|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
15-1019 |
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: 1353.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 15 SFSFYEPSEIRKISVKQIVNPVLFDALGHPTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFDN 94
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 95 LYALLRSKCVYCHQFRISRALMKKYTAQLTLLQHGLINQAQSLDeivldfkkaneakedetledrmeesslslstaeeyi 174
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKLKLLDKGLLVEAAELD------------------------------------ 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 175 dyvdnfmkdaladeearkyaaqdykvtvindvrknvmrdfmkhcihskkcgnchgisppvrrdgaaklfqlalnkkdqav 254
Cdd:cd01435 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 255 mdrmkestgsfgeikgfingqrfltpyevrkdvqalfekegevttllfgardprvpsfikkATYHMFFIEVLAVAPTRFR 334
Cdd:cd01435 125 -------------------------------------------------------------FGYDMFFLDVLLVPPNRFR 143
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 335 PPSVMGDKTFESPQNELLSAILKGSHLVRDFSEELQAASEEEPVDKKKVEVTRNRFVDSIINLQHAVNSFIDSTKNPTQv 414
Cdd:cd01435 144 PPSFLGDKVFENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLISGKTNSEKLINAWLQLQSAVNELFDSTKAPKS- 222
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 415 aqGQNLPPGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMRQAVING 494
Cdd:cd01435 223 --GKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVING 300
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 495 PNKWPGATHVQNEDQSIDVLGDLSIESRIALANSLLAPqsshtaqsgnnPFPTRTQTINKKVFRHLRNGDMLLLNRQPTL 574
Cdd:cd01435 301 PDVYPGANAIEDEDGRLILLSALSEERRKALAKLLLLL-----------SSAKLLLNGPKKVYRHLLDGDVVLLNRQPTL 369
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 575 HKPSIMAHKARVLPGEKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDNQYLVPTSGDPLRGLIQDNVD 654
Cdd:cd01435 370 HKPSIMAHKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVV 449
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 655 SGVWMSSRDTFFNREEYHQLLYGSLRPEVDGTGDGKIRTLPPTILKPEPLWTGKQVISTIIKNLTWGKAQLNMTS----K 730
Cdd:cd01435 450 SGVLLTSRDTFFTREEYQQLVYAALRPLFTSDKDGRIKLLPPAILKPKPLWTGKQVISTILKNLIPGNAPLLNLSgkkkT 529
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 731 SKVAAKFWGPNAKDEEKVLIVDGELMHGVMDKSQFGASAFGLVHSIYEIYGPESAGMLLSILSRLFIKFIQSHGFTCRMD 810
Cdd:cd01435 530 KKKVGGGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIE 609
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 811 DLILTKDGDKWRRDLLDNGVGLGTEAHLEFLGLaetaqtatpevlakefklrmnevirddnklagldnamkaKVNKLTSS 890
Cdd:cd01435 610 DLLLTPKADEKRRKILRKAKKLGLEAAAEFLGL---------------------------------------KLNKVTSS 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 891 ITQKCLPDGLVRPFPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVSGRSLPSFRPFDTSARAGGFVTGRF 970
Cdd:cd01435 651 IIKACLPKGLLKPFPENNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRF 730
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*....
gi 1954159237 971 LTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLRVHYD 1019
Cdd:cd01435 731 LTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
10-1046 |
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: 584.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 10 EVDYVSFSFYEPSEIRKISVKQIVNPVLFDALGHPTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNP 89
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 90 MFFDNLYALLRSKCVYCHqfrisRALMKkytaqltllqhglinqaqsldeivldfkkaneakEDEtledrmeesslslst 169
Cdd:cd02582 83 GFAKHIYDLLRATCRSCG-----RILLP----------------------------------EEE--------------- 108
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 170 AEEYIDYVdnfmkdaladEEARKYAAQDYKvTVINDVRKNVMRdfMKHCIHskkCGnchgisppvrrdgaAKLFQLALNK 249
Cdd:cd02582 109 IEKYLERI----------RRLKEKWPELVK-RVIEKVKKKAKK--RKVCPH---CG--------------APQYKIKLEK 158
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 250 kdqavmdrmkeSTGSFGEIKGfinGQRFLTPYEVRkdvqALFEKEGEVTTLLFGArDPrvpsfiKKATYHMFFIEVLAVA 329
Cdd:cd02582 159 -----------PTTFYEEKEE---GEVKLTPSEIR----ERLEKIPDEDLELLGI-DP------KTARPEWMVLTVLPVP 213
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 330 PTRFRPpSVmgdkTFESPQNellsailkgshlvrdfseelqaaSEEEpVDKKKVEVTR--NRFVDSIIN----------- 396
Cdd:cd02582 214 PVTVRP-SI----TLETGER-----------------------SEDD-LTHKLVDIIRinQRLKENIEAgapqliiedlw 264
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 --LQHAVNSFIDstkNPTQvaqgqNLPP----------GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIG 464
Cdd:cd02582 265 dlLQYHVTTYFD---NEIP-----GIPParhrsgrplkTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVG 336
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 465 IPPVFATKLTYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNEDQS-IDvlgdLSIESRIALANSLlapqsshtaqsgnn 543
Cdd:cd02582 337 VPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRPDGRrIR----LRYVNREELAERL-------------- 398
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 544 pfptrtqTINKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIAR 623
Cdd:cd02582 399 -------EPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQSEEAR 470
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 624 AEAALIANTDNQYLVPTSGDPLRGLIQDNVDSGVWMSSRDTFFNREEYHQLL----YGSLRPEvdgtgdgkirtlpPTIL 699
Cdd:cd02582 471 AEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLsaagYDGLLPE-------------PAIL 537
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 700 KPEPLWTGKQVISTIIKNltwgkaQLNMTSKSKVAAKfwGPNAKDEE-----KVLIVDGELMHGVMDKSQFGASAFG-LV 773
Cdd:cd02582 538 EPKPLWTGKQLFSLFLPK------DLNFEGKAKVCSG--CSECKDEDcpndgYVVIKNGKLLEGVIDKKAIGAEQPGsLL 609
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 774 HSIYEIYGPESAGMLLSILSRLFIKFIQSHGFTCRMDDLILTKDGDKWRRDLLDngvglgtEAHLEFLGLAETAQTATPE 853
Cdd:cd02582 610 HRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIK-------EAEKKVYELIEQYKNGELE 682
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 854 VL-------AKEFKL--RMNEViRDDnklagldnamkakvnklTSSITQKCLPdglvrpfPKNDMQMMTVSGAKGSNVNA 924
Cdd:cd02582 683 PLpgrtleeTLEMKImqVLGKA-RDE-----------------AGKVASKYLD-------PFNNAVIMARTGARGSMLNL 737
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 925 TQISCLLGQQELEGRRVPLMVSGRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQ 1004
Cdd:cd02582 738 TQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQ 817
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|..
gi 1954159237 1005 RCLMKHLEGLRVHYDHTVRDSDGSVLQFHYGEDSLDVIKAKH 1046
Cdd:cd02582 818 RRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSDH 859
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
11-1642 |
5.55e-178 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 571.58 E-value: 5.55e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 11 VDYVSFSFYEPSEIRKISVKQIVNPVLFDALGHPTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPM 90
Cdd:PRK14977 9 IDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPVIHIA 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 91 FFDNLYALLRSKCVYChqfrisralmkkytAQLTLLQhglinqaqsldeivldfkkaneakEDETLEDRMEEsslslstA 170
Cdd:PRK14977 89 FIDNIKDLLNSTCHKC--------------AKLKLPQ------------------------EDLNVFKLIEE-------A 123
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 171 EEYidYVDNFMKdaLADEEarkyaaqdykvtVINDVRKNVMRDFMKHcihsKKCGNChgisppvrrdgAAKLFQLALNKK 250
Cdd:PRK14977 124 HAA--ARDIPEK--RIDDE------------IIEEVRDQVKVYAKKA----KECPHC-----------GAPQHELEFEEP 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 251 DQAVMDRmkestgsfgEIkgfinGQRFLTPYEVRKdvqaLFEKEGEVTTLLFGArDPrvpsfiKKATYHMFFIEVLAVAP 330
Cdd:PRK14977 173 TIFIEKT---------EI-----EEHRLLPIEIRD----IFEKIIDDDLELIGF-DP------KKARPEWAVLQAFLVPP 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 331 TRFRPPSVMgdKTFESPQNELlsailkgSHLVRDFSEELQAASEEepvdkKKVEVTRNRFVDSIINLQHAVNSFIDSTKN 410
Cdd:PRK14977 228 LTARPSIIL--ETGERSEDDL-------THILVDIIKANQKLKES-----KDAGAPPLIVEDEVDHLQYHTSTFFDNATA 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 411 --PTQVAQGQNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEM 487
Cdd:PRK14977 294 giPQAHHKGSGRPlKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKM 373
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 488 RQAVINGPNKWPGATHVQNEDQ---SIDVLGDLSIESRIALANSLlapqsshtaqsgnnpfptrtqTINKKVFRHLRNGD 564
Cdd:PRK14977 374 KELVINGPDEFPGANAIRKGDGtkiRLDFLEDKGKDALREAAEQL---------------------EIGDIVERHLADGD 432
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 565 MLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDNQYLVPTSGDP 644
Cdd:PRK14977 433 IVIFNRQPSLHKLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGP 511
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 645 LRGLIQDNVDSGVWMSSRDTFFNREEYHQLL----YGSLRPEvdgtgdgkirtlPPTILKPEPLWTGKQVISTII-KNLT 719
Cdd:PRK14977 512 IIGALQDFITAAYLITKDDALFDKNEASNIAmlagITDPLPE------------PAIKTKDGPAWTGKQLFSLFLpKDFN 579
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 720 W-GKAQLNMTSKSKVAakfwGPNAKDEEKVLIVDGELMHGVMDKSQFGASAFG---LVHSIYEIYGPESAGMLLSILSRL 795
Cdd:PRK14977 580 FeGIAKWSAGKAGEAK----DPSCLGDGYVLIKEGELISGVIDDNIIGALVEEpesLIDRIAKDYGEAVAIEFLNKILII 655
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 796 FIKFIQSHGFTCRMDDLILTkdgDKWRRDLLDNGVGLgteahLEFLGLAETAQTATPEVLAKEFKLRMNEVIRDDNKL-A 874
Cdd:PRK14977 656 AKKEILHYGFSNGPGDLIIP---DEAKQEIEDDIQGM-----KDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALeA 727
