPREMALEL--FQP---FVINRLifQGLVNNI-------------------------------- 306
Cdd:cd01435 255 RSVISPDPFIETNEIGIPLVFAKKLtfPEPvtpFNVEEL--RQAVINGpdvypganaiededgrlillsalseerrkala 332
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90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1886015742 307 --KAAKKIIQKNESAIWAVLQEVISGHPILLNRAPTLHRLGIQA-FEPILVEGRAIKLHPLVCPAFNADFDG 375
Cdd:cd01435 333 klLLLLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYNADFDG 404
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| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
133-170 |
1.55e-03 |
|
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: 40.69 E-value: 1.55e-03
10 20 30
....*....|....*....|....*....|....*...
gi 1886015742 133 LRLLeNFISTQASPSWMVFSVIPVIPPDLRPMVQLDGG 170
Cdd:cd02582 190 LELL-GIDPKTARPEWMVLTVLPVPPVTVRPSITLETG 226
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