|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
9-869 |
0e+00 |
|
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: 1596.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIH 88
Cdd:cd02582 2 KRIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 89 IEFTKLIYDLLRATCRNCGRILLPDDTIKRVRAKINRTKQLLGMVPDEVSKWVVQEA-KTKQCPHCGAVQYKITFEKPTK 167
Cdd:cd02582 82 VGFAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKEKWPELVKRVIEKVKKKAkKRKVCPHCGAPQYKIKLEKPTT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 168 FSEMIPEsGSEPLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDI 247
Cdd:cd02582 162 FYEEKEE-GEVKLTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 248 IRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSA 327
Cdd:cd02582 241 IRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 328 RTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFVtDRTKIAEALE 407
Cdd:cd02582 321 RTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRPDGRRIRLRYV-NREELAERLE 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 408 PGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQV 487
Cdd:cd02582 400 PGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLV 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 488 QDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDGPLPEPKITEPQPLWTGKQIFSLFLPRDLNY 567
Cdd:cd02582 480 QEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAGYDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNF 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 568 VLKATICQGCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQSESLLHRIIKDYGTKAGREFLNKITRLLKLFISMR 647
Cdd:cd02582 560 EGKAKVCSGCSECKDEDCPNDGYVVIKNGKLLEGVIDKKAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELR 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 648 GFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTLE 727
Cdd:cd02582 640 GFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPF 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 728 NAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGG 807
Cdd:cd02582 720 NNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGG 799
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1325381750 808 REGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDHGK 869
Cdd:cd02582 800 REGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSDHGK 861
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
9-881 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 1593.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIH 88
Cdd:PRK08566 7 KRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 89 IEFTKLIYDLLRATCRNCGRILLPDDTIKRVRAKINRTKQLlGMVPDEVSKWVVQEA-KTKQCPHCGAVQYKITFEKPTK 167
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEW-GSLADDLIKEVKKEAaKRMVCPHCGEKQYKIKFEKPTT 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 168 FSEMIPEsGSEPLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDI 247
Cdd:PRK08566 166 FYEERKE-GLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDI 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 248 IRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSA 327
Cdd:PRK08566 245 IRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 328 RTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLeFVTDRTKIAEALE 407
Cdd:PRK08566 325 RTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGRRIKL-TDKNKEELAEKLE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 408 PGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQV 487
Cdd:PRK08566 404 PGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLV 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 488 QDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDG-PLPEPKITEPQPLWTGKQIFSLFLPRDLN 566
Cdd:PRK08566 484 QEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDElPEPEPAIENGKPYWTGKQIFSLFLPKDLN 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 567 YVLKATICQGCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQsESLLHRIIKDYGTKAGREFLNKITRLLKLFISM 646
Cdd:PRK08566 564 LEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGAEQ-GSILDRIVKEYGPERARRFLDSVTRLAIRFIML 642
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 647 RGFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTL 726
Cdd:PRK08566 643 RGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGL 722
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 727 ENAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMG 806
Cdd:PRK08566 723 DNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMG 802
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1325381750 807 GREGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDHGKAVNVSRLVDQIR 881
Cdd:PRK08566 803 GREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHGKPVDVDRIIERVL 877
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
9-877 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 1401.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIH 88
Cdd:TIGR02390 2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 89 IEFTKLIYDLLRATCRNCGRILLPDDTIKRVRAKINRTKQLLGMVPDEVSKWVVQEA-KTKQCPHCGAVQYKITFEKPTK 167
Cdd:TIGR02390 82 VGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAaKRMKCPHCGEEQKKIKFEKPTY 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 168 FSEMIPEsGSEPLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDI 247
Cdd:TIGR02390 162 FYEEGKE-GDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 248 IRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSA 327
Cdd:TIGR02390 241 IRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 328 RTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFVTdRTKIAEALE 407
Cdd:TIGR02390 321 RTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDEN-KEELAERLE 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 408 PGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQV 487
Cdd:TIGR02390 400 PGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLV 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 488 QDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDGPLPEPKITEPQPLWTGKQIFSLFLPRDLNY 567
Cdd:TIGR02390 480 EEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNF 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 568 VLKATICQGCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQSeSLLHRIIKDYGTKAGREFLNKITRLLKLFISMR 647
Cdd:TIGR02390 560 EGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKG-KILHRIVREYGPEAARRFLDSVTRLFIRFITLR 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 648 GFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTLE 727
Cdd:TIGR02390 639 GFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPE 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 728 NAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGG 807
Cdd:TIGR02390 719 NHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGG 798
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 808 REGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDHGKAVNVSRLV 877
Cdd:TIGR02390 799 REGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHGKPVDVKKIF 868
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
891-1263 |
0e+00 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 544.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 891 EAEYIKKKLKEVEDQLTPLLIEELKQSLSKAKISKEGVDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTF 970
Cdd:PRK04309 3 SEETLEEKLEDASLELPQKLKEELREKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 971 HYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQAIYEDDIHGEIVVELN 1050
Cdd:PRK04309 83 HYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVDLANMTIIIELD 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1051 KAMMEDRDVTLQELKEKLQ-IQNATIKLKGKILRVKPKKDE--GLKKLLDKISSFYIKGVPGIKRVLVTEEHGEWIIRTD 1127
Cdd:PRK04309 163 EEMLEDRGLTVDDVKEAIEkKKGGEVEIEGNTLIISPKEPSyrELRKLAEKIRNIKIKGIKGIKRVIIRKEGDEYVIYTE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1128 GSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGI 1207
Cdd:PRK04309 243 GSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGV 322
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1325381750 1208 SGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYM 1263
Cdd:PRK04309 323 SGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTM 378
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
908-1263 |
4.61e-171 |
|
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain] Cd Length: 363 Bit Score: 511.41 E-value: 4.61e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 908 PLLIEELKQSLSKAKISKEGVDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRL 987
Cdd:cd06528 1 PLLKEKLEEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 988 IEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQAIYEDDIHGEIVVELNKAMMEDRDVTLQELKEK 1067
Cdd:cd06528 81 IEIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1068 LQiqnatiKLKGKI--------LRVKPKKDEGLKKLL---DKISSFYIKGVPGIKRVLVTEEHGEWIIRTDGSNLSKVLE 1136
Cdd:cd06528 161 IE------KLKKGKvgeegdvtLIVLKAEEPSIKELRklaEKILNTKIKGIKGIKRVIVRKEEDEYVIYTEGSNLKAVLK 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1137 VYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVLA 1216
Cdd:cd06528 235 VEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLA 314
|
330 340 350 360
....*....|....*....|....*....|....*....|....*..
gi 1325381750 1217 RAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYM 1263
Cdd:cd06528 315 RAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTM 361
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
210-512 |
8.63e-168 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 500.12 E-value: 8.63e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 210 EWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEasGI 289
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 290 PPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKL 369
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 370 VANGPekyPGALYIIRpdGKRIRLEFVtDRTKIAEALEPGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFR 449
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLA-KKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIR 232
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1325381750 450 LHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAY 512
Cdd:smart00663 233 LNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
906-1263 |
3.26e-159 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 480.70 E-value: 3.26e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 906 LTPLLIEELKQSLSKAKIS-KEGVDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGL 984
Cdd:TIGR02389 2 LPEKLLKELEETVKKREISdKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 985 PRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQAIYEDDIHGEIVVELNKAMMEDRDVTLQEL 1064
Cdd:TIGR02389 82 PRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTVIIELDEEQLKERGITVDDV 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1065 KEKLQ----IQNATIKLKGKILRVKPKKD--EGLKKLLDKISSFYIKGVPGIKRVLVTEEHGEWIIRTDGSNLSKVLEVY 1138
Cdd:TIGR02389 162 EKAIKkaklGKVIEIDMDNNTITIKPGNPslKELRKLKEKIKNLHIKGIKGIKRVVIRKEGDEYVIYTEGSNLKEVLKLE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1139 GVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVLARA 1218
Cdd:TIGR02389 242 GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARA 321
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1325381750 1219 AFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYM 1263
Cdd:TIGR02389 322 AFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDLVM 366
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
9-318 |
7.53e-113 |
|
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: 356.21 E-value: 7.53e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDG-APITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPII 87
Cdd:pfam04997 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSlKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 88 HIEFTKLIYDLLRATCRNCGRILLPD-----DTIKRVRAKINRTKQLLGMVpdevskWVVQEAKTKqCPHCGAVQYKITF 162
Cdd:pfam04997 82 HIGFFKKTLKILECVCKYCSKLLLDPgkpklFNKDKKRLGLENLKMGAKAI------LELCKKKDL-CEHCGGKNGVCGS 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 163 EKPT------KFSEMIPESGSEP----LTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLES 232
Cdd:pfam04997 155 QQPVsrkeglKLKAAIKKSKEEEekeiLNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDG 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 233 GIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEG 312
Cdd:pfam04997 235 GRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEG 314
|
....*.
gi 1325381750 313 RFRSNL 318
Cdd:pfam04997 315 RFRGNL 320
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
794-1215 |
4.88e-110 |
|
RNA polymerase Rpb1, domain 5; 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 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 355.89 E-value: 4.88e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 794 GLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDH------ 867
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKqgrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 868 --------GKAVNVSRLVDQIRIATERGKPAEAEYIKKKLKEVEDQ---------LTPLLIE---ELKQSLSKAKISKEG 927
Cdd:pfam04998 81 efsdlkleDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSkeaqeratlLFELLLKsglESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 928 VDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLT 1007
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLF 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1008 EKHRKSREAAVKIARNIVYTALENLAQA---IYEDDIHgEIVVELNKAMMEDRDVTLQELKEKLQIQNATIKLKGKILRV 1084
Cdd:pfam04998 241 DEVGRELEKAKKVYGAIEKVTLGSVVESgeiLYDPDPF-NTPIISDVKGVVKFFDIIDEVTNEEEIDPETGLLILVIRLL 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1085 KPKK-----------------------------------------------------------DEGLKKLLDKISS-FYI 1104
Cdd:pfam04998 320 KILNksikkvvkseviprsirnkvdegrdiaigeitafiikiskkirqdtgglrrvdelfmeeDPKLAILVASLLGnITL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1105 KGVPGIKRVLVTE-----EHGEWIIRTDGSNLSKVLEVYG-VDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQG 1178
Cdd:pfam04998 400 RGIPGIKRILVNEddkgkVEPDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQG 479
|
490 500 510
....*....|....*....|....*....|....*..