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 875 GLDNAMKAKVNKLTSSITqKCLPdglvrpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVSGR------ 948
Cdd:PRK14977 728 DIVNELDKARDKAGSSAN-DCID-------ADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRlhegyk 799
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 949 --SLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLRVHYDHTVRDSD 1026
Cdd:PRK14977 800 drALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPH 879
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1027 GSVLQFHYGEDSLDVIKAKHINQFsfsahNFEALSQKYHPKAALASLEIKQGEEYAKKALKkpgkydpalsVYNPGTHLG 1106
Cdd:PRK14977 880 GHIIQFKFGEDGIDPQKLDHGEAF-----NLERIIEKQKIEDRGKGASKDEIEELAKEYTK----------TFNANLPKL 944
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1107 VVserfalamkeyveknpDAMpfeKGSESSKNTARyagltknKFKALMNLKYLHSLVEPGEAVGILAAQSVGEPSTQMTL 1186
Cdd:PRK14977 945 LA----------------DAI---HGAELKEDELE-------AICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTL 998
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1187 NTFHFAGYGAANVTLGIPRLREIImTAARKIKTPTMLLPLcaettpkkaAQFCKSaSRLTLAQLVDNVIvKEKISA--KS 1264
Cdd:PRK14977 999 RTFHAAGIKAMDVTHGLERFIELV-DARAKPSTPTMDIYL---------DDECKE-DIEKAIEIARNLK-ELKVRAliAD 1066
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1265 SENNYrrsktYSIRVNMFDEKEYNEEYRVSAKRVKEVLATTflkdleelirrdikdtkkiediSKGQKMdgpqdtneden 1344
Cdd:PRK14977 1067 SAIDN-----ANEIKLIKPDKRALENGCIPMERFAEIEAAL----------------------AKGKKF----------- 1108
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1345 mgdntaagyvsddaedldaktarksaenkpqasydepdedddvvpeenEKSLEDEeaefeqailagavddeeapkrtssk 1424
Cdd:PRK14977 1109 ------------------------------------------------EMELEDD------------------------- 1115
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1425 ggKIEKQAVEKSkyctkfnfddangafceiDMEFPADTKKILMVSLIEKScarvvVHEVKGISKcfEYINPTENDTSKR- 1503
Cdd:PRK14977 1116 --LIILDLVEAA------------------DRDKPLATLIAIRNKILDKP-----VKGVPDIER--AWVELVEKDGRDEw 1168
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1504 -LQTEGVNLRGMWAFSDiIDVNYIDTNDIAAILNTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEG---- 1578
Cdd:PRK14977 1169 iIQTSGSNLAAVLEMKC-IDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGtiea 1247
|
1610 1620 1630 1640 1650 1660
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954159237 1579 --GYKPFSRIGIGSNV-SPFVKMSFESTCKFLTEATLHGDFDSLDSPSSRIVVGRVVEGGTGSFDVL 1642
Cdd:PRK14977 1248 igLQAAGVRHGFAGEKdSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLL 1314
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
10-1046 |
2.29e-176 |
|
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: 553.17 E-value: 2.29e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 10 EVDYVSFSFYEPSEIRKISVKQIVNPVLFDALGHPTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNP 89
Cdd:TIGR02390 3 KIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 90 MFFDNLYALLRSKCVYCHQFRISRALMKKYtaqltllqhglinqaqsldeivldFKKANEAKEDETLEDRmeesslslst 169
Cdd:TIGR02390 83 GFAKEIYKILRATCRKCGRITLTEEEIEQY------------------------LEKINKLKEEGGDLAS---------- 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 170 aeeyidyvdnfmkdaladeearkyaaqdykvTVINDVRKNVMRdfmkhcihSKKCGNChgisppvrrdgAAKLFQLALNK 249
Cdd:TIGR02390 129 -------------------------------TLIEKIVKEAAK--------RMKCPHC-----------GEEQKKIKFEK 158
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 250 KdqavmdrmkestGSFGEIKGfiNGQRFLTPYEVRKdvqaLFEKEGEVTTLLFGArDPRV--PSFIkkatyhmfFIEVLA 327
Cdd:TIGR02390 159 P------------TYFYEEGK--EGDVKLTPSEIRE----RLEKIPDEDAELLGI-NPKVarPEWM--------VLTVLP 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 328 VAPTRFRpPSVmgdkTFESPQNellsailkgshlvrdfseelqaasEEEPVDKKKVEVTR--NRFVDSIIN--------- 396
Cdd:TIGR02390 212 VPPVTVR-PSI----TLETGER------------------------SEDDLTHKLVDIIRinQRLKENIEAgapqliied 262
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 ----LQHAVNSFIDStknptqvaQGQNLPP----------GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSE 462
Cdd:TIGR02390 263 lwelLQYHVATYFDN--------ELPGIPParhrsgrplkTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINE 334
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 463 IGIPPVFATKLTYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNED-QSIdvlgDLSIESRIALANSLlapqsshtaqsg 541
Cdd:TIGR02390 335 VGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDgRRI----KIRDENKEELAERL------------ 398
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 542 nnpfptrtqTINKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEI 621
Cdd:TIGR02390 399 ---------EPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEE 468
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 622 ARAEAALIANTDNQYLVPTSGDPLRGLIQDNVDSGVWMSSRDTFFNREEYHQLLYGSLRPEVDGtgdgkirtlPPTILKP 701
Cdd:TIGR02390 469 ARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPP---------EPAIEKP 539
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 702 EPLWTGKQVISTIIKNltwgkaQLNMTSKSKVAAKFWGPNAKD---EEKVLIVDGELMHGVMDKSQFGASAFGLVHSIYE 778
Cdd:TIGR02390 540 KEYWTGKQIFSAFLPE------DLNFEGRAKICSGSDACKKEEcphDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVR 613
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 779 IYGPESAGMLLSILSRLFIKFIQSHGFTCRMDDLILTKDGDKWRRDLLDngvglgtEAHLEFLGLAETAQTATPEVLAKe 858
Cdd:TIGR02390 614 EYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIE-------KAEKRVDNLIERYRNGELEPLPG- 685
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 859 fklRMNEVIRDDNKLAGLDnamkaKVNKLTSSITQKCLPdglvrpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEG 938
Cdd:TIGR02390 686 ---RTVEETLEMKIMEVLG-----KARDEAGEVAEKYLD-------PENHAVIMARTGARGSLLNITQMAAMVGQQSVRG 750
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 939 RRVPLMVSGRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLRVHY 1018
Cdd:TIGR02390 751 GRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEY 830
|
1050 1060
....*....|....*....|....*...
gi 1954159237 1019 DHTVRDSDGSVLQFHYGEDSLDVIKAKH 1046
Cdd:TIGR02390 831 DGTVRDTRGNLIQFKYGEDGVDPMKSDH 858
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
14-1046 |
2.69e-176 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 553.31 E-value: 2.69e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 14 VSFSFYEPSEIRKISVKQIVNPVLFDALGHPTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFD 93
Cdd:PRK08566 12 IKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIHVGFAK 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 94 NLYALLRSKCVYChqfriSRALMKkytaqltllqhglinqaqsldeivldfkkaneakedetlEDRMEESSLSLSTAEEY 173
Cdd:PRK08566 92 LIYKLLRATCREC-----GRLKLT---------------------------------------EEEIEEYLEKLERLKEW 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 174 IDYVDNFMKdaladeEARKYAAqdyKVTVindvrknvmrdfmkhCIHskkCGnchgisppvrrdgaAKLFQLALNKKDqa 253
Cdd:PRK08566 128 GSLADDLIK------EVKKEAA---KRMV---------------CPH---CG--------------EKQYKIKFEKPT-- 164
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 254 vmdrmkestgSFGEIKGfiNGQRFLTPYEVRkdvqALFEKEGEVTTLLFGArDPRV--PSFikkatyhmFFIEVLAVAPT 331
Cdd:PRK08566 165 ----------TFYEERK--EGLVKLTPSDIR----ERLEKIPDEDLELLGI-NPEVarPEW--------MVLTVLPVPPV 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 332 RFRPpSVmgdkTFESPQNellsailkgshlvrdfseelqaaSEEEpVDKKKVEVTR--NRFVDS--------IIN----- 396
Cdd:PRK08566 220 TVRP-SI----TLETGQR-----------------------SEDD-LTHKLVDIIRinQRLKENieagapqlIIEdlwel 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDStknptQVAqgqNLPP----------GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIP 466
Cdd:PRK08566 271 LQYHVTTYFDN-----EIP---GIPParhrsgrplkTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVP 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 467 PVFATKLTYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNED-QSIDvlgdLSIESRIALANSLlapqsshtaqsgnnpf 545
Cdd:PRK08566 343 EAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDgRRIK----LTDKNKEELAEKL---------------- 402
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 546 ptrtqTINKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAE 625
Cdd:PRK08566 403 -----EPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAE 476
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 626 AALIANTDNQYLVPTSGDPLRGLIQDNVdSGVWMSSRD-TFFNREEYHQLLygslrpevdgtGDGKIRTLP---PTILKP 701
Cdd:PRK08566 477 ARILMLVQEHILSPRYGGPIIGGIQDHI-SGAYLLTRKsTLFTKEEALDLL-----------RAAGIDELPepePAIENG 544
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 702 EPLWTGKQVISTII-KNLTW-GKAQLNmtSKSKVAAKFWGPNakdEEKVLIVDGELMHGVMDKSQFGASAFGLVHSIYEI 779
Cdd:PRK08566 545 KPYWTGKQIFSLFLpKDLNLeFKAKIC--SGCDECKKEDCEH---DAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKE 619
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 780 YGPESAGMLLSILSRLFIKFIQSHGFTCRMDDLILTKDGDKWRRDLLDNG-------VGLGTEAHLEFL---GLAETAQT 849
Cdd:PRK08566 620 YGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAekrveelIEAYENGELEPLpgrTLEETLEM 699
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 850 ATPEVLAKefklrmnevIRDDnklagldnamkakvnklTSSITQKCLPdglvrpfPKNDMQMMTVSGAKGSNVNATQISC 929
Cdd:PRK08566 700 KIMQVLGK---------ARDE-----------------AGEIAEKYLG-------LDNPAVIMARTGARGSMLNLTQMAA 746
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 930 LLGQQELEGRRVPLMVSGRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMK 1009
Cdd:PRK08566 747 CVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLIN 826
|
1050 1060 1070
....*....|....*....|....*....|....*..
gi 1954159237 1010 HLEGLRVHYDHTVRDSDGSVLQFHYGEDSLDVIKAKH 1046
Cdd:PRK08566 827 ALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDH 863
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
12-1019 |
6.24e-163 |
|
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: 513.24 E-value: 6.24e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 12 DYVSFSFYEPSEIRKISVKQIVNPVLFDALGHPTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMF 91
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYENGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 92 FDNLYALLRSKCvychqfrisralmkkyTAQLTLlqhglinqaqsldEIVLD-FKKaneakedetledrmeesslslsta 170
Cdd:cd02733 81 LTKILKILRCVC----------------KRELSA-------------ERVLEiFKR------------------------ 107
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 171 eeyidyvdnfmkdaLADEEARkyaaqdykvtvindvrknvmrdfmkhcihskkcgnchgisppvrrdgaaklfqlalnkk 250
Cdd:cd02733 108 --------------ISDEDCR----------------------------------------------------------- 114
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 251 dqavmdrmkestgsfgeIKGFingqrflTPYEVRKDvqalfekegevttllfgardprvpsfikkatyhMFFIEVLAVAP 330
Cdd:cd02733 115 -----------------ILGF-------DPKFSRPD---------------------------------WMILTVLPVPP 137
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 331 TRFRPpSVMGDKTFESpQNEL---LSAILK-------------GSHLVRDFSEELQAaseeepvdkkkvEVTRnrFVD-S 393
Cdd:cd02733 138 PAVRP-SVVMDGSARS-EDDLthkLADIIKannqlkrqeqngaPAHIIEEDEQLLQF------------HVAT--YMDnE 201
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 394 IINLQHAVNsfidstKNptqvaqGQNLPPgIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKL 473
Cdd:cd02733 202 IPGLPQATQ------KS------GRPLKS-IRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNL 268
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 474 TYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNEDqsidvlgdlsiESRIALAnslLAPQSShtaqsgnnpfptrTQTIN 553
Cdd:cd02733 269 TFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDD-----------GERIDLR---YLKKAS-------------DLHLQ 321
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 554 K--KVFRHLRNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIAN 631
Cdd:cd02733 322 YgyIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPY-STFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMM 400
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 632 TDNQYLVPTSGDPLRGLIQDNVdSGVW-MSSRDTFFNREEYHQLLYGSlrpevdGTGDGKIRtlPPTILKPEPLWTGKQV 710
Cdd:cd02733 401 VPRQIVSPQSNKPVMGIVQDTL-LGVRkLTKRDTFLEKDQVMNLLMWL------PDWDGKIP--QPAILKPKPLWTGKQI 471
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 711 ISTIIKNLTwgkaqlNMTSKSKVAAKFWGPNAKDEEKVLIVDGELMHGVMDKSQFGASAFGLVHSIYEIYGPESAGMLLS 790
Cdd:cd02733 472 FSLIIPKIN------NLIRSSSHHDGDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIG 545
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 791 ILSRLFIKFIQSHGFTcrmddliltkdgdkwrrdlldngVGLG-TEAHleflglAETAQTATPEVlaKEFKLRMNEVIRD 869
Cdd:cd02733 546 NIQRVVNNWLLHNGFS-----------------------IGIGdTIAD------KETMKKIQETI--KKAKRDVIKLIEK 594
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 870 --DNKL---AGldNAMK----AKVNKL-------TSSITQKCLPDglvrpfpKNDMQMMTVSGAKGSNVNATQISCLLGQ 933
Cdd:cd02733 595 aqNGELepqPG--KTLResfeNKVNRIlnkardkAGKSAQKSLSE-------DNNFKAMVTAGSKGSFINISQIIACVGQ 665
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 934 QELEGRRVPLMVSGRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEG 1013
Cdd:cd02733 666 QNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMED 745
|
....*.
gi 1954159237 1014 LRVHYD 1019
Cdd:cd02733 746 VMVKYD 751
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
21-1023 |
1.47e-158 |
|
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: 503.62 E-value: 1.47e-158
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 21 PSEIRKISVKQIVNPVLFDAL-GHPTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFDNLYALL 99
Cdd:cd02583 3 PEDIIRLSEVEVTNRNLYDIEtRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIINIL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 100 RSKCVYChqfriSRALMKKytaqltllqhglinqaqsldeivldfkkaneaKEDETLEDRMEESSLSLStaeeyidyvdn 179
Cdd:cd02583 83 QCICKTC-----SRVLLPE--------------------------------EEKRKFLKRLRRPNLDNL----------- 114
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 180 fmkdaladeearKYAAQDYKvtvINDVRKNVmrdfmkhcihsKKCGNCHgisppvrrdgaaklfqlaLNKKDQAVMDRMK 259
Cdd:cd02583 115 ------------QKKALKKK---ILEKCKKV-----------RKCPHCG------------------LLKKAQEDLNPLK 150
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 260 estgsfgeikgfingqrfltpyevrkdVQALFEK--EGEVTTLLFGARDPRvPSfikkatyhMFFIEVLAVAPTRFRPpS 337
Cdd:cd02583 151 ---------------------------VLNLFKNipPEDVELLLMNPLAGR-PE--------NLILTRIPVPPLCIRP-S 193
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 338 VMGDKTFESpqNE-----LLSAILKGSHLVRD-FSEELQAASEEEPVDKKKVEVTRnrfvdsIINlqhAVNSFIDSTKNP 411
Cdd:cd02583 194 VVMDEKSGT--NEddltvKLSEIIFLNDVIKKhLEKGAKTQKIMEDWDFLQLQCAL------YIN---SELPGLPLSMQP 262
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 412 TQVAQGqnlppgIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMRQAV 491
Cdd:cd02583 263 KKPIRG------FCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLV 336
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 492 INGPNKWPGATHVQNEDQSidvlgdlsieSRIALANsllapqsshtaqsGNNPFPTRTQTINKKVFRHLRNGDMLLLNRQ 571
Cdd:cd02583 337 LNGPDVHPGANFVIKRDGG----------KKKFLKY-------------GNRRKIARELKIGDIVERHLEDGDIVLFNRQ 393
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 572 PTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDNQYLVPTSGDPLRGLIQD 651
Cdd:cd02583 394 PSLHRLSIMAHRAKVMPW-RTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQD 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 652 NVDSGVWMSSRDTFFNREEYHQLL-YGSLrpevdgtGDGKIRTLPPTILKPEPLWTGKQVISTIIKNLTWGKAQLNMTSK 730
Cdd:cd02583 473 FLTASYLLTSKDVFFDRAQFCQLCsYMLD-------GEIKIDLPPPAILKPVELWTGKQIFSLLLRPNKKSPVLVNLEAK 545
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 731 SKV---AAKFWGPNakdEEKVLIVDGELMHGVMDKSQFGA-SAFGLVHSIYEIYGPESAGMLLSILSRLFIKFIQSHGFT 806
Cdd:cd02583 546 EKSytkKSPDMCPN---DGYVVIRNSELLCGRLDKSTLGSgSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFS 622
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 807 CRMDDLILTKDGDKWRRDLLDNGVGLGTEAHLEFlglaetaqtatpevlaKEFKLrmnevirddNKLAGLDNA--MKAKV 884
Cdd:cd02583 623 IGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQY----------------KKGKL---------ELQPGCTAEqtLEAKI 677
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 885 NKLTSSITQKC-------LPdglvrpfPKNDMQMMTVSGAKGSNVNATQ-ISClLGQQELEGRRVPLMVSGRSLPSFRPF 956
Cdd:cd02583 678 SGELSKIREDAgkaclkeLH-------KSNSPLIMALCGSKGSNINISQmIAC-VGQQIISGKRIPNGFEDRTLPHFPRN 749
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954159237 957 DTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLRVHYDHTVR 1023
Cdd:cd02583 750 SKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1157-1642 |
3.91e-142 |
|
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: 440.09 E-value: 3.91e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1157 KYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIIMTAARKIKTPTMLLPLCAETTPKKAA 1236
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1237 QFCKSASRLTLAQLVDNVIVKEkisakssennyrrsktysirvnmfdekeyneeyrvsakrVKEVLATTFLKDLEELirr 1316
Cdd:cd02735 81 TLKKRLSRVTLSDVVEKVEVTE---------------------------------------ILKTIERVFKKLLGKW--- 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1317 dikdtkkiediskgqkmdgpqdtnedenmgdntaagyvsddaedldaktarksaenkpqasydepdedddvvpeeneksl 1396
Cdd:cd02735 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1397 edeeaefeqailagavddeeapkrtsskggkiekqavekskyctkfnfddangafCEIDMEFPADTKKILMVSLIEKSCA 1476
Cdd:cd02735 119 -------------------------------------------------------CEVTIKLPLSSPKLLLLSIVEKLAR 143
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1477 RVVVHEVKGISKCFEYINPTENDTSKRLQTEGVNLRGMWAFSDIIDVNYIDTNDIAAILNTYGVEAARNAVIKEVGSVFA 1556
Cdd:cd02735 144 KAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFK 223
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1557 VYGIKVDRRHLTLIADYMTFEGGYKPFSRIGIGSNVSPFVKMSFESTCKFLTEATLHGDFDSLDSPSSRIVVGRVVEGGT 1636
Cdd:cd02735 224 VYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGT 303
|
....*.