gi 1325381750 1179 LDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVL 1215
Cdd:pfam04998 480 IYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
12-1184 |
1.05e-79 |
|
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: 286.29 E-value: 1.05e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 12 DEIQFGLFSPQEIRKLSVVEIQTPDTYD-EDGAPITAGLMDGR-LGTleprqrCKT----CGNTA---------ARCPGH 76
Cdd:COG0086 8 DAIKIGLASPEKIRSWSYGEVKKPETINyRTFKPERDGLFCERiFGP------CKDyecyCGKYKrmvykgvvcEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 77 ----------FGHIELAVPIIHIEFTKLIYD----LLRATCRNCGRILL--------PDDT-IKRvrakinrtKQLLGmv 133
Cdd:COG0086 82 vtlskvrrerMGHIELAMPVFHIWGLKSLPSriglLLDMSLRDLERVLYfesyvvidPGDTpLEK--------GQLLT-- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 134 PDEVSKwVVQEAKTKQCPHCGAVQYK-----ITFEKPTKFS-EMIPESGSEPLTPSMVReRLERIPdddlellGFNPKAA 207
Cdd:COG0086 152 EDEYRE-ILEEYGDEFVAKMGAEAIKdllgrIDLEKESEELrEELKETTSEQKRKKLIK-RLKVVE-------AFRESGN 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 208 RPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEAS 287
Cdd:COG0086 223 RPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRR 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 288 GiPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKvtewnieeMR 367
Cdd:COG0086 303 G-RAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFI--------YR 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 368 KLVANGPEKypgalyIIRPDGKRIRLEfvtdRTKIAEALEPgfVVERHLkngdiAIFNRQPSLHRMSIMAHYVRVLPYKT 447
Cdd:COG0086 374 KLEERGLAT------TIKSAKKMVERE----EPEVWDILEE--VIKEHP-----VLLNRAPTLHRLGIQAFEPVLIEGKA 436
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 448 FRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYLFTR-KTN------- 519
Cdd:COG0086 437 IQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTReREGakgegmi 516
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 520 YLTKDEVGRLLAA------AGYDGPLPEPKITEPQPLWT--GKQIFSLFLPRDLNYVLKaticqgctkcleencpydayv 591
Cdd:COG0086 517 FADPEEVLRAYENgavdlhARIKVRITEDGEQVGKIVETtvGRYLVNEILPQEVPFYNQ--------------------- 575
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 592 vvkngelisgVIDRRSIgaeqsESLLHRIIKDYGTKAGREFLNKItRLLKLFISMR-GFTYSYQELVLSPTAENKIRKTm 670
Cdd:COG0086 576 ----------VINKKHI-----EVIIRQMYRRCGLKETVIFLDRL-KKLGFKYATRaGISIGLDDMVVPKEKQEIFEEA- 638
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 671 ervQKKVEELIESYRNGTLprlpgqTLEESFEiYVMNELATARDEAGKIADQDFTLENAGIVMTRTGARGSSLNIGQMSA 750
Cdd:COG0086 639 ---NKEVKEIEKQYAEGLI------TEPERYN-KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAG 708
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 751 CVGQQSVRGKRILRGYVGRalpHFRAgdpspkargfvyssyqkGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLIN 830
Cdd:COG0086 709 MRGLMAKPSGNIIETPIGS---NFRE-----------------GLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVD 768
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 831 -ALEHIRLEYD-GTVRNSagDIIQFKYGEDGVDPAKSDHGKAVNVSRLVDQIRIatERGKPAEAEYIKKKLKEVEDqltp 908
Cdd:COG0086 769 vAQDVIVTEEDcGTDRGI--TVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTG--EVLVPAGTLIDEEVAEIIEE---- 840
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 909 LLIEELKQSLSKAKISKEGVdkavtlTVEHYKRSL-----MEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVR------- 976
Cdd:COG0086 841 AGIDSVKVRSVLTCETRGGV------CAKCYGRDLarghlVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAsraaees 914
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 977 -EQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQaiYEDDIHGEIVVELNKAMME 1055
Cdd:COG0086 915 sIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSELVIVDDGGRREEEYKVPYGGVLVVVG--GGVVVGGGIVAEWDPHTPP 992
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1056 --------DRDVTLQELKEKLQIQNATIKLKGKILRVKPKKDEGLKKLLDKISSFYIKGVPGIKRVLVTEEHGewIIRTD 1127
Cdd:COG0086 993 iieevgggVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAG--VIIGG 1070
|
1210 1220 1230 1240 1250
....*....|....*....|....*....|....*....|....*....|....*..
gi 1325381750 1128 GSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVR 1184
Cdd:COG0086 1071 LDVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIG 1127
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
9-869 |
0e+00 |
|
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: 1596.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIH 88
Cdd:cd02582 2 KRIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 89 IEFTKLIYDLLRATCRNCGRILLPDDTIKRVRAKINRTKQLLGMVPDEVSKWVVQEA-KTKQCPHCGAVQYKITFEKPTK 167
Cdd:cd02582 82 VGFAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKEKWPELVKRVIEKVKKKAkKRKVCPHCGAPQYKIKLEKPTT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 168 FSEMIPEsGSEPLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDI 247
Cdd:cd02582 162 FYEEKEE-GEVKLTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 248 IRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSA 327
Cdd:cd02582 241 IRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 328 RTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFVtDRTKIAEALE 407
Cdd:cd02582 321 RTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRPDGRRIRLRYV-NREELAERLE 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 408 PGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQV 487
Cdd:cd02582 400 PGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLV 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 488 QDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDGPLPEPKITEPQPLWTGKQIFSLFLPRDLNY 567
Cdd:cd02582 480 QEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAGYDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNF 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 568 VLKATICQGCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQSESLLHRIIKDYGTKAGREFLNKITRLLKLFISMR 647
Cdd:cd02582 560 EGKAKVCSGCSECKDEDCPNDGYVVIKNGKLLEGVIDKKAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELR 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 648 GFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTLE 727
Cdd:cd02582 640 GFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPF 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 728 NAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGG 807
Cdd:cd02582 720 NNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGG 799
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1325381750 808 REGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDHGK 869
Cdd:cd02582 800 REGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSDHGK 861
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
9-881 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 1593.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIH 88
Cdd:PRK08566 7 KRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 89 IEFTKLIYDLLRATCRNCGRILLPDDTIKRVRAKINRTKQLlGMVPDEVSKWVVQEA-KTKQCPHCGAVQYKITFEKPTK 167
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEW-GSLADDLIKEVKKEAaKRMVCPHCGEKQYKIKFEKPTT 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 168 FSEMIPEsGSEPLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDI 247
Cdd:PRK08566 166 FYEERKE-GLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDI 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 248 IRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSA 327
Cdd:PRK08566 245 IRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 328 RTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLeFVTDRTKIAEALE 407
Cdd:PRK08566 325 RTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGRRIKL-TDKNKEELAEKLE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 408 PGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQV 487
Cdd:PRK08566 404 PGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLV 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 488 QDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDG-PLPEPKITEPQPLWTGKQIFSLFLPRDLN 566
Cdd:PRK08566 484 QEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDElPEPEPAIENGKPYWTGKQIFSLFLPKDLN 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 567 YVLKATICQGCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQsESLLHRIIKDYGTKAGREFLNKITRLLKLFISM 646
Cdd:PRK08566 564 LEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGAEQ-GSILDRIVKEYGPERARRFLDSVTRLAIRFIML 642
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 647 RGFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTL 726
Cdd:PRK08566 643 RGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGL 722
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 727 ENAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMG 806
Cdd:PRK08566 723 DNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMG 802
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1325381750 807 GREGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDHGKAVNVSRLVDQIR 881
Cdd:PRK08566 803 GREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHGKPVDVDRIIERVL 877
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
4-1263 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 1496.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 4 EEIV-HKVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIEL 82
Cdd:PRK14977 1 EEILaVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 83 AVPIIHIEFTKLIYDLLRATCRNCGRILLPDD------TIKRVRA--KINRTKQLLGMVPDEVSKWVVQEAKT-KQCPHC 153
Cdd:PRK14977 81 AEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEdlnvfkLIEEAHAaaRDIPEKRIDDEIIEEVRDQVKVYAKKaKECPHC 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 154 GAVQYKITFEKPTKFSEMiPESGSEPLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESG 233
Cdd:PRK14977 161 GAPQHELEFEEPTIFIEK-TEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 234 IRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHR-SGRALKTLSQRLKGKEG 312
Cdd:PRK14977 240 ERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKgSGRPLKSLFQRLKGKEG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 313 RFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIR 392
Cdd:PRK14977 320 RFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIRKGDGTKIR 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 393 LEFVTDRTK-----IAEALEPGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEM 467
Cdd:PRK14977 400 LDFLEDKGKdalreAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEM 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 468 NLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDGPLPEPKI-TE 546
Cdd:PRK14977 480 NLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPAIkTK 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 547 PQPLWTGKQIFSLFLPRDLNYVLKATICQG-CTKCLEENCPYDAYVVVKNGELISGVIDRRSIGA--EQSESLLHRIIKD 623
Cdd:PRK14977 560 DGPAWTGKQLFSLFLPKDFNFEGIAKWSAGkAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGAlvEEPESLIDRIAKD 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 624 YGTKAGREFLNKITRLLKLFISMRGFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYR--------NGTLPRLPGQ 695
Cdd:PRK14977 640 YGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKitrkitiyKGKEELLRGM 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 696 TLEESFEIYVMNELATARDEAGKIADQDFTLENAGIVMTRTGARGSSLNIGQMSACVGQQSVR--------GKRILRGYV 767
Cdd:PRK14977 720 KEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKtrigfvltGGRLHEGYK 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 768 GRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSA 847
Cdd:PRK14977 800 DRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPH 879
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 848 GDIIQFKYGEDGVDPAKSDHGKAVNVSRLVDQIRIaTERGKPAEAEYIKKKLKEVEDQLTPLLIEELKQSLSKAKISKEG 927
Cdd:PRK14977 880 GHIIQFKFGEDGIDPQKLDHGEAFNLERIIEKQKI-EDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDE 958
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 928 VDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLT 1007
Cdd:PRK14977 959 LEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLD 1038
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1008 EKHRKSREAAVKIARNIVYTALENLAqAIYEDDIHGEIVVELNKAMMEDRDVTLQE------------LKEKLQIQNATI 1075
Cdd:PRK14977 1039 DECKEDIEKAIEIARNLKELKVRALI-ADSAIDNANEIKLIKPDKRALENGCIPMErfaeieaalakgKKFEMELEDDLI 1117
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1076 KLKGKILRVKPKKDEGLKKLLDKISSFYIKGVPGIKRVLV----TEEHGEWIIRTDGSNLSKVLEVYGVDTSRTTTNNIH 1151
Cdd:PRK14977 1118 ILDLVEAADRDKPLATLIAIRNKILDKPVKGVPDIERAWVelveKDGRDEWIIQTSGSNLAAVLEMKCIDIANTITNDCF 1197
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1152 EIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIG------RHGISGKKSSVLARAAFEITVP 1225
Cdd:PRK14977 1198 EIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGlqaagvRHGFAGEKDSPLAKAAFEITTH 1277
|
1290 1300 1310
....*....|....*....|....*....|....*...
gi 1325381750 1226 NIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYM 1263
Cdd:PRK14977 1278 TIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLM 1315
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
9-877 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 1401.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIH 88
Cdd:TIGR02390 2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 89 IEFTKLIYDLLRATCRNCGRILLPDDTIKRVRAKINRTKQLLGMVPDEVSKWVVQEA-KTKQCPHCGAVQYKITFEKPTK 167
Cdd:TIGR02390 82 VGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAaKRMKCPHCGEEQKKIKFEKPTY 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 168 FSEMIPEsGSEPLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDI 247
Cdd:TIGR02390 162 FYEEGKE-GDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 248 IRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSA 327
Cdd:TIGR02390 241 IRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 328 RTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFVTdRTKIAEALE 407
Cdd:TIGR02390 321 RTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDEN-KEELAERLE 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 408 PGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQV 487
Cdd:TIGR02390 400 PGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLV 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 488 QDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDGPLPEPKITEPQPLWTGKQIFSLFLPRDLNY 567
Cdd:TIGR02390 480 EEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNF 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 568 VLKATICQGCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQSeSLLHRIIKDYGTKAGREFLNKITRLLKLFISMR 647
Cdd:TIGR02390 560 EGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKG-KILHRIVREYGPEAARRFLDSVTRLFIRFITLR 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 648 GFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTLE 727
Cdd:TIGR02390 639 GFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPE 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 728 NAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGG 807
Cdd:TIGR02390 719 NHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGG 798
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 808 REGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDHGKAVNVSRLV 877
Cdd:TIGR02390 799 REGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHGKPVDVKKIF 868
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
12-840 |
0e+00 |
|
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: 1002.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 12 DEIQFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIHIEF 91
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYENGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 92 TKLIYDLLRATCrncgrillpddtiKRVrakinrtkqllgmvpdevskwvvqeaktkqcphcgavqykitfekptkfsem 171
Cdd:cd02733 81 LTKILKILRCVC-------------KRE---------------------------------------------------- 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 172 ipesgsepLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRIN 251
Cdd:cd02733 96 --------LSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSARSEDDLTHKLADIIKAN 167
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 252 QRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVI 331
Cdd:cd02733 168 NQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVI 247
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 332 SPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFVTDRTKIaeALEPGFV 411
Cdd:cd02733 248 TPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGERIDLRYLKKASDL--HLQYGYI 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 412 VERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQI 491
Cdd:cd02733 326 VERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQI 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 492 LSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLL-AAAGYDGPLPEPKITEPQPLWTGKQIFSLFLPRDLNYVLK 570
Cdd:cd02733 406 VSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLmWLPDWDGKIPQPAILKPKPLWTGKQIFSLIIPKINNLIRS 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 571 ATICQGCTKcleENCPYDAYVVVKNGELISGVIDRRSIGAeQSESLLHRIIKDYGTKAGREFLNKITRLLKLFISMRGFT 650
Cdd:cd02733 486 SSHHDGDKK---WISPGDTKVIIENGELLSGILCKKTVGA-SSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFS 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 651 YSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTLENAG 730
Cdd:cd02733 562 IGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKAGKSAQKSLSEDNNF 641
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 731 IVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGGREG 810
Cdd:cd02733 642 KAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREG 721
|
810 820 830
....*....|....*....|....*....|
gi 1325381750 811 LVDTAVRTQQSGYMQRRLINALEHIRLEYD 840
Cdd:cd02733 722 LIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
19-844 |
0e+00 |
|
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: 980.50 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 19 FSPQEIRKLSVVEIQTPDTYD-EDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIHIEFTKLIYD 97
Cdd:cd02583 1 LSPEDIIRLSEVEVTNRNLYDiETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIIN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 98 LLRATCRNCGRILLPDDTI----KRVRAKINRTKQLLGMvpdevSKWVVQEAK-TKQCPHCGAVQykitfekptKFSEMi 172
Cdd:cd02583 81 ILQCICKTCSRVLLPEEEKrkflKRLRRPNLDNLQKKAL-----KKKILEKCKkVRKCPHCGLLK---------KAQED- 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 173 pesgsepLTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRS-EDDLTHKLVDIIRIN 251
Cdd:cd02583 146 -------LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEKSGTnEDDLTVKLSEIIFLN 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 252 QRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARhRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVI 331
Cdd:cd02583 219 DVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSM-QPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVI 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 332 SPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFVTDRTKIAEALEPGFV 411
Cdd:cd02583 298 SPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFVIKRDGGKKKFLKYGNRRKIARELKIGDI 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 412 VERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQI 491
Cdd:cd02583 378 VERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNL 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 492 LSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGyDGP----LPEPKITEPQPLWTGKQIFSLFL------ 561
Cdd:cd02583 458 VTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYML-DGEikidLPPPAILKPVELWTGKQIFSLLLrpnkks 536
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 562 PRDLNYVLKATIcqgCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQSESLLHRIIKDYGTKAGREFLNKITRLLK 641
Cdd:cd02583 537 PVLVNLEAKEKS---YTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSGSKNSLFYVLLRDYGPEAAAAAMNRLAKLSS 613
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 642 LFISMRGFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIAD 721
Cdd:cd02583 614 RWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAEQTLEAKISGELSKIREDAGKACL 693
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 722 QDFTLENAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFF 801
Cdd:cd02583 694 KELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLPHFPRNSKTPAAKGFVANSFYSGLTPTEFF 773
|
810 820 830 840
....*....|....*....|....*....|....*....|...
gi 1325381750 802 FHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVR 844
Cdd:cd02583 774 FHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
15-840 |
0e+00 |
|
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: 648.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 15 QFGLFSPQEIRKLSVVEIQTPDTYDEDGAPITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIHIEFTKL 94
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 95 IYDLLRATCRNCGRILLPDDTIKRVRAKInrtkQLLgmvpdevskwvvqeaktkqcpHCGAVQYKITFEKPtkfsemipe 174
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKL----KLL---------------------DKGLLVEAAELDFG--------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 175 sgsepltpsmvrerleripdddlellgfnpkaarPEWMVLQVLPVPPVYVRPSITLeSGIRSEDDLTHKLVDIIRINQRL 254
Cdd:cd01435 127 ----------------------------------YDMFFLDVLLVPPNRFRPPSFL-GDKVFENPQNVLLSKILKDNQQI 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 255 KENMDAGAPTLIIQDLSEL---------------LQYHVTTYFNNEASGIPPARHRSGralktLSQRLKGKEGRFRSNLS 319
Cdd:cd01435 172 RDLLASMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDSTKAPKSGKKSPPG-----IKQLLEKKEGLFRMNMM 246
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 320 GKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFVTDR 399
Cdd:cd01435 247 GKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINGPDVYPGANAIEDEDGRLILLSALSEE 326
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 400 TKIAEALE------------PGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLP-YKTFRLHLCVCPPYNADFDGDE 466
Cdd:cd01435 327 RRKALAKLllllssaklllnGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRVLPgEKTLRLHYANCKSYNADFDGDE 406
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 467 MNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAA-------GYDGP- 538
Cdd:cd01435 407 MNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTFFTREEYQQLVYAAlrplftsDKDGRi 486
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 539 -LPEPKITEPQPLWTGKQIFSLFL---------PRDLNYVLKATICQGCTKCLEENCpyDAYVVVKNGELISGVIDRRSI 608
Cdd:cd01435 487 kLLPPAILKPKPLWTGKQVISTILknlipgnapLLNLSGKKKTKKKVGGGKWGGGSE--ESQVIIRNGELLTGVLDKSQF 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 609 GAeQSESLLHRIIKDYGTKAGREFLNKITRLLKLFISMRGFTYSYQELVLSPTAENKIRKTMERVQKKVEELIESYRNGT 688
Cdd:cd01435 565 GA-SAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEFLGLK 643
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 689 LPRLPGQTLEESfeiyVMNELATardeagKIADQDFTLenagivMTRTGARGSSLNIGQMSACVGQQSVRGKRILRGYVG 768
Cdd:cd01435 644 LNKVTSSIIKAC----LPKGLLK------PFPENNLQL------MVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSG 707
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1325381750 769 RALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYD 840
Cdd:cd01435 708 KTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
19-840 |
0e+00 |
|
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: 562.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 19 FSPQEIRKLSVVEIQTPDTYDEDGAPIT-AGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPIIHIEFTKLIYD 97
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAErGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 98 LLRatcrncgrillpddtikrvrakinrtkqllgmvpdevskwvvqeaktkqcphcgavqykitfekptkfsemipesgs 177
Cdd:cd00399 81 FLG----------------------------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 178 epltpsmvrerleripdddlellgfnpkaarPEWMVLQVLPVPPVYVRPSItlesgirseddlthklvdiirinqrlken 257
Cdd:cd00399 84 -------------------------------PEWMILTCLPVPPPCLRPSV----------------------------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 258 mdagaptlIIQDLSELLQYHVTTYFNNEASGIPPArHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNL 337
Cdd:cd00399 104 --------IIEERWRLLQEHVDTYLDNGIAGQPQT-QKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNL 174
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 338 DISEVGVPQEVAMRLsvpekvtewnieemrklvangpekypgalyiirpdgkrirlefvtdrtkiaealepgfvverhlk 417
Cdd:cd00399 175 RLDQVGVPKSIALTL----------------------------------------------------------------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 418 NGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFG 497
Cdd:cd00399 190 DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNG 269
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 498 GPIIGAIRDFITAAYLFTRktnyltkdevgrllaaagydgplpepkitepqplwtGKQIFSLFLPrdlnyvlkaticqgc 577
Cdd:cd00399 270 EPLIGLSQDTLLGAYLLTL------------------------------------GKQIVSAALP--------------- 298
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 578 tkcleencpydayvvvkngelisgvidrrsigaeqsESLLHRIIKDYGTKAGREFLNKITRLLKLFISMRGFTYSYQELV 657
Cdd:cd00399 299 ------------------------------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVI 342
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 658 LSPTAENKIRKTMERVQKKVEELIESYRNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTLE---NAGIVMT 734
Cdd:cd00399 343 DDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDFLNEARDKAGSAASVNLDLVskfNSIYVMA 422
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 735 RTGARGSSLNIGQMSACVGQQSVRGKRILRGYVGRALPHFRAGDPSPKARGFVYSSYQKGLDAIEFFFHAMGGREGLVDT 814
Cdd:cd00399 423 MSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDT 502
|
810 820
....*....|....*....|....*.
gi 1325381750 815 AVRTQQSGYMQRRLINALEHIRLEYD 840
Cdd:cd00399 503 AVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
891-1263 |
0e+00 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 544.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 891 EAEYIKKKLKEVEDQLTPLLIEELKQSLSKAKISKEGVDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTF 970
Cdd:PRK04309 3 SEETLEEKLEDASLELPQKLKEELREKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 971 HYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQAIYEDDIHGEIVVELN 1050
Cdd:PRK04309 83 HYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVDLANMTIIIELD 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1051 KAMMEDRDVTLQELKEKLQ-IQNATIKLKGKILRVKPKKDE--GLKKLLDKISSFYIKGVPGIKRVLVTEEHGEWIIRTD 1127
Cdd:PRK04309 163 EEMLEDRGLTVDDVKEAIEkKKGGEVEIEGNTLIISPKEPSyrELRKLAEKIRNIKIKGIKGIKRVIIRKEGDEYVIYTE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1128 GSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGI 1207
Cdd:PRK04309 243 GSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGV 322
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1325381750 1208 SGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYM 1263
Cdd:PRK04309 323 SGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTM 378
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
908-1263 |
4.61e-171 |
|
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain] Cd Length: 363 Bit Score: 511.41 E-value: 4.61e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 908 PLLIEELKQSLSKAKISKEGVDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRL 987
Cdd:cd06528 1 PLLKEKLEEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 988 IEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQAIYEDDIHGEIVVELNKAMMEDRDVTLQELKEK 1067
Cdd:cd06528 81 IEIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1068 LQiqnatiKLKGKI--------LRVKPKKDEGLKKLL---DKISSFYIKGVPGIKRVLVTEEHGEWIIRTDGSNLSKVLE 1136
Cdd:cd06528 161 IE------KLKKGKvgeegdvtLIVLKAEEPSIKELRklaEKILNTKIKGIKGIKRVIVRKEEDEYVIYTEGSNLKAVLK 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1137 VYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVLA 1216
Cdd:cd06528 235 VEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLA 314
|
330 340 350 360
....*....|....*....|....*....|....*....|....*..