gi 1954159237 1637 GSFDVL 1642
Cdd:cd02735 304 GLFDLL 309
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
396-1019 |
1.88e-121 |
|
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: 392.18 E-value: 1.88e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 396 NLQHAVNSFIDSTKNPTQVAQGQNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLt 474
Cdd:cd00399 111 LLQEHVDTYLDNGIAGQPQTQKSGRPlRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL- 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 475 ypepvtphnikemrqavingpnkwpgathvqnedqsidvlgdlsiesrialansllapqsshtaqsgnnpfptrtqtink 554
Cdd:cd00399 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 555 kvfrhlrNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDN 634
Cdd:cd00399 190 -------DGDPVLFNRQPSLHKLSIMAHRVRVLPG-STFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPN 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 635 QYLVPTSGDPLRGLIQDNVDSGVWMSsrdtffnreeyhqllygslrpevdgtgdgkirtlpptilkpeplwTGKQVISTI 714
Cdd:cd00399 262 NILSPQNGEPLIGLSQDTLLGAYLLT---------------------------------------------LGKQIVSAA 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 715 IKNltwgkaqlnmtskskvaakfwgpnakdeekvlivdgelmhgvmdksqfgasafGLVHSIYEIYGPESAGMLLSILSR 794
Cdd:cd00399 297 LPG-----------------------------------------------------GLLHTVTRELGPEKAAKLLSNLQR 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 795 LFIKFIQSHGFTCRMDDLILTKDGDKWRRDLLDngvglgtEAHLEFLGLAETAQTAtpEVLAKEFKLRMNEvirddnkla 874
Cdd:cd00399 324 VGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIE-------EAKKKVDEVEEAFQAG--LLTAQEGMTLEES--------- 385
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 875 gLDNAMKAKVNKLTSSITQKCLP-DGLVRPFpkNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVSGRSLPSF 953
Cdd:cd00399 386 -LEDNILDFLNEARDKAGSAASVnLDLVSKF--NSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHF 462
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1954159237 954 RPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLRVHYD 1019
Cdd:cd00399 463 SKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
973-1588 |
2.00e-119 |
|
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: 386.32 E-value: 2.00e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 973 GIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLRVHYDHTVRDSDGSVLQFHYGEDSLDVIKAKHINQFSF 1052
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1053 SAHNFEALSQKYhpkaaLASLEIKQGEEYAKKALKKPGKYDPALSVYNPGTHLGVVSERFALAMKEYVEKNpdamPFEKG 1132
Cdd:pfam04998 81 EFSDLKLEDKFK-----NDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSKEAQERATLLFELLLKSGLE----SKRVR 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1133 SESSKNTARYagltkNKFKALMNLKYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIIMT 1212
Cdd:pfam04998 152 SELTCNSKAF-----VCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINV 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1213 AArKIKTPTMLLPL--CAETTPKKAAQFCKSASRLTLAQLVDNVIVKEKISaKSSENNYRRSKTYSIRVNMFDEKEYNEE 1290
Cdd:pfam04998 227 SK-NIKSPSLTVYLfdEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPD-PFNTPIISDVKGVVKFFDIIDEVTNEEE 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1291 YRVSAKRVKEVlattflkdleelIRRDIKDTKKIEDISKGQKMDGPQDtnedeNMGDNTAAGYVSDDAEDLDAKtarksa 1370
Cdd:pfam04998 305 IDPETGLLILV------------IRLLKILNKSIKKVVKSEVIPRSIR-----NKVDEGRDIAIGEITAFIIKI------ 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1371 enkpqasydepdedddvvpeeneksledeeaefeqailagavddeeapkrtsskggkiekqavekskyctkfNFDDANGA 1450
Cdd:pfam04998 362 ------------------------------------------------------------------------SKKIRQDT 369
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1451 FCEIDMEFPADTKKILMVSLIEKSCARVVVHEVKGISKCfeYINPTEN---DTSKRLQTEGVNLRGMWAFSDIIDVNYID 1527
Cdd:pfam04998 370 GGLRRVDELFMEEDPKLAILVASLLGNITLRGIPGIKRI--LVNEDDKgkvEPDWVLETEGVNLLRVLLVPGFVDAGRIL 447
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1954159237 1528 TNDIAAILNTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIGI 1588
Cdd:pfam04998 448 SNDIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGI 508
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
320-651 |
3.89e-109 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 348.74 E-value: 3.89e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 320 MFFIEVLAVAPTRFRPPSVMGDKTF-ESPQNELLSAILKGSHLVRDFSEELQAAseeepvdkkkvevtrNRFVDSIINLQ 398
Cdd:smart00663 2 WMILTVLPVPPPCLRPSVQLDGGRFaEDDLTHLLRDIIKRNNRLKRLLELGAPS---------------IIIRNEKRLLQ 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 399 HAVNSFIDSTKNPTQVAQGQNLPPGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEP 478
Cdd:smart00663 67 EAVDTLIDNEGLPRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEI 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 479 VTPHNIKEMRQAVINGPnkwPGATHVQNEDQSidvlgDLSIESRIALANSLLapqsshtaqsgnnpfptrtqtINKKVFR 558
Cdd:smart00663 147 VTPLNIDKLRKLVRNGP---NGAKYIIRGKKT-----NLKLAKKSKIANHLK---------------------IGDIVER 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 559 HLRNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDNQYLV 638
Cdd:smart00663 198 HVIDGDVVLFNRQPTLHRMSIQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILS 276
|
330
....*....|...
gi 1954159237 639 PTSGDPLRGLIQD 651
Cdd:smart00663 277 PKNGKPIIGPIQD 289
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
441-632 |
6.71e-79 |
|
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: 257.62 E-value: 6.71e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 441 GKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNEDQSIDVLGDLSIE 520
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 521 SRIALAnsllapqsshtaqsgnnpfptrtqtINKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANC 600
Cdd:pfam00623 81 LDKELE-------------------------IGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG-KTFRLNLSVT 134
|
170 180 190
....*....|....*....|....*....|..
gi 1954159237 601 NTYNADFDGDEMNIHFPQNEIARAEAALIANT 632
Cdd:pfam00623 135 TPYNADFDGDEMNLHVPQSEEARAEAEELMLV 166
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1145-1642 |
3.13e-54 |
|
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: 195.89 E-value: 3.13e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1145 LTKNKFKALMN---LKYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIImTAARKIKTPT 1221
Cdd:cd02584 3 LNKEAFDWILGeieTRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII-NVAKNIKTPS 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1222 M---LLPLCAEtTPKKAAQFCKSASRLTLAQLV-----------DNVIVKEKisaKSSENNYrrsktysirvNMFDEkEY 1287
Cdd:cd02584 82 LtvyLEPGFAK-DEEKAKKIQSRLEHTTLKDVTaateiyydpdpQNTVIEED---KEFVESY----------FEFPD-ED 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1288 NEEYRVSAKRVKEVLattflkDLEELIRRDIK---DTKKIEDISKGqkmdgpqdtneDENMgdntaagYVSDDAedldak 1364
Cdd:cd02584 147 VEQDRLSPWLLRIEL------DRKKMTDKKLSmeqIAKKIKEEFKD-----------DLNV-------IFSDDN------ 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1365 tarksaenkpqasydepdedddvvpeeneksledeeaeFEQAILAGAVDDEEAPKRTSSKGGKIEKQavEKSKYCTKFNf 1444
Cdd:cd02584 197 --------------------------------------AEKLVIRIRIINDDEEKEEDSEDDVFLKK--IESNMLSDMT- 235
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1445 ddANGafceidmeFPADTKKILMVSLIekscaRVVVHEVKGISKCFEYInptendtskrLQTEGVNLRGMWAFSDiIDVN 1524
Cdd:cd02584 236 --LKG--------IEGIRKVFIREENK-----KKVDIETGEFKKREEWV----------LETDGVNLREVLSHPG-VDPT 289
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1525 YIDTNDIAAILNTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIGIG-SNVSPFVKMSFEST 1603
Cdd:cd02584 290 RTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINrQDTGPLMRCSFEET 369
|
490 500 510
....*....|....*....|....*....|....*....
gi 1954159237 1604 CKFLTEATLHGDFDSLDSPSSRIVVGRVVEGGTGSFDVL 1642
Cdd:cd02584 370 VDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLL 408
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1134-1642 |
1.91e-52 |
|
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: 189.00 E-value: 1.91e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1134 ESSKNTARYAGLTKNKFKALMNL---KYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIi 1210
Cdd:cd06528 5 EKLEEVLKEHGLTLSEAEEIIKEvlrEYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEI- 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1211 MTAARKIKTPTMLLPLcaettpkkaaqfcksasrltlaqlvdnvivkekisakssennyrrsktysirvnmfdekeyNEE 1290
Cdd:cd06528 84 VDARKEPSTPTMTIYL-------------------------------------------------------------EEE 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1291 YRVSAKRVKEVLattflkdleelirrdikdtKKIEdiskgqkmdgpqdtnedenmgdntaAGYVSDDAEDLDAKTARKSA 1370
Cdd:cd06528 103 YKYDREKAEEVA-------------------RKIE-------------------------ETTLENLAEDISIDLFNMRI 138
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1371 ENKPqasydepdedddvvpeeNEKSLEDEEAEFEQAIlagavddeeapkrtsskggkiekQAVEKSKYCTKFNFDDANGa 1450
Cdd:cd06528 139 TIEL-----------------DEEMLEDRGITVDDVL-----------------------KAIEKLKKGKVGEEGDVTL- 177
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1451 fceidMEFPADTKKILMVSLIEKSCARVVVHEVKGISKCF------EYInptendtskrLQTEGVNLRGMWAFSDIiDVN 1524
Cdd:cd06528 178 -----IVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIvrkeedEYV----------IYTEGSNLKAVLKVEGV-DPT 241
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1525 YIDTNDIAAILNTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIGI-GSNVSPFVKMSFEST 1603
Cdd:cd06528 242 RTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIaGEKPSVLARAAFEVT 321
|
490 500 510
....*....|....*....|....*....|....*....
gi 1954159237 1604 CKFLTEATLHGDFDSLDSPSSRIVVGRVVEGGTGSFDVL 1642
Cdd:cd06528 322 VKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELT 360
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1157-1642 |
1.57e-49 |
|
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: 180.63 E-value: 1.57e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1157 KYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIImTAARKIKTPTMLLPLcaettpkkaa 1236
Cdd:TIGR02389 35 EYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIV-DARKTPSTPSMTIYL---------- 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1237 qfcksasrltlaqlvdnvivkekisakssennyrrsktysirvnmfdEKEYNEEYRVSAKRVKEVLATtflkdleelirr 1316
Cdd:TIGR02389 104 -----------------------------------------------EDEYEKDREKAEEVAKKIEAT------------ 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1317 dikdtkKIEDISKgqkmdgpqdtnedenmgdntaagyvsDDAEDLDAKTARksaenkpqasydepdedddvvPEENEKSL 1396
Cdd:TIGR02389 125 ------KLEDVAK--------------------------DISIDLADMTVI---------------------IELDEEQL 151
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1397 EDEEAEfeqailagaVDDEEapkrtsskggkiekQAVEKSKYCTKFNFDDANGafcEIDMEFPADTKKILMvsLIEKSCA 1476
Cdd:TIGR02389 152 KERGIT---------VDDVE--------------KAIKKAKLGKVIEIDMDNN---TITIKPGNPSLKELR--KLKEKIK 203
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1477 RVVVHEVKGISKCF------EYInptendtskrLQTEGVNLRGMWAFSDiIDVNYIDTNDIAAILNTYGVEAARNAVIKE 1550
Cdd:TIGR02389 204 NLHIKGIKGIKRVVirkegdEYV----------IYTEGSNLKEVLKLEG-VDKTRTTTNDIHEIAEVLGIEAARNAIIEE 272
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1551 VGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIGI-GSNVSPFVKMSFESTCKFLTEATLHGDFDSLDSPSSRIVVG 1629
Cdd:TIGR02389 273 IKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGIsGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVG 352
|
490
....*....|...