gi 1325381750 1217 RAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYM 1263
Cdd:cd06528 315 RAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTM 361
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
210-512 |
8.63e-168 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 500.12 E-value: 8.63e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 210 EWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEasGI 289
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 290 PPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKL 369
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 370 VANGPekyPGALYIIRpdGKRIRLEFVtDRTKIAEALEPGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFR 449
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLA-KKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIR 232
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1325381750 450 LHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAY 512
Cdd:smart00663 233 LNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
906-1263 |
3.26e-159 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 480.70 E-value: 3.26e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 906 LTPLLIEELKQSLSKAKIS-KEGVDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGL 984
Cdd:TIGR02389 2 LPEKLLKELEETVKKREISdKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 985 PRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQAIYEDDIHGEIVVELNKAMMEDRDVTLQEL 1064
Cdd:TIGR02389 82 PRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTVIIELDEEQLKERGITVDDV 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1065 KEKLQ----IQNATIKLKGKILRVKPKKD--EGLKKLLDKISSFYIKGVPGIKRVLVTEEHGEWIIRTDGSNLSKVLEVY 1138
Cdd:TIGR02389 162 EKAIKkaklGKVIEIDMDNNTITIKPGNPslKELRKLKEKIKNLHIKGIKGIKRVVIRKEGDEYVIYTEGSNLKEVLKLE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1139 GVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVLARA 1218
Cdd:TIGR02389 242 GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARA 321
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1325381750 1219 AFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYM 1263
Cdd:TIGR02389 322 AFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDLVM 366
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
875-1264 |
8.22e-137 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 427.30 E-value: 8.22e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 875 RLVDQIRIATERGKPAEAEYIKKKLKEVEDQLTPLLIEELKQSLSKAKISKEGVDKAVTLTVEHYKRSLMEPGEAVGIIA 954
Cdd:PRK14897 110 LLTAEEKEYYEENSNEDVLKVIDDVKKLGFRLPPSVIEEIAKAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVA 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 955 AQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQ 1034
Cdd:PRK14897 190 AQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVAD 269
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1035 AIyeDDIhGE--IVVELNKAMMEDRDVTLQELKEKL-QIQNATIKLKGKILRVKPKKD--EGLKKLLDKISSFYIKGVPG 1109
Cdd:PRK14897 270 II--TDI-AEmsVVVELDEEKMKERLIEYDDILAAIsKLTFKTVEIDDGIIRLKPQQPsfKKLYLLAEKVKSLTIKGIKG 346
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1110 IKRVLVTEEHGE--WIIRTDGSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVM 1187
Cdd:PRK14897 347 IKRAIARKENDErrWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIM 426
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1325381750 1188 LVADMMTSTGEVQQIGRHGISGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYMS 1264
Cdd:PRK14897 427 LVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYK 503
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
9-318 |
7.53e-113 |
|
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: 356.21 E-value: 7.53e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 9 KVVDEIQFGLFSPQEIRKLSVVEIQTPDTYDEDG-APITAGLMDGRLGTLEPRQRCKTCGNTAARCPGHFGHIELAVPII 87
Cdd:pfam04997 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSlKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 88 HIEFTKLIYDLLRATCRNCGRILLPD-----DTIKRVRAKINRTKQLLGMVpdevskWVVQEAKTKqCPHCGAVQYKITF 162
Cdd:pfam04997 82 HIGFFKKTLKILECVCKYCSKLLLDPgkpklFNKDKKRLGLENLKMGAKAI------LELCKKKDL-CEHCGGKNGVCGS 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 163 EKPT------KFSEMIPESGSEP----LTPSMVRERLERIPDDDLELLGFNPKAARPEWMVLQVLPVPPVYVRPSITLES 232
Cdd:pfam04997 155 QQPVsrkeglKLKAAIKKSKEEEekeiLNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDG 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 233 GIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEG 312
Cdd:pfam04997 235 GRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEG 314
|
....*.
gi 1325381750 313 RFRSNL 318
Cdd:pfam04997 315 RFRGNL 320
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
794-1215 |
4.88e-110 |
|
RNA polymerase Rpb1, domain 5; 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 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 355.89 E-value: 4.88e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 794 GLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKSDH------ 867
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKqgrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 868 --------GKAVNVSRLVDQIRIATERGKPAEAEYIKKKLKEVEDQ---------LTPLLIE---ELKQSLSKAKISKEG 927
Cdd:pfam04998 81 efsdlkleDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSkeaqeratlLFELLLKsglESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 928 VDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLT 1007
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLF 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1008 EKHRKSREAAVKIARNIVYTALENLAQA---IYEDDIHgEIVVELNKAMMEDRDVTLQELKEKLQIQNATIKLKGKILRV 1084
Cdd:pfam04998 241 DEVGRELEKAKKVYGAIEKVTLGSVVESgeiLYDPDPF-NTPIISDVKGVVKFFDIIDEVTNEEEIDPETGLLILVIRLL 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1085 KPKK-----------------------------------------------------------DEGLKKLLDKISS-FYI 1104
Cdd:pfam04998 320 KILNksikkvvkseviprsirnkvdegrdiaigeitafiikiskkirqdtgglrrvdelfmeeDPKLAILVASLLGnITL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1105 KGVPGIKRVLVTE-----EHGEWIIRTDGSNLSKVLEVYG-VDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQG 1178
Cdd:pfam04998 400 RGIPGIKRILVNEddkgkVEPDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQG 479
|
490 500 510
....*....|....*....|....*....|....*..
gi 1325381750 1179 LDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVL 1215
Cdd:pfam04998 480 IYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
963-1273 |
7.76e-110 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 366.14 E-value: 7.76e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 963 TQMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQAIYEDDIH 1042
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAIDLWT 620
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1043 GEIVVELNKAMMEDRDVTLQELKEKLQIQ-NATIKLKGKILRVKPKKD--EGLKKLLDKISSFYIKGVPGIKRVLV---- 1115
Cdd:PRK14898 621 QSIKVELDEETLADRGLTIESVEEAIEKKlGVKIDRKGTVLYLKPKTPsyKALRKRIPKIKNIVLKGIPGIERVLVkkee 700
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1116 TEEHGEWIIRTDGSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTS 1195
Cdd:PRK14898 701 HENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTA 780
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1325381750 1196 TGEVQQIGRHGISGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLVELYMSTFEMGGKTK 1273
Cdd:PRK14898 781 DGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDREYEEGKND 858
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
13-1258 |
3.09e-108 |
|
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: 368.22 E-value: 3.09e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 13 EIQFGLFSPQEIRKLSVVEIQTPDTYD-EDGAPITAGLMDGRL-GTLEPRQ--------------RCKTCGNTAARCP-- 74
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINyRTLKPEKDGLFCEKIfGPTKDWEcycgkykkirykgvVCERCGVEVTESKvr 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 75 -GHFGHIELAVPIIHIEFTKL----IYDLLRATCRNCGRILL--------PDDTiKRVRAKINRTKQLLGMVPDEVSKWV 141
Cdd:TIGR02386 81 rERMGHIELAAPVAHIWYFKGlpsrIGLLLDITAKELESVLYfenyvvldPGDT-KLDKKEVLDETEYREVLKRYGDGFR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 142 VqeaktkqCPHCGAVQYKITFEKPTKFSEMIPESGSEPLTPSMVRERLERipdddLELL-GFNPKAARPEWMVLQVLPVP 220
Cdd:TIGR02386 160 A-------GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKR-----LEIVeAFKDSGNRPEWMVLDVIPVI 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 221 PVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGIPPARhRSGRAL 300
Cdd:TIGR02386 228 PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVG-KNNRPL 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 301 KTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPeKVTEWNIEemRKLVANgpekypga 380
Cdd:TIGR02386 307 KSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP-FIIKRLID--RELAAN-------- 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 381 lyiIRPDGKRIRLEfvtdRTKIAEALEpgFVVERHlkngdIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNA 460
Cdd:TIGR02386 376 ---IKSAKKMIEQE----DPEVWDVLE--DVIKEH-----PVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNA 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 461 DFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYlftrktnYLTKDE-----VGRLL----- 530
Cdd:TIGR02386 442 DFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLY-------YLTTEKpgakgEGKIFsnvde 514
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 531 AAAGYD----------GPLPEPKITEPQPlwtGKQIFSLFLPRDLNYVlkaticqgctkclEENCPYDAYVVvknGELIS 600
Cdd:TIGR02386 515 AIRAYDngkvhlhaliGVRTSGEILETTV---GRVIFNEILPEGFPYI-------------NDNEPLSKKEI---SSLID 575
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 601 GVIDRrsigaeqsesllhriikdYGTKAGREFLNKITRLLKLFISMRGFTYSYQELVLSPTAENKIrktmERVQKKVEEL 680
Cdd:TIGR02386 576 LLYEV------------------HGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEIL----KEADKEVAKI 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 681 IESYRNGTLprlpgqTLEESFEIYV-----MNELATarDEAGKIADQDFTLENAGIVMTRTGARGSSLNIGQMSAcvgqq 755
Cdd:TIGR02386 634 QKFYNKGLI------TDEERYRKVVsiwseTKDKVT--DAMMKLLKKDTYKFNPIFMMADSGARGNISQFRQLAG----- 700
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 756 svrgkriLRGYVGRAlphfrAGD--PSPkargfVYSSYQKGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINA-- 831
Cdd:TIGR02386 701 -------MRGLMAKP-----SGDiiELP-----IKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVaq 763
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 832 -----------LEHIRLEY----DGTVRNSAGDIIQFKY-GEDGVDPAKSdhgkavnvsrlvdqiRIATERGKpaeaeyi 895
Cdd:TIGR02386 764 dvvvreedcgtEEGIEVEAivegKDEIIESLKDRIVGRYsAEDVYDPDTG---------------KLIAEANT------- 821
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 896 kkklkevedqltpLLIEELKQSLSKAKISKEGVDKAVTLTVEH------YKRSL-----MEPGEAVGIIAAQSIGEPGTQ 964
Cdd:TIGR02386 822 -------------LITEEIAEKIENSGIEKVKVRSVLTCESEHgvcqkcYGRDLatgklVEIGEAVGVIAAQSIGEPGTQ 888
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 965 MTLRTFHYAGV--REQNVTLGLPRLIEIVDARripsTPimtiyltekhrksREAAVkiarnivytalenlaqaIYEDDIH 1042
Cdd:TIGR02386 889 LTMRTFHTGGVagASGDITQGLPRVKELFEAR----TP-------------KDKAV-----------------IAEVDGT 934
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1043 GEIVVELNKAMMEDRDVTLQELKEKLQIqnatikLKGKILRVKPKkdeglkkllDKISsfyikgvpgikrvlvteeHGEW 1122
Cdd:TIGR02386 935 VEIIEDIVKNKRVVVIKDENDEEKKYTI------PFGAQLRVKDG---------DSVS------------------AGDK 981
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1123 IirTDGSnlskvlevygVDtsrtttnnIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHV-MLVADMM-----TST 1196
Cdd:TIGR02386 982 L--TEGS----------ID--------PHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIeVIVRQMLrkvriTDS 1041
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1197 GEV-----QQIGRH------------------------GI---SGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTE 1244
Cdd:TIGR02386 1042 GDSnllpgELIDIHefneenrklleqgkkpasaipqllGItkaSLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKE 1121
|
1370
....*....|....
gi 1325381750 1245 NVIVGQSIPIGTGL 1258
Cdd:TIGR02386 1122 NVIIGNLIPAGTGL 1135
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
320-487 |
3.93e-93 |
|
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: 296.14 E-value: 3.93e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 320 GKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGPEKYPGALYIIRPDGKRIRLEFvtDR 399
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRY--QK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 400 TKIAEALEPGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEART 479
Cdd:pfam00623 79 RRLDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARA 158
|
....*...
gi 1325381750 480 EALMLMQV 487
Cdd:pfam00623 159 EAEELMLV 166
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
22-844 |
1.20e-91 |
|
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: 312.42 E-value: 1.20e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 22 QEIRKLSVVEIQTPDTydedgapitagLMDGRLGTLEPRQRCKTCGNTAAR-CPGHFGHIELAVPIIHIEFtkliydllr 100
Cdd:cd10506 4 IDIEKISVSEIKAPNQ-----------VTNPRLGLPNESGQCTTCGAKDNKkCEGHFGVIKLPVTIYHPYF--------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 101 atcrncgrillpddtikrvrakINRTKQLLGMVpdevskwvvqeaktkqCPHCGAVQYKItfEKPTKFS----------- 169
Cdd:cd10506 64 ----------------------ISEVAQILNKI----------------CPGCKSIKQKK--KKPPRETlppdywdfipk 103
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 170 -EMIPESGSEPLTPSMVRERLERIPDD-DLELLgfNPKAARPEWMVLQVLPVPPVYVR-PSIT--LESGIR-SEDDLTHK 243
Cdd:cd10506 104 dGQQEESCVTKNLPILSLAQVKKILKEiDPKLI--AKGLPRQEGLFLKCLPVPPNCHRvTEFThgFSTGSRlIFDERTRA 181
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 244 LvdIIRINQRLKENMDAGAPTLiiqdlsellqyhvttyfnneasgipparhrSGRALKTLsqrlkgkegrfrsnLSGKRV 323
Cdd:cd10506 182 Y--KKLVDFIGTANESAASKKS------------------------------GLKWMKDL--------------LLGKRS 215
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 324 DFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEWNIEEMRKLVANGP-EKYpgalyiirpdGKRIRLEFVTDRTKI 402
Cdd:cd10506 216 GHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLTLlLKG----------VIGVRRNGRLVGVRS 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 403 AEALEPGFVVERHLKNGDIAIFNRQPSLHRMSIMAHYVRVLPYK-TFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEA 481
Cdd:cd10506 286 HNTLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSVKVLPTNsVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAEL 365
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 482 LMLMQVQDQILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLAAAGYDGPLPEPKITEPQ--PLWTGKQIFSL 559
Cdd:cd10506 366 EELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPSQLPPPAIIKSPPSngPLWTGKQLFQM 445
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 560 FLPRDLNYVlkaticqgctkcleencpYDAY-VVVKNGELISGViDRRSIGAEQSESLLHRIIKDYGTKAgREFLNKITR 638
Cdd:cd10506 446 LLPTDLDYS------------------FPSNlVFISDGELISSS-GGSSWLRDSEGNLFSILVKHGPGKA-LDFLDSAQG 505
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 639 LLKLFISMRGFTYSYQELVLSPTAENKiRKTMERVQKKVEE----------LIESYRNGTLPRLPGQTLEESFE--IYVM 706
Cdd:cd10506 506 LLCEWLSMRGFSVSLSDLYLSSDSYSR-QKMIEEISLGLREaeiacnikqlLVDSRKDFLSGSGEENDVSSDVErvIYER 584
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 707 NELA------------TARD---EAGKIADQDftleNAGIVMTRTGARGSSLNIGQMSACVGQQSVRGKRILR------- 764
Cdd:cd10506 585 QKSAalsqasvsafkqVFRDiqnLVYKYASKD----NSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVKLSYRiprqlsc 660
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 765 -GYVGRALPHFRAGDP-----SPKARGFVYSSYQKGLDAIEFFFHAMGGREGLVDTAVRTqqSGYMQRRLINALEHIRLE 838
Cdd:cd10506 661 aAWNSQKSPRVIEKDGsecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFSSNADL--PGTLFRKLMFFMRDIYVA 738
|
....*.
gi 1325381750 839 YDGTVR 844
Cdd:cd10506 739 YDGTVR 744
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
922-1262 |
1.29e-91 |
|
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain] Cd Length: 410 Bit Score: 301.82 E-value: 1.29e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 922 KISKEGVDKaVTLTVEH-YKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTP 1000
Cdd:cd02584 2 RLNKEAFDW-ILGEIETrFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1001 IMTIYLTEKHRKSREAAVKIARNIVYTALENLAQA--IYED-DIHGEIV-----------------------------VE 1048
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAAteIYYDpDPQNTVIeedkefvesyfefpdedveqdrlspwllrIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1049 LNKAMMEDRDVTLQELKEKLQ---------I--QNATIKLkgkILRVKPKKDEGLKKLLDKISSFYI------------K 1105
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKeefkddlnvIfsDDNAEKL---VIRIRIINDDEEKEEDSEDDVFLKkiesnmlsdmtlK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1106 GVPGIKRVLVTEEHG--------------EWIIRTDGSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESK 1171
Cdd:cd02584 238 GIEGIRKVFIREENKkkvdietgefkkreEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1172 SVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQS 1251
Cdd:cd02584 318 NVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQL 397
|
410
....*....|.
gi 1325381750 1252 IPIGTGLVELY 1262
Cdd:cd02584 398 APIGTGCFDLL 408
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
208-1258 |
7.18e-88 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 310.46 E-value: 7.18e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 208 RPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLThklvD-----IIRiNQRLKENMDAGAPTLIIQDLSELLQYHVTTYF 282
Cdd:PRK00566 223 KPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLN----DlyrrvINR-NNRLKRLLELGAPEIIVRNEKRMLQEAVDALF 297
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 283 NNEASGiPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAM---------RLS 353
Cdd:PRK00566 298 DNGRRG-RPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALelfkpfimkKLV 376
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 354 VPEKVTewNIEEMRKLVangpEKYpgalyiiRPDgkrirlefvtdrtkIAEALEPgfVVERHLkngdiAIFNRQPSLHRM 433
Cdd:PRK00566 377 ERGLAT--TIKSAKKMV----ERE-------DPE--------------VWDVLEE--VIKEHP-----VLLNRAPTLHRL 422
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 434 SIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYl 513
Cdd:PRK00566 423 GIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLY- 501
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 514 ftrktnYLTKDEVGR-------------LLA-AAGYDG-------PLPEPKITEPQPlwtGKQIFSLFLPRDLNYVLkat 572
Cdd:PRK00566 502 ------YLTREREGAkgegmvfsspeeaLRAyENGEVDlharikvRITSKKLVETTV---GRVIFNEILPEGLPFIN--- 569
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 573 icqgctkcleencpyDAYVVVKNGelISGVIDrrsigaeqsesllhRIIKDYGTKAGREFLNKITRLlklfismrGFTYS 652
Cdd:PRK00566 570 ---------------VNKPLKKKE--ISKIIN--------------EVYRRYGLKETVIFLDKIKDL--------GFKYA 610
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 653 YQ-------ELVLSPTAENKIrktMERVQKKVEELIESYRNGTLprlpgqTLEESfeiY--VMNELATARDEAGKIADQD 723
Cdd:PRK00566 611 TRsgisigiDDIVIPPEKKEI---IEEAEKEVAEIEKQYRRGLI------TDGER---YnkVIDIWSKATDEVAKAMMKN 678
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 724 FTLENAGI----VMTRTGARGSSLNIGQMSAcvgqqsvrgkriLRGYVgrALPhfrAGD--PSPkargfVYSSYQKGLDA 797
Cdd:PRK00566 679 LSKDQESFnpiyMMADSGARGSASQIRQLAG------------MRGLM--AKP---SGEiiETP-----IKSNFREGLTV 736
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 798 IEFFFHAMGGREGLVDTAVRTQQSGYMQRRLIN-ALEHIRLEYD-GTvrnsagdiiqfkygEDGVDPAKSDHGKAVNVSr 875
Cdd:PRK00566 737 LEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVREDDcGT--------------DRGIEVTAIIEGGEVIEP- 801
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 876 LVDQI--RIATErgkPAEAEYIKKKLKEVEDQLTPLLIEelkqslskaKISKEGVDK-----AVTLTVEH------YKRS 942
Cdd:PRK00566 802 LEERIlgRVLAE---DVVDPETGEVIVPAGTLIDEEIAD---------KIEEAGIEEvkirsVLTCETRHgvcakcYGRD 869
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 943 L-----MEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVreqNVTLGLPRLIEIVDARRiPstpimtiyltekhrksREAA 1017
Cdd:PRK00566 870 LatgklVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFEARK-P----------------KGPA 929
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1018 VkIArnivytalenlaqaiyedDIHGeiVVELNKammEDRDvtlqelKEKLQIQNatiklkgkilrvkpkKDEGLKKLLd 1097
Cdd:PRK00566 930 I-IA------------------EIDG--TVSFGK---ETKG------KRRIVITP---------------DDGEEREYL- 963
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1098 kissfyikgVPGIKRVLVTEehGEWIIR----TDGSnlskvlevygvdtsrtttNNIHEIAKTLGIEAARNALILESKSV 1173
Cdd:PRK00566 964 ---------IPKGKHLLVQE--GDHVEAgdklTDGS------------------IDPHDILRVLGVEAVQNYLVNEVQKV 1014
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1174 LEEQGLDVDVRHVMLVADMMTSTGEV-----------QQIGRH------------------------GISgKKS----SV 1214
Cdd:PRK00566 1015 YRLQGVKINDKHIEVIVRQMLRKVRItdpgdtdflpgELVDRSefeeenrkliaegkepatgrpvllGIT-KASlateSF 1093
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....