gi 1954159237 1630 RVVEGGTGSFDVL 1642
Cdd:TIGR02389 353 QPIPLGTGDVDLV 365
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
425-1023 |
8.38e-49 |
|
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: 187.61 E-value: 8.38e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 425 RQALEKKEGL--FRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMrqavingpnkwpgat 502
Cdd:cd10506 194 ESAASKKSGLkwMKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERL--------------- 258
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 503 hvqnedQSIDVLGDLSIESRIALANSLLAPQSSHTaqsgnnpfptrTQTINKKVFRHLRNGDMLLLNRQPTLHKPSIMAH 582
Cdd:cd10506 259 ------QEYCDLTLLLKGVIGVRRNGRLVGVRSHN-----------TLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIAL 321
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 583 KARVLPGEKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDNQYLVPTSGDPLRGLIQDNVDSGVWMSSR 662
Cdd:cd10506 322 SVKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTER 401
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 663 DTFFNREEYHQL-LYGSLRPevdgtgdgkirtLPPTILK----PEPLWTGKQVIStiiknltwgkaqlnMTSKSKVAAKF 737
Cdd:cd10506 402 GVFLDKAQMQQLqMLCPSQL------------PPPAIIKsppsNGPLWTGKQLFQ--------------MLLPTDLDYSF 455
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 738 wgpnakDEEKVLIVDGELMHGvMDKSQFGASAFGLVHSIYEIYGPESAGMLLSILSRLFIKFIQSHGFTCRMDDLILTKD 817
Cdd:cd10506 456 ------PSNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSSD 528
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 818 GDKwRRDLLDNgvglgteahlEFLGLAETAQTATPEVLAKEFKLRMNEVIRDDN--------------KLAGLDNAMKAK 883
Cdd:cd10506 529 SYS-RQKMIEE----------ISLGLREAEIACNIKQLLVDSRKDFLSGSGEENdvssdverviyerqKSAALSQASVSA 597
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 884 VNKLTSSItQKCLPDGLVRpfpKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGR---RVPL-----MVSGRSLPSFRP 955
Cdd:cd10506 598 FKQVFRDI-QNLVYKYASK---DNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVKlsyRIPRqlscaAWNSQKSPRVIE 673
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1954159237 956 FDTSARAG-----GFVTGRFLTGIRPQEYYFHCMAGREGlidtAVKTSR--SGYLQRCLMKHLEGLRVHYDHTVR 1023
Cdd:cd10506 674 KDGSECTEsyipyGVVESSFLDGLNPLECFVHSITSRDS----SFSSNAdlPGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1116-1642 |
9.87e-47 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 173.11 E-value: 9.87e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1116 MKEYVEKNPDAMPfEKGSESSKNTARYAGLTKNKFKALMNL---KYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFA 1192
Cdd:PRK04309 7 LEEKLEDASLELP-QKLKEELREKLEERKLTEEEVEEIIEEvvrEYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1193 GYGAANVTLGIPRLREiIMTAARKIKTPTMLLPLcaettpkkaaqfcksasrltlaqlvdnvivkekisakssennyrrs 1272
Cdd:PRK04309 86 GVAEINVTLGLPRLIE-IVDARKEPSTPMMTIYL---------------------------------------------- 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1273 ktysirvnmfdekeyNEEYRVSAKRVKEVLattflkdleelirRDIKDTkKIEDISKgqkmdgpqdtnedenmgdntaag 1352
Cdd:PRK04309 119 ---------------KDEYAYDREKAEEVA-------------RKIEAT-TLENLAK----------------------- 146
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1353 YVSDDAEDLdaktarksaenkpqasydepdeddDVVPEENEKSLEDEEAEFEQaiLAGAVDdeeapkrtSSKGGKIEKQA 1432
Cdd:PRK04309 147 DISVDLANM------------------------TIIIELDEEMLEDRGLTVDD--VKEAIE--------KKKGGEVEIEG 192
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1433 VEkskyctkfnfddangafceidMEFPADTKKILMVSLIEKSCARVVVHEVKGISKCF------EYInptendtskrLQT 1506
Cdd:PRK04309 193 NT---------------------LIISPKEPSYRELRKLAEKIRNIKIKGIKGIKRVIirkegdEYV----------IYT 241
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1507 EGVNLRGMWAFsDIIDVNYIDTNDIAAILNTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRI 1586
Cdd:PRK04309 242 EGSNLKEVLKV-EGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRH 320
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 1954159237 1587 GI-GSNVSPFVKMSFESTCKFLTEATLHGDFDSLDSPSSRIVVGRVVEGGTGSFDVL 1642
Cdd:PRK04309 321 GVsGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELT 377
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1157-1639 |
1.20e-42 |
|
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: 158.54 E-value: 1.20e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1157 KYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIImTAARKIKTPTmllplcaettpkkaa 1236
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEII-NASKNISTPI--------------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1237 qfcksasrltlaqlvdnvivkekISAKsSENNYrrsktysirvnmfDEKeyneeyrvSAKRVKEVLATTFLKDLeelirr 1316
Cdd:cd02736 65 -----------------------ITAK-LENDR-------------DEK--------SARIVKGRIEKTYLGEV------ 93
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1317 dikdTKKIEDIskgqkmdgpqdtnedenmgdntaagYVSDDAE---DLDAKTARKsaenkpqasydepdedddvvpeene 1393
Cdd:cd02736 94 ----ASYIEEV-------------------------YSPDDCYiliKLDKKIIEK------------------------- 119
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1394 KSLEDEEAEFEQAILagavddeeapkrtsskggkiekqavekskyctkfnfddangafceidmefpadtKKILmvsliek 1473
Cdd:cd02736 120 LQLSKSNLYFLLQSL------------------------------------------------------KRKL------- 138
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1474 scARVVVHEVKGISKCFeyINPTENDTSKRLQTEGVNLRGMWAfSDIIDVNYIDTNDIAAILNTYGVEAARNAVIKEVGS 1553
Cdd:cd02736 139 --PDVVVSGIPEVKRAV--INKDKKKGKYKLLVEGYGLRAVMN-TPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQY 213
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1554 VFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIGIGSN-VSPFVKMSFESTCKFLTEATLHGDFDSLDSPSSRIVVGRVV 1632
Cdd:cd02736 214 TMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMkESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPM 293
|
....*..
gi 1954159237 1633 EGGTGSF 1639
Cdd:cd02736 294 PIGTGLF 300
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
397-1332 |
9.81e-41 |
|
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: 164.84 E-value: 9.81e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDSTKNPTQVaQGQNLPP--GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLT 474
Cdd:TIGR02386 281 LQEAVDALFDNGRRGKPV-VGKNNRPlkSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELF 359
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 475 YP-------EPVTPHNIKEMRQAVINGPNK-WpgathvqnedqsiDVLgDLSIESRialansllapqsshtaqsgnnpfP 546
Cdd:TIGR02386 360 KPfiikrliDRELAANIKSAKKMIEQEDPEvW-------------DVL-EDVIKEH-----------------------P 402
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 547 trtqtinkkvfrhlrngdmLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEA 626
Cdd:TIGR02386 403 -------------------VLLNRAPTLHRLGIQAFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEA 462
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 627 ALIANTDNQYLVPTSGDPLRGLIQDNVDSGVWMSSRD--------TFFNREE-----------YHQLLYGSLRPEVDGTG 687
Cdd:TIGR02386 463 RALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKpgakgegkIFSNVDEairaydngkvhLHALIGVRTSGEILETT 542
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 688 DGKI---RTLP---PTILKPEPLwtGKQVISTIIKNLtwgkaqlnmtskskvaakfwgpnakdeekvlivdgelmhgvmd 761
Cdd:TIGR02386 543 VGRVifnEILPegfPYINDNEPL--SKKEISSLIDLL------------------------------------------- 577
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 762 ksqfgasafglvhsiYEIYGPESAGMLLSILSRLFIKFIQSHGFTCRMDDLIltkdgdkwrrdLLDNGVGLGTEAHLEFL 841
Cdd:TIGR02386 578 ---------------YEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIV-----------VPDEKYEILKEADKEVA 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 842 GLaeTAQTATPEVLAKEfklRMNEVIRddnklagldnaMKAKVNKLTSSITQKCLPDGLVRpfpKNDMQMMTVSGAKGSN 921
Cdd:TIGR02386 632 KI--QKFYNKGLITDEE---RYRKVVS-----------IWSETKDKVTDAMMKLLKKDTYK---FNPIFMMADSGARGNI 692
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 922 VNATQISCLLGqqelegrrvpLMV--SGRSLPsfRPFDTSARAGGFVTgrfltgirpqEYYFHCMAGREGLIDTAVKTSR 999
Cdd:TIGR02386 693 SQFRQLAGMRG----------LMAkpSGDIIE--LPIKSSFREGLTVL----------EYFISTHGARKGLADTALKTAD 750
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1000 SGYLQRCLMKhleglrVHYDHTVRDSDgsvlqfhygedsldvikakhinqfsfsahnfealsqkYHPKAALASLEIKQGE 1079
Cdd:TIGR02386 751 SGYLTRRLVD------VAQDVVVREED-------------------------------------CGTEEGIEVEAIVEGK 787
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1080 EYAKKALKKP--GKYdPALSVYNPGTHlGVVSERFALAMKEYVEKNPDAMPFEKGSESSKNTARYAGLTKNKFKalMNLK 1157
Cdd:TIGR02386 788 DEIIESLKDRivGRY-SAEDVYDPDTG-KLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYG--RDLA 863
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1158 YLHsLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAA--NVTLGIPRLREIIMTaarkiktptmllplcaeTTPKKA 1235
Cdd:TIGR02386 864 TGK-LVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGAsgDITQGLPRVKELFEA-----------------RTPKDK 925
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1236 AqfcksasrlTLAQlvdnviVKEKISAKSSENNYRRsktysiRVNMFDEKEYNEEYRVSAKRVKEVLATTFLKDLEELI- 1314
Cdd:TIGR02386 926 A---------VIAE------VDGTVEIIEDIVKNKR------VVVIKDENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTe 984
|
970
....*....|....*....
gi 1954159237 1315 -RRDIKDTKKIEDISKGQK 1332
Cdd:TIGR02386 985 gSIDPHDLLRIKGIQAVQE 1003
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
635-812 |
2.30e-39 |
|
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: 143.92 E-value: 2.30e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 635 QYLVPTSGDPLRGLIQDNVDSGVWMSSRDTFFNREEYHQLLYGslrpevdgtgdgKIRTLPPTILKP-EPLWTGKQVIST 713
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMY------------GIVLPHPAILKPiKPLWTGKQTFSR 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 714 IIKNltwgkaQLNMTSKSKVAAKFWGPNakdEEKVLIVDGELMHGVMDKSQFGASAFGLVHSIYEIYGPESAGMLLSILS 793
Cdd:pfam04983 69 LLPN------EINPKGKPKTNEEDLCEN---DSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQ 139
|
170
....*....|....*....