gi 1325381750 1215 LARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGL 1258
Cdd:PRK00566 1094 LSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGL 1137
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
208-1258 |
1.79e-87 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 312.58 E-value: 1.79e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 208 RPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEAS 287
Cdd:PRK14906 311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 288 GiPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKvtewnieeMR 367
Cdd:PRK14906 391 G-RPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFV--------MK 461
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 368 KLVANG-PEKYPGAlyiirpdgKRirlefVTDR--TKIAEALEPgfVVERHLkngdiAIFNRQPSLHRMSIMAHYVRVLP 444
Cdd:PRK14906 462 RLVELEyAANIKAA--------KR-----AVDRgaSYVWDVLEE--VIQDHP-----VLLNRAPTLHRLGIQAFEPVLVE 521
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 445 YKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAY-LFTRKTNYLTK 523
Cdd:PRK14906 522 GKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYyLTTERDGFEGE 601
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 524 D---------------------------EVGRLLAAAGYDGPLPEPKITEPQPLWTGKQIFSlflprdlnyvlkaticqg 576
Cdd:PRK14906 602 GrtfadfddalnaydaradldlqakivvRLSRDMTVRGSYGDLEETKAGERIETTVGRIIFN------------------ 663
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 577 ctKCLEENCPYDAYVVVKN--GELISGVIDRRSIGAeqSESLLHRIIKD---YGTKAgreflnkitrllklfismrGFTY 651
Cdd:PRK14906 664 --QVLPEDYPYLNYKMVKKdiGRLVNDCCNRYSTAE--VEPILDGIKKTgfhYATRA-------------------GLTV 720
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 652 SYQELVLSPTAEnkirKTMERVQKKVEELIESYRNGTLPrlpgqtlEESFEIYVMNELATARDEAGKIADQDFTLENAGI 731
Cdd:PRK14906 721 SVYDATIPDDKP----EILAEADEKVAAIDEDYEDGFLS-------ERERHKQVVDIWTEATEEVGEAMLAGFDEDNPIY 789
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 732 VMTRTGARGSSLNIGQMSACVGQQS-VRGKRIlrgyvgrALPhfragdpspkargfVYSSYQKGLDAIEFFFHAMGGREG 810
Cdd:PRK14906 790 MMADSGARGNIKQIRQLAGMRGLMAdMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKG 848
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 811 LVDTAVRTQQSGYMQRRLINALEH--IRLEYDGTVRNSAGDIiqfkygedgVDPAKSDHGKAVNVSRLVDQIRIATERGK 888
Cdd:PRK14906 849 LVDTALRTADSGYLTRRLVDVAQDviVREEDCGTDEGVTYPL---------VKPKGDVDTNLIGRCLLEDVCDPNGEVLL 919
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 889 PAeAEYI--KKKLKE-VEDQLTPLLIEELKQSLSKAKISKE--GVDKAVTLTVehykrslmEPGEAVGIIAAQSIGEPGT 963
Cdd:PRK14906 920 SA-GDYIesMDDLKRlVEAGVTKVQIRTLMTCHAEYGVCQKcyGWDLATRRPV--------NIGTAVGIIAAQSIGEPGT 990
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 964 QMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTPIMtiyltekhrksreAAVKIARNIVYTALENLAQAIYEDDIHG 1043
Cdd:PRK14906 991 QLTMRTFHSGGVAGDDITQGLPRVAELFEARKPKGEAVL-------------AEISGTLQITGDKTEKTLTIHDQDGNSR 1057
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1044 EIVVELNKAMM---EDrdvtlqelkeklqiqNATIKLKGKILR--VKPKKdegLKKLLDKISSFY-----IKGVPGIKRV 1113
Cdd:PRK14906 1058 EYVVSARVQFMpgvED---------------GVEVRVGQQITRgsVNPHD---LLRLTDPNTTLRyivsqVQDVYVSQGV 1119
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1114 LVTEEHGEWIIRtdgSNLSKVLEVYGVDTSRTTTNNIHEIAktlgIEAARNALILESKSVLEEQGLDVDVRHVMLVADmm 1193
Cdd:PRK14906 1120 DINDKHIEVIAR---QMLRKVAVTNPGDSDYLPGRQVNRYE----FEDTANNLILEGKQPPVGQPLLLGITKASLATD-- 1190
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1325381750 1194 tstgevqqigrhgisgkksSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGL 1258
Cdd:PRK14906 1191 -------------------SWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
939-1259 |
6.71e-85 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 278.72 E-value: 6.71e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 939 YKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAV 1018
Cdd:cd02736 2 YMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLENDRDEKSARIV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1019 KIarNIVYTALENLAQAIYE----DDIHgeIVVELNKammedrdvtlqELKEKLQIQNATIKLKGKILRvkpkkdeglKK 1094
Cdd:cd02736 82 KG--RIEKTYLGEVASYIEEvyspDDCY--ILIKLDK-----------KIIEKLQLSKSNLYFLLQSLK---------RK 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1095 LLDKIssfyIKGVPGIKRVLV--TEEHGEWIIRTDGSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKS 1172
Cdd:cd02736 138 LPDVV----VSGIPEVKRAVInkDKKKGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQY 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1173 VLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGISGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSI 1252
Cdd:cd02736 214 TMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPM 293
|
....*..
gi 1325381750 1253 PIGTGLV 1259
Cdd:cd02736 294 PIGTGLF 300
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
12-1184 |
1.05e-79 |
|
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: 286.29 E-value: 1.05e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 12 DEIQFGLFSPQEIRKLSVVEIQTPDTYD-EDGAPITAGLMDGR-LGTleprqrCKT----CGNTA---------ARCPGH 76
Cdd:COG0086 8 DAIKIGLASPEKIRSWSYGEVKKPETINyRTFKPERDGLFCERiFGP------CKDyecyCGKYKrmvykgvvcEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 77 ----------FGHIELAVPIIHIEFTKLIYD----LLRATCRNCGRILL--------PDDT-IKRvrakinrtKQLLGmv 133
Cdd:COG0086 82 vtlskvrrerMGHIELAMPVFHIWGLKSLPSriglLLDMSLRDLERVLYfesyvvidPGDTpLEK--------GQLLT-- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 134 PDEVSKwVVQEAKTKQCPHCGAVQYK-----ITFEKPTKFS-EMIPESGSEPLTPSMVReRLERIPdddlellGFNPKAA 207
Cdd:COG0086 152 EDEYRE-ILEEYGDEFVAKMGAEAIKdllgrIDLEKESEELrEELKETTSEQKRKKLIK-RLKVVE-------AFRESGN 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 208 RPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEAS 287
Cdd:COG0086 223 RPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRR 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 288 GiPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKvtewnieeMR 367
Cdd:COG0086 303 G-RAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFI--------YR 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 368 KLVANGPEKypgalyIIRPDGKRIRLEfvtdRTKIAEALEPgfVVERHLkngdiAIFNRQPSLHRMSIMAHYVRVLPYKT 447
Cdd:COG0086 374 KLEERGLAT------TIKSAKKMVERE----EPEVWDILEE--VIKEHP-----VLLNRAPTLHRLGIQAFEPVLIEGKA 436
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 448 FRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYLFTR-KTN------- 519
Cdd:COG0086 437 IQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTReREGakgegmi 516
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 520 YLTKDEVGRLLAA------AGYDGPLPEPKITEPQPLWT--GKQIFSLFLPRDLNYVLKaticqgctkcleencpydayv 591
Cdd:COG0086 517 FADPEEVLRAYENgavdlhARIKVRITEDGEQVGKIVETtvGRYLVNEILPQEVPFYNQ--------------------- 575
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 592 vvkngelisgVIDRRSIgaeqsESLLHRIIKDYGTKAGREFLNKItRLLKLFISMR-GFTYSYQELVLSPTAENKIRKTm 670
Cdd:COG0086 576 ----------VINKKHI-----EVIIRQMYRRCGLKETVIFLDRL-KKLGFKYATRaGISIGLDDMVVPKEKQEIFEEA- 638
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 671 ervQKKVEELIESYRNGTLprlpgqTLEESFEiYVMNELATARDEAGKIADQDFTLENAGIVMTRTGARGSSLNIGQMSA 750
Cdd:COG0086 639 ---NKEVKEIEKQYAEGLI------TEPERYN-KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAG 708
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 751 CVGQQSVRGKRILRGYVGRalpHFRAgdpspkargfvyssyqkGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLIN 830
Cdd:COG0086 709 MRGLMAKPSGNIIETPIGS---NFRE-----------------GLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVD 768
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 831 -ALEHIRLEYD-GTVRNSagDIIQFKYGEDGVDPAKSDHGKAVNVSRLVDQIRIatERGKPAEAEYIKKKLKEVEDqltp 908
Cdd:COG0086 769 vAQDVIVTEEDcGTDRGI--TVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTG--EVLVPAGTLIDEEVAEIIEE---- 840
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 909 LLIEELKQSLSKAKISKEGVdkavtlTVEHYKRSL-----MEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVR------- 976
Cdd:COG0086 841 AGIDSVKVRSVLTCETRGGV------CAKCYGRDLarghlVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAsraaees 914
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 977 -EQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEKHRKSREAAVKIARNIVYTALENLAQaiYEDDIHGEIVVELNKAMME 1055
Cdd:COG0086 915 sIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSELVIVDDGGRREEEYKVPYGGVLVVVG--GGVVVGGGIVAEWDPHTPP 992
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1056 --------DRDVTLQELKEKLQIQNATIKLKGKILRVKPKKDEGLKKLLDKISSFYIKGVPGIKRVLVTEEHGewIIRTD 1127
Cdd:COG0086 993 iieevgggVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAG--VIIGG 1070
|
1210 1220 1230 1240 1250
....*....|....*....|....*....|....*....|....*....|....*..
gi 1325381750 1128 GSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVR 1184
Cdd:COG0086 1071 LDVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIG 1127
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
12-835 |
6.81e-79 |
|
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: 274.01 E-value: 6.81e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 12 DEIQFGLFSPQEIRKLSVVEIQTPDTYD------EDGapitaGLMDGRL-----------GTLEpRQR-----CKTCG-- 67
Cdd:cd01609 4 DAIRISLASPEQIRSWSHGEVTKPETINyrtlkpEKD-----GLFCERIfgptkdyecacGKYK-RIRykgiiCDRCGve 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 68 -NTAA----RcpghFGHIELAVPIIHIEFTKLIydllratcrncgrillpddtikrvrakINRTKQLLGMVPDEVSKwvv 142
Cdd:cd01609 78 vTRSKvrreR----MGHIELAAPVAHIWFFKGL---------------------------PSRIGLLLDLSPKDLER--- 123
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 143 qeaktkqcphcgaVQYKItfekptkFSEMIpESGsepltpsmvrerleripdddlellgfnpkaARPEWMVLQVLPVPPV 222
Cdd:cd01609 124 -------------VIYFV-------VESFR-KSG------------------------------NRPEWMILTVLPVIPP 152
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 223 YVRPSITLESG-IRSED--DLTHKLvdIIRiNQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEASGiPPARHRSGRA 299
Cdd:cd01609 153 DLRPMVQLDGGrFATSDlnDLYRRV--INR-NNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRG-KPVTGANNRP 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 300 LKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKvtewnieeMRKLVANGpekypg 379
Cdd:cd01609 229 LKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFV--------IRELIERG------ 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 380 ALYIIRPDGKRIRLEfvtdRTKIAEALEPgfVVERHLkngdiAIFNRQPSLHRMSIMAHYVRVLPYKTFRLHLCVCPPYN 459
Cdd:cd01609 295 LAPNIKSAKKMIERK----DPEVWDILEE--VIKGHP-----VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFN 363
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 460 ADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYlftrktnYLTKDEvgrllaaagyDGPL 539
Cdd:cd01609 364 ADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLY-------YLTKER----------KGDK 426
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 540 PEPKI-TEPqplwtGKQIFSLFLPRDLNYVlkaticqgctkcleeNCPYDAYVVvknGELISGVIDRrsIGAEQSESLLH 618
Cdd:cd01609 427 GEGIIeTTV-----GRVIFNEILPEGLPFI---------------NKTLKKKVL---KKLINECYDR--YGLEETAELLD 481
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 619 RIiKDYG----TKAGreflnkITrllklfISMrgftysyqELVLSPTAENKIrktMERVQKKVEELIESYRNGTLPRlpG 694
Cdd:cd01609 482 DI-KELGfkyaTRSG------IS------ISI--------DDIVVPPEKKEI---IKEAEEKVKEIEKQYEKGLLTE--E 535
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 695 QTLEESFEIY----------VMNELATARDeagkiadqdftleNAGIVMTRTGARGSSLNIGQMSAcvgqqsvrgkriLR 764
Cdd:cd01609 536 ERYNKVIEIWtevtekvadaMMKNLDKDPF-------------NPIYMMADSGARGSKSQIRQLAG------------MR 590
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1325381750 765 GYVGralphfragDPSPKARGF-VYSSYQKGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHI 835
Cdd:cd01609 591 GLMA---------KPSGKIIELpIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDV 653
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-1259 |
9.27e-78 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 284.21 E-value: 9.27e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1 MAVEEIVHKVV----DEIQFGLFSPQEIRKLSVVEIQTPDTYD------EDGA---PITAGLMD------GRLGTLEPRQ 61
Cdd:PRK14844 1434 VVIEDISHTNIaqsfNEVSISIASPESIKRMSYGEIEDVSTANyrtfkvEKGGlfcPKIFGPVNddeclcGKYKKRRHRG 1513
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 62 R-CKTCG---NTAARCPGHFGHIELAVPIIHIEFTK----LIYDLLRATCRNCGRILLPDDTIkrvrakinrtkqllgMV 133
Cdd:PRK14844 1514 RiCEKCGvevTSSKVRRERMGHIELASPVAHIWFLKslpsRIGALLDMSLRDIENILYSDNYI---------------VI 1578
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 134 PDEVSKWVVQEAKTKQCPHCGAVQYKItfekptkfSEMIPESGSEPLTPSMVRERLERIPDD---DLELLG--------- 201
Cdd:PRK14844 1579 DPLVSPFEKGEIISEKAYNEAKDSYGI--------DSFVAMQGVEAIRELLTRLDLHEIRKDlrlELESVAseirrkkii 1650
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 202 --------FNPKAARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSEL 273
Cdd:PRK14844 1651 krlrivenFIKSGNRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRM 1730
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 274 LQYHVTTYFNNEASGIPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLS 353
Cdd:PRK14844 1731 LQEAVDSLFDNSRRNALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELF 1810
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 354 VPekvtewNIEEMRKLVANGPekypgalyIIRPDGKRIRLEfvtdRTKIAEALEPgfVVERHlkngdIAIFNRQPSLHRM 433
Cdd:PRK14844 1811 KP------FVYSKLKMYGMAP--------TIKFASKLIRAE----KPEVWDMLEE--VIKEH-----PVLLNRAPTLHRL 1865
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 434 SIMAHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYL 513
Cdd:PRK14844 1866 GIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYY 1945
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 514 FTRKTnyLTKDEVGRLLAAAGYDGPLPEPkitepqplwtgkqifSLFLPRDLNYVLKATICQGCTkCLEENCPYDAYVVV 593
Cdd:PRK14844 1946 LTLQE--PKEDDLPSFGAFCEVEHSLSDG---------------TLHIHSSIKYRMEYINSSGET-HYKTICTTPGRLIL 2007
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 594 ---------KNGELISGVIDRRSIgaeqsESLLHRIIKDYGTKAGREFLNKITRLLKLFISMRGFTYSYQELVLSPTAEN 664
Cdd:PRK14844 2008 wqifpkhenLGFDLINQVLTVKEI-----TSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKAT 2082
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 665 KIrktmERVQKKVEELIESYRNGTLPRlpgqtlEESFEiYVMNELATARD-------EAGKIADQDfTLENAGIVMTRTG 737
Cdd:PRK14844 2083 HV----DHARGEIKKFSMQYQDGLITR------SERYN-KVIDEWSKCTDmiandmlKAISIYDGN-SKYNSVYMMVNSG 2150
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 738 ARGSSLNIGQMSACVGQQSVRGKRILRgyvgralphfragdpSPkargfVYSSYQKGLDAIEFFFHAMGGREGLVDTAVR 817
Cdd:PRK14844 2151 ARGSTSQMKQLAGMRGLMTKPSGEIIE---------------TP-----IISNFREGLNVFEYFNSTHGARKGLADTALK 2210
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 818 TQQSGYMQRRLINALEH-IRLEYDGTVRNsaGDIIQfkygedgvdpaksdhgKAVNVSRLVDQIRiATERGKPAEAEYIK 896
Cdd:PRK14844 2211 TANSGYLTRRLVDVSQNcIVTKHDCKTKN--GLVVR----------------ATVEGSTIVASLE-SVVLGRTAANDIYN 2271
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 897 KKLKEVEDQLTPLLIEELKQSLSKAKISKEGVDKAVTLTVEH------YKRSL-----MEPGEAVGIIAAQSIGEPGTQM 965
Cdd:PRK14844 2272 PVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPgvcslcYGRDLatgkiVSIGEAVGVIAAQSVGEPGTQL 2351
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 966 TLRTFHYAGVREQNV-----------------------------------------TLGLPRL----------------- 987
Cdd:PRK14844 2352 TMRTFHIGGVMTRGVessniiasinakiklnnsniiidkngnkivisrscevvlidSLGSEKLkhsvpygaklyvdeggs 2431
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 988 IEIVD--ARRIPST-PIMT--------------IYLTEKHRKSREAAVKIARNI-VYTALENLAQAIYEDDIHGEIV--- 1046
Cdd:PRK14844 2432 VKIGDkvAEWDPYTlPIITektgtvsyqdlkdgISITEVMDESTGISSKVVKDWkLYSGGANLRPRIVLLDDNGKVMtla 2511
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1047 --VE----------LN---KAMMEDRDVTLQELKEKLQIQNATIKLKG--KILRVKPKKDEGLKKLLDKISSFYIKGVPG 1109
Cdd:PRK14844 2512 sgVEacyfipigavLNvqdGQKVHAGDVITRTPRESVKTRDITGGLPRviELFEARRPKEHAIVSEIDGYVAFSEKDRRG 2591
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1110 IKRVLV--TEEHG---EWII-RTDGSNLSKVLEVYGVDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDV 1183
Cdd:PRK14844 2592 KRSILIkpVDEQIspvEYLVsRSKHVIVNEGDFVRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDN 2671
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1184 RHVMLVADMMTSTGEV-----------QQIGRHGI---------SGKK------------------SSVLARAAFEITVP 1225
Cdd:PRK14844 2672 KHLEVILKQMLQKVEItdpgdtmylvgESIDKLEVdrendamsnSGKRpahylpilqgitrasletSSFISAASFQETTK 2751
|
1450 1460 1470
....*....|....*....|....*....|....
gi 1325381750 1226 NIVDAAVKGESDPLEGVTENVIVGQSIPIGTGLV 1259
Cdd:PRK14844 2752 VLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGLI 2785
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
208-974 |
1.34e-72 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 267.94 E-value: 1.34e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 208 RPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNN--E 285
Cdd:PRK09603 1622 RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNgrS 1701
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 286 ASGIPPArhrSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEkvtewniee 365
Cdd:PRK09603 1702 TNAVKGA---NKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPH--------- 1769
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 366 mrkLVANGPEK-YPGALyiirpdgKRIRLEFVTDRTKIAEALEpgfvverHLKNGDIAIFNRQPSLHRMSIMAHYVRVLP 444
Cdd:PRK09603 1770 ---LLSKLEERgYATTL-------KQAKRMIEQKSNEVWECLQ-------EITEGYPVLLNRAPTLHKQSIQAFHPKLID 1832
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 445 YKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYLFTRKTN----- 519
Cdd:PRK09603 1833 GKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSgvkge 1912
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 520 ---YLTKDEVGRLLAAAGYDGPLPEPKITEPQPLWT--GKQIFSLFLPrdlNYVlkaticqgctkcleencPYDayvvvk 594
Cdd:PRK09603 1913 hklFSSVNEIITAIDTKELDIHAKIRVLDQGNIIATsaGRMIIKSILP---DFI-----------------PTD------ 1966
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 595 ngeLISGVIDRRSIGAeqsesLLHRIIKDYGTKAGREFLNKITRLLKLFISMRGFTYSYQELVlspTAENKiRKTMERVQ 674
Cdd:PRK09603 1967 ---LWNRPMKKKDIGV-----LVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDII---TPKDK-QKMVEKAK 2034
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 675 KKVEELIESYRNGTLprlpgqTLEESFE--IYVMNELATA-RDEAGKIADQDFTLENAGIVMTRTGARGSSLNIGQMSAC 751
Cdd:PRK09603 2035 VEVKKIQQQYDQGLL------TDQERYNkiIDTWTEVNDKmSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAM 2108
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 752 VGQQSVRGKRILRgyvgralphfragdpSPkargfVYSSYQKGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINA 831
Cdd:PRK09603 2109 RGLMTKPDGSIIE---------------TP-----IISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDV 2168
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 832 LEHIRLEYDGTVRNSAGDIIQFKYGEDGVDPAKsdhgkavnvSRLVdqiriaterGKPAEAEYIKKKLKEVEDQLTPLLI 911
Cdd:PRK09603 2169 SQNVKVVSDDCGTHEGIEITDIAVGSELIEPLE---------ERIF---------GRVLLEDVIDPITNEILLYADTLID 2230
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325381750 912 EELKQSLSKAKISKEGVDKAVTLTVEH------YKRSLME-----PGEAVGIIAAQSIGEPGTQMTLRTFHYAG 974
Cdd:PRK09603 2231 EEGAKKVVEAGIKSITIRTPVTCKAPKgvcakcYGLNLGEgkmsyPGEAVGVVAAQSIGEPGTQLTLRTFHVGG 2304
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
939-1262 |
2.86e-68 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 232.47 E-value: 2.86e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 939 YKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIV-DARRIPSTPIMTIYLteKHRKSREAA 1017
Cdd:cd02735 2 YMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILmTASKNIKTPSMTLPL--KNGKSAERA 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1018 VKIARNI--VYtalenLAQAIyeddihgeivvelnkammedRDVTLQELKEKlqIQNATIKLKGKILRVKPKKDEGLKKL 1095
Cdd:cd02735 80 ETLKKRLsrVT-----LSDVV--------------------EKVEVTEILKT--IERVFKKLLGKWCEVTIKLPLSSPKL 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1096 L------DKISSFYIKGVPGIKRVLVTEE----HGEWIIRTDGSNLSKVLEVYG-VDTSRTTTNNIHEIAKTLGIEAARN 1164
Cdd:cd02735 133 LllsiveKLARKAVIREIPGITRCFVVEEdkggKTKYLVITEGVNLAALWKFSDiLDVNRIYTNDIHAMLNTYGIEAARR 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1165 ALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGISgKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTE 1244
Cdd:cd02735 213 AIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGME-SSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSS 291
|
330
....*....|....*...