gi 1954159237 794 RLFIKFIQSHGFTCRMDDL 812
Cdd:pfam04983 140 KLGFRYLTKSGFSIGIDDI 158
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1145-1642 |
1.21e-38 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 152.66 E-value: 1.21e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1145 LTKNKFKALM---NLKYLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIiMTAARKIKTPT 1221
Cdd:PRK14897 158 LSDDEYEEILrriREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEI-VDARKKPSTPT 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1222 MLLPLcaettpkkaaqfcksasrltlaqlvdnvivkekisakssennyrrsktysirvnmfdekeyNEEYRVSAKRVKEV 1301
Cdd:PRK14897 237 MTIYL-------------------------------------------------------------KKDYREDEEKVREV 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1302 LattflKDLEELIRRDIKDTkkIEDISkgqkmdgpqdtnedenmgdntaagyvsddaedldaktarksaenkpqasydep 1381
Cdd:PRK14897 256 A-----KKIENTTLIDVADI--ITDIA----------------------------------------------------- 275
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1382 dedddvvpeeneksledeeaefEQAILAgAVDDEEAPKRtsskggKIEKQAVEKSKYCTKFNFDDANGAfcEIDMEFPAD 1461
Cdd:PRK14897 276 ----------------------EMSVVV-ELDEEKMKER------LIEYDDILAAISKLTFKTVEIDDG--IIRLKPQQP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1462 TKKILMvsLIEKSCARVVVHEVKGISKCfeyINPTENDTSK-RLQTEGVNLRgmwafsDIIDVNYID-----TNDIAAIL 1535
Cdd:PRK14897 325 SFKKLY--LLAEKVKSLTIKGIKGIKRA---IARKENDERRwVIYTQGSNLK------DVLEIDEVDptrtyTNDIIEIA 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1536 NTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIGI-GSNVSPFVKMSFESTCKFLTEATLHG 1614
Cdd:PRK14897 394 TVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGIsGEKSSVLARAAFEITGKHLLRAGILG 473
|
490 500
....*....|....*....|....*...
gi 1954159237 1615 DFDSLDSPSSRIVVGRVVEGGTGSFDVL 1642
Cdd:PRK14897 474 EVDKLAGVAENIIVGQPITLGTGAVSLV 501
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
397-1193 |
1.41e-35 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 148.92 E-value: 1.41e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDSTKNPTQVaQGQNLPP--GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLt 474
Cdd:PRK09603 1688 LQEAVDVLFDNGRSTNAV-KGANKRPlkSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALEL- 1765
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 475 ypepVTPHNIKEMRQAVIngpnkwpgATHVQNEDQSIDvlgdlsiesrialansllapqsshtaQSGNNPFptrtqtink 554
Cdd:PRK09603 1766 ----FKPHLLSKLEERGY--------ATTLKQAKRMIE--------------------------QKSNEVW--------- 1798
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 555 KVFRHLRNGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDN 634
Cdd:PRK09603 1799 ECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDG-KAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSM 1877
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 635 QYLVPTSGDPLRGLIQDNVdSGVWMSSRDTFFNREEYHqlLYGSLRPEVDG--TGDGKIRTLPPTILKPEPLWT--GKQV 710
Cdd:PRK09603 1878 NILLPASGKAVAIPSQDMV-LGLYYLSLEKSGVKGEHK--LFSSVNEIITAidTKELDIHAKIRVLDQGNIIATsaGRMI 1954
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 711 ISTIIKNLtwgkaqlnmtskskVAAKFWgpnakdeekvlivdgelmHGVMDKSQFGAsafgLVHSIYEIYGPESAGMLLS 790
Cdd:PRK09603 1955 IKSILPDF--------------IPTDLW------------------NRPMKKKDIGV----LVDYVHKVGGIGITATFLD 1998
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 791 ILSRLFIKFIQSHGFTCRMDDLILTKDgdkwRRDLLDNGVGLGTEAHLEFLGLAETAQTatpevlakefklRMNEVIrdd 870
Cdd:PRK09603 1999 NLKTLGFRYATKAGISISMEDIITPKD----KQKMVEKAKVEVKKIQQQYDQGLLTDQE------------RYNKII--- 2059
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 871 nklagldNAMKAKVNKLTSSITQKCLPD--GLvrpfpkNDMQMMTVSGAKGSNVNATQISCLLGqqelegrrvpLMVSgr 948
Cdd:PRK09603 2060 -------DTWTEVNDKMSKEMMTAIAKDkeGF------NSIYMMADSGARGSAAQIRQLSAMRG----------LMTK-- 2114
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 949 slPSFRPFDTSaraggfVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKHLEGLRVhydhtVRDSDGS 1028
Cdd:PRK09603 2115 --PDGSIIETP------IISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKV-----VSDDCGT 2181
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1029 vlqfHYGEDSLDVikakhinqfSFSAHNFEALSQKYHPKAALASLeikqgeeyakkalkkpgkYDPALS--VYNPGThlg 1106
Cdd:PRK09603 2182 ----HEGIEITDI---------AVGSELIEPLEERIFGRVLLEDV------------------IDPITNeiLLYADT--- 2227
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1107 VVSERFALAMKE-----YVEKNPDAMPFEKGSessknTARYAGLTKNKFKalmnlkylhsLVEPGEAVGILAAQSVGEPS 1181
Cdd:PRK09603 2228 LIDEEGAKKVVEagiksITIRTPVTCKAPKGV-----CAKCYGLNLGEGK----------MSYPGEAVGVVAAQSIGEPG 2292
|
810
....*....|..
gi 1954159237 1182 TQMTLNTFHFAG 1193
Cdd:PRK09603 2293 TQLTLRTFHVGG 2304
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
397-1226 |
7.95e-32 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 136.15 E-value: 7.95e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDSTKNPTQVAQGQNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTY 475
Cdd:PRK14906 377 LQEAVDSLFDNGRRGRPVTGPGNRPlKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFK 456
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 476 P-------EPVTPHNIKEMRQAVING-PNKWpgathvqnedqsiDVLGDLsIESRialansllapqsshtaqsgnnpfpt 547
Cdd:PRK14906 457 PfvmkrlvELEYAANIKAAKRAVDRGaSYVW-------------DVLEEV-IQDH------------------------- 497
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 548 rtqtinkkvfrhlrngdMLLLNRQPTLHKPSIMAHKArVLPGEKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAA 627
Cdd:PRK14906 498 -----------------PVLLNRAPTLHRLGIQAFEP-VLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEAR 559
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 628 LIANTDNQYLVPTSGDPLRGLIQDNVDSGVWMSS-RDTF------FNREEYHQLLYGSlRPEVDGTGDGKIRtLPPTILK 700
Cdd:PRK14906 560 VLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTeRDGFegegrtFADFDDALNAYDA-RADLDLQAKIVVR-LSRDMTV 637
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 701 PEPLWTGKQVISTIIKNLTWGKAQLNmtskskvaakfwgpnakdeeKVLIVDGELMHGVMDKSQFGAsafgLVHSIYEIY 780
Cdd:PRK14906 638 RGSYGDLEETKAGERIETTVGRIIFN--------------------QVLPEDYPYLNYKMVKKDIGR----LVNDCCNRY 693
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 781 GPESAGMLLSILSRLFIKFIQSHGFTCRMDDLILTKDGDkwrrdlldngvglgteahlEFLGLAETAQTATPEVLAKEFk 860
Cdd:PRK14906 694 STAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKP-------------------EILAEADEKVAAIDEDYEDGF- 753
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 861 lrmnevIRDDNKLAGLDNAMKAKVNKLTSSITqkclpDGLVRpfpKNDMQMMTVSGAKGsnvNATQIscllgqQELEGRR 940
Cdd:PRK14906 754 ------LSERERHKQVVDIWTEATEEVGEAML-----AGFDE---DNPIYMMADSGARG---NIKQI------RQLAGMR 810
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 941 vPLMVSgrslPSFRPFDTSARAGgfvtgrFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKhleglrVHYDH 1020
Cdd:PRK14906 811 -GLMAD----MKGEIIDLPIKAN------FREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVD------VAQDV 873
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1021 TVRDSDgsvlqfhYGEDsldvikakhinqfsfsahnfealsqkyhpkaalasleikQGEEYAkkALKKPGKYDPALSVYN 1100
Cdd:PRK14906 874 IVREED-------CGTD---------------------------------------EGVTYP--LVKPKGDVDTNLIGRC 905
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1101 PGTHLGVVSERFALAMKEYVEKNPDAMPFEKgsesskntaryAGLTKNKFKALMNLKYLHSL--------------VEPG 1166
Cdd:PRK14906 906 LLEDVCDPNGEVLLSAGDYIESMDDLKRLVE-----------AGVTKVQIRTLMTCHAEYGVcqkcygwdlatrrpVNIG 974
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1167 EAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREiiMTAARKIKTPTMLLPL 1226
Cdd:PRK14906 975 TAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAE--LFEARKPKGEAVLAEI 1032
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1526-1638 |
8.52e-32 |
|
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: 122.14 E-value: 8.52e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1526 IDTNDIAAILNTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIG-IGSNVSPFVKMSFESTC 1604
Cdd:cd00630 45 LNAASIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGfRASKTSPLMRASFEKTT 124
|
90 100 110
....*....|....*....|....*....|....