gi 1325381750 1245 NVIVGQSIPIGTGLVELY 1262
Cdd:cd02735 292 RLVVGKPVNGGTGLFDLL 309
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
207-501 |
4.93e-48 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 183.18 E-value: 4.93e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 207 ARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKE--NMDAGAPTLIIQDLSELLQYHVTTYFNN 284
Cdd:CHL00018 259 IEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDllTTSRSTPGELVMCQKKLLQEAVDALLDN 338
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 285 EASGiPPARHRSGRALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPekvteWNIE 364
Cdd:CHL00018 339 GIRG-QPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQP-----FVIR 412
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 365 EM--RKLVANgpekypgalyiIRPDGKRIRlefvtDRTKIA-EALEpgFVVERHlkngdIAIFNRQPSLHRMSIMAHYVR 441
Cdd:CHL00018 413 GLirQHLASN-----------IRAAKSKIR-----EKEPIVwEILQ--EVMQGH-----PVLLNRAPTLHRLGIQAFQPI 469
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 442 VLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPII 501
Cdd:CHL00018 470 LVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPIS 529
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
947-1258 |
1.15e-47 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the 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, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 167.21 E-value: 1.15e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 947 GEAVGIIAAQSIGEPGTQMTLRTFHYAGVREQNVTLGLPRLIEIVDARripstpimtiyltekhrksreaavkiarnivy 1026
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA-------------------------------- 48
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1027 talenlaqaiyeddihgeivvelnkammedrdvtlqelkeklqiqnatiklkgkilrvkpkkdeglkklldkissfyikg 1106
Cdd:cd00630 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1107 vpgikrvlvteehgewiirtdgsnlskvlevygvdtsrtttnNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHV 1186
Cdd:cd00630 49 ------------------------------------------SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHI 86
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1325381750 1187 MLVADMMTSTGEVQQIGRHGISGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGL 1258
Cdd:cd00630 87 ELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
207-541 |
3.54e-47 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 179.94 E-value: 3.54e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 207 ARPEWMVLQVLPVPPVYVRPSITLESGIRSEDDLTHKLVDIIRINQRLKENMDAGAPTLIIQDLSELLQYHVTTYFNNEA 286
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 287 SGippaRHRSG---RALKTLSQRLKGKEGRFRSNLSGKRVDFSARTVISPDPNLDISEVGVPQEVAMRLSVPEKVTEW-- 361
Cdd:PRK02625 320 RG----RTVVGannRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLir 395
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 362 -----NIEEMRKLvangpekypgalyIIRPDgkrirlefvtdrTKIAEALEPgfVVERHlkngdIAIFNRQPSLHRMSIM 436
Cdd:PRK02625 396 qgivnNIKAAKKL-------------IQRAD------------PEVWQVLEE--VIEGH-----PVLLNRAPTLHRLGIQ 443
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 437 AHYVRVLPYKTFRLHLCVCPPYNADFDGDEMNLHIPQSEEARTEALMLMQVQDQILSPRFGGPIIGAIRDFITAAYlftr 516
Cdd:PRK02625 444 AFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCY---- 519
|
330 340
....*....|....*....|....*
gi 1325381750 517 ktnYLTKDEVGRLLAAAGYDGPLPE 541
Cdd:PRK02625 520 ---YLTAENPGAQKGAGRYFASLED 541
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
490-650 |
7.07e-47 |
|
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 165.11 E-value: 7.07e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 490 QILSPRFGGPIIGAIRDFITAAYLFTRKTNYLTKDEVGRLLaAAGYDgpLPEPKITEP-QPLWTGKQIFSLFLPRDLNYv 568
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLL-MYGIV--LPHPAILKPiKPLWTGKQTFSRLLPNEINP- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 569 lkatiCQGCTKCLEENCPYDAYVVVKNGELISGVIDRRSIGAEQSeSLLHRIIKDYGTKAGREFLNKITRLLKLFISMRG 648
Cdd:pfam04983 77 -----KGKPKTNEEDLCENDSYVLINNGELISGVIDKKTVGKSLG-SLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSG 150
|
..
gi 1325381750 649 FT 650
Cdd:pfam04983 151 FS 152
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
681-787 |
6.38e-35 |
|
RNA polymerase Rpb1, domain 4; 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 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 129.02 E-value: 6.38e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 681 IESY-RNGTLPRLPGQTLEESFEIYVMNELATARDEAGKIADQDFTLENAGIVMTRTGARGSSLNIGQMSACVGQQSVRG 759
Cdd:pfam05000 1 ITDAeRYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 1325381750 760 KRILRGYVGRALPHFRAGDPSPKARGFV 787
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
942-1258 |
1.59e-24 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape 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. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 102.61 E-value: 1.59e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 942 SLMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGVrEQNVTLGLPRLIEIVDARRIPSTPIMTIYLTEkHRKSREAAVKIA 1021
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEELFEARKINPHDLLRIKFLG-PEAVQKYLVEEI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1022 RNiVYTalenlAQAIYEDDIHGEIVVelnKAMMedrdvtlqelkeklqiqnatiklkgkilrvkpkkdeglkklldkiss 1101
Cdd:cd02655 79 QK-VYR-----SQGVNINDKHIEIIV---RQMT----------------------------------------------- 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1102 fyikgvpgiKRVLVTEehgewiirtdgSNLSKVLEvyGVDTSRTTTNNIHEIAKTLGIEAArnalilesksvleeqgldv 1181
Cdd:cd02655 103 ---------SKVKIID-----------PGDSGFLP--GELVDLNEFEEENKRLLLLGKKPA------------------- 141
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1325381750 1182 dvrhvmlvadmmtsTGEVQQIGRHGISGKKSSVLARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTGL 1258
Cdd:cd02655 142 --------------KYEPVLLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
606-975 |
5.21e-22 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 103.39 E-value: 5.21e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 606 RSIGAEQSESLLHRIIKDYGTKAGREFLNKITRLLKLFISMRGFTYSYQELVLSPT-------AENKIRKTMERVQK--- 675
Cdd:TIGR02388 5 RVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAkqdlleaAEKEIRATEERYRRgei 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 676 -KVE---ELIESYrNGTLPRLpgqtleesfeiyvmnelataRDEAGKIADQDFTLeNAGIVMTRTGARGsslNIGQMSAC 751
Cdd:TIGR02388 85 tEVErfqKVIDTW-NGTNEEL--------------------KDEVVNNFRQTDPL-NSVYMMAFSGARG---NMSQVRQL 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 752 VGqqsvrgkriLRGYVgrALPHFRAGDPSPKargfvySSYQKGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINA 831
Cdd:TIGR02388 140 VG---------MRGLM--ANPQGEIIDLPIK------TNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDV 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 832 LEH--IRLEYDGTVRnsaGDIIQfkygedgvdpAKSDHGKAVNV-SRLVDqiRIATERGKPAEAEYIKKKLKEVEDqltp 908
Cdd:TIGR02388 203 SQDviVREEDCGTER---SIVVR----------AMTEGDKKISLgDRLLG--RLVAEDVLHPEGEVIVPKNTAIDP---- 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 909 llieelkqSLSKaKISKEGVDKAVT---LTVEH--------YKRSL-----MEPGEAVGIIAAQSIGEPGTQMTLRTFHY 972
Cdd:TIGR02388 264 --------DLAK-TIETAGISEVVVrspLTCEAarsvcrkcYGWSLahahlVDLGEAVGIIAAQSIGEPGTQLTMRTFHT 334
|
...
gi 1325381750 973 AGV 975
Cdd:TIGR02388 335 GGV 337
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
791-975 |
7.13e-22 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 103.15 E-value: 7.13e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 791 YQKGLDAIEFFFHAMGGREGLVDTAVRTQQSGYMQRRLIN-ALEHIRLEYD-GTVRN------SAGDIIQFKYGEdgvdp 862
Cdd:PRK02597 163 FREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDvSQDVIVREEDcGTTRGivveamDDGDRVLIPLGD----- 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 863 aksdhgkavnvsRLVDqiRIATERGKPAEAEYIKKKLKEVEDQLTpllieelkqslskAKISKEGVDKAVT---LTVEHy 939
Cdd:PRK02597 238 ------------RLLG--RVLAEDVVDPEGEVIAERNTAIDPDLA-------------KKIEKAGVEEVMVrspLTCEA- 289
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1325381750 940 KRS--------------LMEPGEAVGIIAAQSIGEPGTQMTLRTFHYAGV 975
Cdd:PRK02597 290 ARSvcrkcygwslahnhLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 339
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
806-975 |
2.24e-21 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 101.55 E-value: 2.24e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 806 GGREGLVDTAVRTQQSGYMQRRLINALEHI--RlEYD-GTVRNsagdIIqfkygedgVDPAKSDHGKAVNVSRLVDqiRI 882
Cdd:CHL00117 184 GARKGVVDTAVRTADAGYLTRRLVEVVQHIvvR-ETDcGTTRG----IS--------VSPRNGMMIERILIQTLIG--RV 248
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 883 AtergkpAEAEYIKKKLKEVEDQ-LTPLLIEELKQSLSKaKISkegVDKAVTLTVEH------YKRS-----LMEPGEAV 950
Cdd:CHL00117 249 L------ADDIYIGSRCIATRNQdIGIGLANRFITFRAQ-PIS---IRSPLTCRSTSwicqlcYGWSlahgdLVELGEAV 318
|
170 180
....*....|....*....|....*
gi 1325381750 951 GIIAAQSIGEPGTQMTLRTFHYAGV 975
Cdd:CHL00117 319 GIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1140-1257 |
1.60e-13 |
|
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; 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 (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb 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. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain] Cd Length: 381 Bit Score: 73.99 E-value: 1.60e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1140 VDTSRTTTNNIHEIAKTLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTSTGEVQQIGRHGI-----SGKKSSV 1214
Cdd:cd02737 252 IDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYkaqrrSLKISAP 331
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1325381750 1215 LARAAFEITVPNIVDAAVKGESDPLEGVTENVIVGQSIPIGTG 1257
Cdd:cd02737 332 FTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTG 374
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
895-990 |
1.59e-10 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 65.68 E-value: 1.59e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 895 IKKKLKEVEDQLTP-LLIEELKQSLSKAK-ISKEGVDKAVTLTVEHYKRSLMEPGEAVGIIAAQSIGEPGTQMTLRTFHY 972
Cdd:PRK14898 3 IEALREKIEDLDLPrSLKDELFEKLSKRDgVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLPYDEK 82
|
90
....*....|....*...
gi 1325381750 973 AGVREQNVTlglpRLIEI 990
Cdd:PRK14898 83 IIVKEGGET----RVTEI 96
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1126-1275 |
3.60e-07 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 55.00 E-value: 3.60e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1126 TDG-SNLSKVLEVYGVDTSrtTTNNIHEIAKtLGIEAARNALILESKSVLEEQGLDVDVRHVMLVADMMTST-------- 1196
Cdd:PRK02597 1055 TDGpINPHELLEIFFEDLR--DRKGLYEAAL-EALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKvriddggd 1131
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1197 -----GE------VQQIGRH-GISG--------------KKS----SVLARAAFEITVPNIVDAAVKGESDPLEGVTENV 1246
Cdd:PRK02597 1132 ttmlpGElielrqVEQVNEAmAITGgapaeytpvllgitKASlntdSFISAASFQETTRVLTEAAIEGKSDWLRGLKENV 1211
|
170 180
....*....|....*....|....*....
gi 1325381750 1247 IVGQSIPIGTGLvelymSTFEMGGKTKNG 1275
Cdd:PRK02597 1212 IIGRLIPAGTGF-----SGFEEELSAEAG 1235
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1134-1261 |
2.25e-04 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 45.70 E-value: 2.25e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1134 VLEVYGVDTSRTttnNIHE--------IAKTLGI-----EAA-------RNALILESKSVLEEQGLDVDVRHVMLVADMM 1193
Cdd:CHL00117 1141 LLEARSIDSISM---NLEKrlegwnerITRILGIpwgflIGAelsiaqsQISLVNKIQKVYRSQGVQISDKHIEIIVRQM 1217
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325381750 1194 TST--------------GEV------QQIGRH------------GISgKKS----SVLARAAFEITVPNIVDAAVKGESD 1237
Cdd:CHL00117 1218 TSKvlvsedgmsnvflpGELigllraERINRAleeaicyrpillGIT-KASlntqSFISEASFQETTRVLAKAALRGRID 1296
|
170 180
....*....|....*....|....
gi 1325381750 1238 PLEGVTENVIVGQSIPIGTGLVEL 1261
Cdd:CHL00117 1297 WLKGLKENVILGGLIPAGTGFKGL 1320
|
|
| |