gi 1954159237 1605 KFLTEATLHGDFDSLDSPSSRIVVGRVVEGGTGS 1638
Cdd:cd00630 125 KHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
397-1007 |
1.81e-25 |
|
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: 114.15 E-value: 1.81e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDSTKNPTQVAQGQNLPP-GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTY 475
Cdd:cd01609 204 LQEAVDALIDNGRRGKPVTGANNRPLkSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFK 283
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 476 P-------EPVTPHNIKEMRQAVINGPNK-WpgathvqnedqsiDVLGDLSIESRIalansllapqsshtaqsgnnpfpt 547
Cdd:cd01609 284 PfvireliERGLAPNIKSAKKMIERKDPEvW-------------DILEEVIKGHPV------------------------ 326
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 548 rtqtinkkvfrhlrngdmlLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAA 627
Cdd:cd01609 327 -------------------LLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEAR 386
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 628 LIANTDNQYLVPTSGDPlrgliqdnvdsgVWMSSRDTFFNreeyhqlLYGSLRPEVDGTGDGKIRTlpptilkpeplwtg 707
Cdd:cd01609 387 VLMLSSNNILSPASGKP------------IVTPSQDMVLG-------LYYLTKERKGDKGEGIIET-------------- 433
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 708 kqvistiiknlTWGKAQLNMTskskVAAKFWGPNakdeekvlivdgelmhGVMDKSQFGAsafgLVHSIYEIYGPESAGM 787
Cdd:cd01609 434 -----------TVGRVIFNEI----LPEGLPFIN----------------KTLKKKVLKK----LINECYDRYGLEETAE 478
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 788 LLSILSRLFIKFIQSHGFTCRMDDLILTKDgdkwRRDLLDNgvglgteahleflglaetaqtATPEVlaKEFKLRMNE-V 866
Cdd:cd01609 479 LLDDIKELGFKYATRSGISISIDDIVVPPE----KKEIIKE---------------------AEEKV--KEIEKQYEKgL 531
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 867 IRDDNKlagldnamKAKVNKLTSSIT---QKCLPDGLvRPFPKNDMQMMTVSGAKGSNVNATQISCLLGqqelegrrvpL 943
Cdd:cd01609 532 LTEEER--------YNKVIEIWTEVTekvADAMMKNL-DKDPFNPIYMMADSGARGSKSQIRQLAGMRG----------L 592
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1954159237 944 MVSgrslPSFRPFDTSaraggfVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCL 1007
Cdd:cd01609 593 MAK----PSGKIIELP------IKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL 646
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
397-1438 |
2.62e-24 |
|
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: 111.41 E-value: 2.62e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDSTKNPTQVAQGQNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTY 475
Cdd:COG0086 289 LQEAVDALFDNGRRGRAVTGANKRPlKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFK 368
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 476 P-------EPVTPHNIKEMRQAVingpnkwpgathVQNEDQSIDVLGDLSIESRIalansllapqsshtaqsgnnpfptr 548
Cdd:COG0086 369 PfiyrkleERGLATTIKSAKKMV------------EREEPEVWDILEEVIKEHPV------------------------- 411
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 549 tqtinkkvfrhlrngdmlLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAAL 628
Cdd:COG0086 412 ------------------LLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARL 472
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 629 IANTDNQYLVPTSGDPLRGLIQDNVDSGVWMSsrdtffnreeyhqllygslRPEVDGTGDGKIRTlpptilkpeplwtgk 708
Cdd:COG0086 473 LMLSTNNILSPANGKPIIVPSQDMVLGLYYLT-------------------REREGAKGEGMIFA--------------- 518
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 709 qVISTIIKNLTWGKAQLNmtSKSKVAAKFWGpnaKDEEKV-------LIVDGELMHGV------MDKSQFGAsafgLVHS 775
Cdd:COG0086 519 -DPEEVLRAYENGAVDLH--ARIKVRITEDG---EQVGKIvettvgrYLVNEILPQEVpfynqvINKKHIEV----IIRQ 588
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 776 IYEIYGPESAGMLLSILSRLFIKFIQSHGFTCRMDDLILtkdgDKWRRDLLDngvglgtEAHleflglaetaqtatpevl 855
Cdd:COG0086 589 MYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVV----PKEKQEIFE-------EAN------------------ 639
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 856 akefklrmNEVIR-DDNKLAGLDNAmKAKVNKL------TSSITQKCLPDGLvRPFpkNDMQMMTVSGAKGSnvnATQIs 928
Cdd:COG0086 640 --------KEVKEiEKQYAEGLITE-PERYNKVidgwtkASLETESFLMAAF-SSQ--NTTYMMADSGARGS---ADQL- 703
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 929 cllgqQELEGRRvPLMV--SGR--SLP---SFrpfdtsaRAGgfvtgrflTGIRpqeYYFHCMAG-REGLIDTAVKTSRS 1000
Cdd:COG0086 704 -----RQLAGMR-GLMAkpSGNiiETPigsNF-------REG--------LGVL---EYFISTHGaRKGLADTALKTADS 759
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1001 GYLQRCLmkhlegLRVHYDHTVRDSDgsvlqfhYGEDSLDVIKAkhinqfsfsahnfealsqkyhpkaalasleIKQGEE 1080
Cdd:COG0086 760 GYLTRRL------VDVAQDVIVTEED-------CGTDRGITVTA------------------------------IKEGGE 796
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1081 yAKKALKKP--GKYdPALSVYNPGTHLGVVSERfALAMKEYVEKnpdampfeKGSESSKNTARYAGLTKNKFKALMNLKY 1158
Cdd:COG0086 797 -VIEPLKERilGRV-AAEDVVDPGTGEVLVPAG-TLIDEEVAEI--------IEEAGIDSVKVRSVLTCETRGGVCAKCY 865
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1159 LHSL-----VEPGEAVGILAAQSVGEPSTQMTLNTFH-------FAGYGAANVTLGIPRLREIIMTAARKIKTPTMLLPL 1226
Cdd:COG0086 866 GRDLarghlVNIGEAVGVIAAQSIGEPGTQLTMRTFHiggaasrAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRN 945
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1227 CAETTPKKAAQFCKSASRLTLAQLVDNVIVKEKISAKSSENNYRRSKTYSIRVNMFDEKEYNEEYRVSAKRVKEVLATTF 1306
Cdd:COG0086 946 SELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSI 1025
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1307 LKDLEELIRRDIKDTKKIEDISKGQKMDGPQDTNEDEnmgdnTAAGYVSDDAEDLDAKTARKSAENKPQASYDEPDEDDD 1386
Cdd:COG0086 1026 VVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAA-----AAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDG 1100
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|..
gi 1954159237 1387 VVPEENEKSLEDEEAEFEQAILAGAVDDEEAPKRTSSKGGKIEKQAVEKSKY 1438
Cdd:COG0086 1101 TGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIE 1152
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
878-966 |
2.02e-23 |
|
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: 96.66 E-value: 2.02e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 878 NAMKAKVNKLTSSITQKCLPdglvrpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVSGRSLPSFRPFD 957
Cdd:pfam05000 27 NNILNKARDPAGNIASKSLD-------PNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGKRIPFGFSGRTLPHFKKDD 99
|
....*....
gi 1954159237 958 TSARAGGFV 966
Cdd:pfam05000 100 EGPESRGFV 108
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
397-1193 |
2.16e-23 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 108.94 E-value: 2.16e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDSTKNPTQV--AQGQNLPPGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLT 474
Cdd:PRK14844 1731 LQEAVDSLFDNSRRNALVnkAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELF 1810
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 475 YPepvtphnikemrqavingpnkwpgathvqnedqsidvlgdlSIESRIALANslLAPQSSHTAQSGNNPFPTRTQTINK 554
Cdd:PRK14844 1811 KP-----------------------------------------FVYSKLKMYG--MAPTIKFASKLIRAEKPEVWDMLEE 1847
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 555 KVFRHlrngdMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDN 634
Cdd:PRK14844 1848 VIKEH-----PVLLNRAPTLHRLGIQAFEPILIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTN 1921
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 635 QYLVPTSGDPLRGLIQDNVDSGVWMssrdTFFNREEYHQLLYGSLRPEVDGTGDGKIRTLPPTILKPEPLWTGKQVISTI 714
Cdd:PRK14844 1922 NVLSPSNGRPIIVPSKDIVLGIYYL----TLQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSSGETHYKT 1997
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 715 IKNlTWGKAQLnmtskskvaakfWGPNAKDEEkvliVDGELMHGVMDKSQFGasafGLVHSIYEIYGPESAGMLLSILSR 794
Cdd:PRK14844 1998 ICT-TPGRLIL------------WQIFPKHEN----LGFDLINQVLTVKEIT----SIVDLVYRNCGQSATVAFSDKLMV 2056
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 795 LFIKFIQSHGFTCRMDDLILTKDgdkwRRDLLDNGVGLGTEAHLEFL-GLAETAQtatpevlakefklRMNEVIRDDNKL 873
Cdd:PRK14844 2057 LGFEYATFSGVSFSRCDMVIPET----KATHVDHARGEIKKFSMQYQdGLITRSE-------------RYNKVIDEWSKC 2119
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 874 AGLdnamkaKVNKLTSSITqkcLPDGLVRpfpKNDMQMMTVSGAKGSNVNATQISCLLGqqelegrrvpLMVSgrslPSF 953
Cdd:PRK14844 2120 TDM------IANDMLKAIS---IYDGNSK---YNSVYMMVNSGARGSTSQMKQLAGMRG----------LMTK----PSG 2173
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 954 RPFDTSaraggfVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMkhleglrvhydhtvrdsdgsvlqfh 1033
Cdd:PRK14844 2174 EIIETP------IISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLV------------------------- 2222
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1034 ygEDSLDVIKAKHinqfSFSAHNFEALSQKYHPKAALASLEikqgeeyaKKALKKPGKYDpalsVYNPgthlgvVSERFA 1113
Cdd:PRK14844 2223 --DVSQNCIVTKH----DCKTKNGLVVRATVEGSTIVASLE--------SVVLGRTAAND----IYNP------VTKELL 2278
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1114 LAMKEYVEknpdampfekgsESSKNTARYAGLTKNKFKA---------LMNLKYLHSL-----VEPGEAVGILAAQSVGE 1179
Cdd:PRK14844 2279 VKAGELID------------EDKVKQINIAGLDVVKIRSpltceispgVCSLCYGRDLatgkiVSIGEAVGVIAAQSVGE 2346
|
810
....*....|....
gi 1954159237 1180 PSTQMTLNTFHFAG 1193
Cdd:PRK14844 2347 PGTQLTMRTFHIGG 2360
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1478-1641 |
3.84e-22 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 103.82 E-value: 3.84e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1478 VVVHEVKGISKCFEYINPTENDTSKRLQTEGVNLRGMWAFsDIIDVNYIDTNDIAAILNTYGVEAARNAVIKEVGSVFAV 1557
Cdd:PRK14898 683 IVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKI-EGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQ 761
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1558 YGIKVDRRHLTLIADYMTFEGGYKPFSRIGI-GSNVSPFVKMSFESTCKFLTEATLHGDFDSLDSPSSRIVVGRVVEGGT 1636
Cdd:PRK14898 762 QGLEVDIRHLMLVADIMTADGEVKPIGRHGVaGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGT 841
|
....*
gi 1954159237 1637 GSFDV 1641
Cdd:PRK14898 842 GCVDL 846
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
396-644 |
5.72e-22 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 103.06 E-value: 5.72e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 396 NLQHAVNSFIDSTKNPTQVAQGQNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLT 474
Cdd:CHL00018 327 LLQEAVDALLDNGIRGQPMRDGHNKPyKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELF 406
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 475 YPepvtphnikemrqAVINGpnkwpgathvqnedqsidvlgdlSIESRiaLANSLLApqsshtAQS---GNNPfptrtqt 551
Cdd:CHL00018 407 QP-------------FVIRG-----------------------LIRQH--LASNIRA------AKSkirEKEP------- 435
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 552 INKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKArVLPGEKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIAN 631
Cdd:CHL00018 436 IVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQP-ILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMF 514
|
250
....*....|...
gi 1954159237 632 TDNQYLVPTSGDP 644
Cdd:CHL00018 515 SHMNLLSPAIGDP 527
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1166-1213 |
2.58e-21 |
|
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: 92.10 E-value: 2.58e-21
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1954159237 1166 GEAVGILAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIIMTA 1213
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
397-653 |
3.32e-21 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 100.21 E-value: 3.32e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 397 LQHAVNSFIDSTKNPTQVAQGQNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTy 475
Cdd:PRK02625 307 LQEAVDALIDNGRRGRTVVGANNRPlKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELF- 385
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 476 pEPVTPHNIkeMRQAVINgpNKWPGATHVQNEDQSI-DVLGDLsIEsrialansllapqsshtaqsgnnpfptrtqtink 554
Cdd:PRK02625 386 -QPFVIHRL--IRQGIVN--NIKAAKKLIQRADPEVwQVLEEV-IE---------------------------------- 425
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 555 kvfrhlrnGDMLLLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAALIANTDN 634
Cdd:PRK02625 426 --------GHPVLLNRAPTLHRLGIQAFEPILVEG-RAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASN 496
|
250
....*....|....*....
gi 1954159237 635 QYLVPTSGDPLRGLIQDNV 653
Cdd:PRK02625 497 NILSPATGEPIVTPSQDMV 515
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
10-436 |
1.11e-18 |
|
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: 88.89 E-value: 1.11e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 10 EVDYVSFSFYEPSEIRKISVKQIVNPVLFDALGH-PTKGGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYN 88
Cdd:pfam04997 3 KIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLkPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 89 PMFFDNLYALLRSKCVYChqfriSRalmkkytaqltllqhglinqaqsldeIVLDfkkaneakedetledrmeESSLSLS 168
Cdd:pfam04997 83 IGFFKKTLKILECVCKYC-----SK--------------------------LLLD------------------PGKPKLF 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 169 TAEEYIDYVDNFMKDALAdeearkyaaqdykvtvINDVRKNVMRdfMKHCihSKKCGNCHGISPPVRRDGAAklFQLALN 248
Cdd:pfam04997 114 NKDKKRLGLENLKMGAKA----------------ILELCKKKDL--CEHC--GGKNGVCGSQQPVSRKEGLK--LKAAIK 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 249 KKDQAVMDRMkestgsfgeikgfingqrfLTPYEVRKdvqaLFEK--EGEVTTLLFGARDPRVPSFIkkatyhmffIEVL 326
Cdd:pfam04997 172 KSKEEEEKEI-------------------LNPEKVLK----IFKRisDEDVEILGFNPSGSRPEWMI---------LTVL 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 327 AVAPTRFRPPSVMGDKTF-ESPQNELLSAILKGSHLVRDFsEELQAASeeepvdkkkvevtrNRFVDSIINLQHAVNSFI 405
Cdd:pfam04997 220 PVPPPCIRPSVQLDGGRRaEDDLTHKLRDIIKRNNRLKKL-LELGAPS--------------HIIREEWRLLQEHVATLF 284
|
410 420 430
....*....|....*....|....*....|...
gi 1954159237 406 DSTKNPTQVAQGQNLPP--GIRQALEKKEGLFR 436
Cdd:pfam04997 285 DNEIPGLPPALQKSKRPlkSISQRLKGKEGRFR 317
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
21-99 |
3.01e-16 |
|
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: 84.02 E-value: 3.01e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 21 PSEIRKISVKQIVNPVLFDALGHPTK-GGLYDPSLGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFDNLYALL 99
Cdd:cd00399 3 PEEIRKWSVAKVIKPETIDNRTLKAErGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPSFL 82
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
567-1287 |
1.26e-15 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 83.19 E-value: 1.26e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 567 LLNRQPTLHKPSIMAHKARVLPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEA-ALIANTDNqYLVPTSGDPL 645
Cdd:PRK00566 412 LLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEArVLMLSSNN-ILSPANGKPI 489
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 646 rglI---QDNVdSGVWMSSRD---------TFFNREE---YHQLLYGSLRPEVdgtgdgKIRTlpptilkpeplwTGKQV 710
Cdd:PRK00566 490 ---IvpsQDMV-LGLYYLTREregakgegmVFSSPEEalrAYENGEVDLHARI------KVRI------------TSKKL 547
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 711 ISTiiknlTWGKAQLNmtskskvaakfwgpNAKDEEKVLIVDGElmhgVMDKSQFGAsafgLVHSIYEIYGPESAGMLLS 790
Cdd:PRK00566 548 VET-----TVGRVIFN--------------EILPEGLPFINVNK----PLKKKEISK----IINEVYRRYGLKETVIFLD 600
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 791 ILSRLFIKFIQSHGFTCRMDDLILTKDgdkwRRDLLDngvglgtEAHleflglAETAQtatpevLAKEFKL-------RM 863
Cdd:PRK00566 601 KIKDLGFKYATRSGISIGIDDIVIPPE----KKEIIE-------EAE------KEVAE------IEKQYRRglitdgeRY 657
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 864 NEVI----RDDNKLAgldNAMKAKVNKltssitqkclpdglvRPFPKNDMQMMTVSGAKGsnvNATQISCLLGqqeLEGr 939
Cdd:PRK00566 658 NKVIdiwsKATDEVA---KAMMKNLSK---------------DQESFNPIYMMADSGARG---SASQIRQLAG---MRG- 712
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 940 rvpLMV--SGRSLPsfRPFDTSARAGgfvtgrfLTGIrpqEYYF--HcmaG-REGLIDTAVKTSRSGYLQRCLMKhlegl 1014
Cdd:PRK00566 713 ---LMAkpSGEIIE--TPIKSNFREG-------LTVL---EYFIstH---GaRKGLADTALKTADSGYLTRRLVD----- 769
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1015 rVHYDHTVRDSD-GSvlqfHYGedsldvIKAKHInqfsfsahnfealsqkyhpkaalasleIKQGEEYAK---KALkkpG 1090
Cdd:PRK00566 770 -VAQDVIVREDDcGT----DRG------IEVTAI---------------------------IEGGEVIEPleeRIL---G 808
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1091 KYdPALSVYNPGTHlGVVSERFALAMKEYVEKNPDAmpfekGSESSK-------NTAR------YaGltknkfkalMNLK 1157
Cdd:PRK00566 809 RV-LAEDVVDPETG-EVIVPAGTLIDEEIADKIEEA-----GIEEVKirsvltcETRHgvcakcY-G---------RDLA 871
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1158 yLHSLVEPGEAVGILAAQSVGEPSTQMTLNTFHFagyGAANVTLGIPRLREIImtAARKiktptmllplcaettPKKAAQ 1237
Cdd:PRK00566 872 -TGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHT---GGVDITGGLPRVAELF--EARK---------------PKGPAI 930
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1238 FCKsasrltlaqlVDNVIVKEKIsakssennYRRSKTYSIRVNMFDEKEY 1287
Cdd:PRK00566 931 IAE----------IDGTVSFGKE--------TKGKRRIVITPDDGEEREY 962
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1161-1217 |
2.43e-14 |
|
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: 73.72 E-value: 2.43e-14
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1954159237 1161 SLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYgAANVTLGIPRLREIImtAARKI 1217
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEELF--EARKI 54
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|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
892-1199 |
1.57e-13 |
|
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: 76.04 E-value: 1.57e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 892 TQKCLPDGLVRPF----PKNDMQMMTVSGAKGsnvNATQISCLLGQQEL----EGRRVPLmvsgrslpsfrPFDTSARAG 963
Cdd:TIGR02388 100 TNEELKDEVVNNFrqtdPLNSVYMMAFSGARG---NMSQVRQLVGMRGLmanpQGEIIDL-----------PIKTNFREG 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 964 GFVTgrfltgirpqEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKhleglrVHYDHTVRDSDGSVlqfhygEDSLDVIK 1043
Cdd:TIGR02388 166 LTVT----------EYVISSYGARKGLVDTALRTADSGYLTRRLVD------VSQDVIVREEDCGT------ERSIVVRA 223
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170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1044 AKHINQ-FSFSAHNFEALSQK--YHPkaalasleikQGEEYAKKAlkkpGKYDPALSvynpgthlgvvSERFALAMKEYV 1120
Cdd:TIGR02388 224 MTEGDKkISLGDRLLGRLVAEdvLHP----------EGEVIVPKN----TAIDPDLA-----------KTIETAGISEVV 278
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1121 EKNPDAmpfekgSESSKNTARYA---GLTKNKfkalmnlkylhsLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAGYGAA 1197
Cdd:TIGR02388 279 VRSPLT------CEAARSVCRKCygwSLAHAH------------LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTG 340
|
..
gi 1954159237 1198 NV 1199
Cdd:TIGR02388 341 EV 342
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
896-1193 |
1.33e-11 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 70.02 E-value: 1.33e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 896 LPDGLVRPFPKND----MQMMTVSGAKGsnvNATQISCLLGQQEL----EGRRVPLmvsgrslpsfrPFDTSARAGGFVT 967
Cdd:PRK02597 105 LKDEVVKNFRQNDplnsVYMMAFSGARG---NMSQVRQLVGMRGLmanpQGEIIDL-----------PIKTNFREGLTVT 170
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 968 grfltgirpqEYYFHCMAGREGLIDTAVKTSRSGYLQRCLMKhleglrVHYDHTVRDSD-----GSVLQfhyGEDSLDVI 1042
Cdd:PRK02597 171 ----------EYVISSYGARKGLVDTALRTADSGYLTRRLVD------VSQDVIVREEDcgttrGIVVE---AMDDGDRV 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1043 KAKhinqfsfsahnfeaLSQKYHPKAALASLEIKQGEEYAKKAlkkpGKYDPALSvynpgthlgvvsERFALAMKEYVE- 1121
Cdd:PRK02597 232 LIP--------------LGDRLLGRVLAEDVVDPEGEVIAERN----TAIDPDLA------------KKIEKAGVEEVMv 281
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250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1954159237 1122 KNPDAmpfekgSESSKNTARYA---GLTKNKfkalmnlkylhsLVEPGEAVGILAAQSVGEPSTQMTLNTFHFAG 1193
Cdd:PRK02597 282 RSPLT------CEAARSVCRKCygwSLAHNH------------LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGG 338
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|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1161-1190 |
2.44e-10 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 65.73 E-value: 2.44e-10
10 20 30
....*....|....*....|....*....|
gi 1954159237 1161 SLVEPGEAVGILAAQSVGEPSTQMTLNTFH 1190
Cdd:CHL00117 310 DLVELGEAVGIIAGQSIGEPGTQLTLRTFH 339
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1523-1642 |
3.80e-10 |
|
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: 63.98 E-value: 3.80e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954159237 1523 VNYIDT-----NDIAAILNTYGVEAARNAVIKEVGSVFAVYGIKVDRRHLTLIADYMTFEGGYKPFSRIGIG------SN 1591
Cdd:cd02737 249 MDLIDWersmpYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKaqrrslKI 328
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 1954159237 1592 VSPFVKMSFESTCKFLTEATLHGDFDSLDSPSSRIVVGRVVEGGTGS-FDVL 1642
Cdd:cd02737 329 SAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSkFEIL 380
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1157-1186 |
1.39e-06 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 53.36 E-value: 1.39e-06
10 20 30
....*....|....*....|....*....|
gi 1954159237 1157 KYLHSLVEPGEAVGILAAQSVGEPSTQMTL 1186
Cdd:PRK14898 48 AYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
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