|
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 ... |
15-1018 |
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: 1357.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 15 SFSFYEPSEIRKISVKQIFNPILFDALGHPTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFDN 94
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 95 LYAILRAKCIYCHQFRISRALMKKYSAQLTLLQHGLVNEAQSLNelvldfkkteakddetledrmeeqalslstvedyie 174
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKLKLLDKGLLVEAAELD------------------------------------ 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 175 hidtfmknaladeesrkyaakdykvtvinevrksvmrdfmkqcihskkcancsgisppirrdgaaklfqlalnkkdqaam 254
Cdd:cd01435 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 255 drlnnqtgsfeeikgftngqrfltpyevrkhvqalfekegdittllfgardprvpsfikkATYHMFFIEVLAVAPTRFRP 334
Cdd:cd01435 125 ------------------------------------------------------------FGYDMFFLDVLLVPPNRFRP 144
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 335 PSVMGDKTFESPQNELLSNILKGSHLVRDLSEELQAISDQEPVDKKKLEATRNRFVDSIIGLQHAVNSFIDSTKNPTQva 414
Cdd:cd01435 145 PSFLGDKVFENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLISGKTNSEKLINAWLQLQSAVNELFDSTKAPKS-- 222
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 415 qGKNLPPGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMRQAVINGP 494
Cdd:cd01435 223 -GKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINGP 301
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 495 NKWPGATHVQNEDQSIDVLGDLSIESRIALANSLLAPqsshtaqsgnnPYPTRTQTINKKVFRHLRNGDMLLLNRQPTLH 574
Cdd:cd01435 302 DVYPGANAIEDEDGRLILLSALSEERRKALAKLLLLL-----------SSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLH 370
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 575 KPSIMAHKARILPGEKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDNQYLVPTSGNPLRGLIQDNVDS 654
Cdd:cd01435 371 KPSIMAHKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVS 450
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 655 GVWMSSRDTFFTKEEYQQLLYGSLRPETDGTGGGKIRMLPPAIMKPQPLWTGKQVISTILKNLTWGKAQ-LNMTSKSKVP 733
Cdd:cd01435 451 GVLLTSRDTFFTREEYQQLVYAALRPLFTSDKDGRIKLLPPAILKPKPLWTGKQVISTILKNLIPGNAPlLNLSGKKKTK 530
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 734 AK---FWGPNAKEEDKVLVMDGELIHGIMDKSQFGASAFGLVHSVYEIYSPEAAGMLLSILSRLFIKFLQSHGFTCRMDD 810
Cdd:cd01435 531 KKvggGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIED 610
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 811 LVLTKEGDQWRRELLDQGVGLGDEAHLEFLGLadtaktaspevlskefklrmnevirddnklagldnamkaKVNKLTSSI 890
Cdd:cd01435 611 LLLTPKADEKRRKILRKAKKLGLEAAAEFLGL---------------------------------------KLNKVTSSI 651
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 891 TQKCLPDGLIRPFPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVSGRSLPSFRPFDTSARAGGFVTGRFL 970
Cdd:cd01435 652 IKACLPKGLLKPFPENNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFL 731
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*...
gi 1954185479 971 TGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVHYD 1018
Cdd:cd01435 732 TGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
10-1045 |
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: 588.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 10 EVDYVSFSFYEPSEIRKISVKQIFNPILFDALGHPTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNP 89
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 90 MFFDNLYAILRAKCIYCHqfrisRALMKkysaqltllqhglvneaqslnelvldfkkteakddetledrmEEQalslstv 169
Cdd:cd02582 83 GFAKHIYDLLRATCRSCG-----RILLP------------------------------------------EEE------- 108
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 170 edyiehIDTFMKNALADEESRKYAAKdykvTVINEVRKSVMRdfmkqcihSKKCANCSGISPPIRrdgaaklfqlalnkk 249
Cdd:cd02582 109 ------IEKYLERIRRLKEKWPELVK----RVIEKVKKKAKK--------RKVCPHCGAPQYKIK--------------- 155
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 250 dqaamdrLNNQTGSFEEIKGftnGQRFLTPYEVRkhvqALFEKEGDITTLLFGArDPrvpsfiKKATYHMFFIEVLAVAP 329
Cdd:cd02582 156 -------LEKPTTFYEEKEE---GEVKLTPSEIR----ERLEKIPDEDLELLGI-DP------KTARPEWMVLTVLPVPP 214
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 330 TRFRPpSVmgdkTFESPQ---NEL---LSNILKGShlvRDLSEELQAISDQepvdkkkleatrnrfvdSIIG-----LQH 398
Cdd:cd02582 215 VTVRP-SI----TLETGErseDDLthkLVDIIRIN---QRLKENIEAGAPQ-----------------LIIEdlwdlLQY 269
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 399 AVNSFIDSTKNPTQVAQ---GKNLPpGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYP 475
Cdd:cd02582 270 HVTTYFDNEIPGIPPARhrsGRPLK-TLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVP 348
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 476 EPVTPHNIKEMRQAVINGPNKWPGATHVQNEDQS-IDvlgdLSIESRIALANSLlapqsshtaqsgnnpyptrtqTINKK 554
Cdd:cd02582 349 ERVTEWNIEKMRKLVLNGPDKWPGANYVIRPDGRrIR----LRYVNREELAERL---------------------EPGWI 403
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 555 VFRHLRNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDNQ 634
Cdd:cd02582 404 VERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEH 482
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 635 YLVPTSGNPLRGLIQDNVDSGVWMSSRDTFFTKEEYQQLLygslrpetdGTGGGKIRMLPPAIMKPQPLWTGKQVISTIL 714
Cdd:cd02582 483 ILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLL---------SAAGYDGLLPEPAILEPKPLWTGKQLFSLFL 553
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 715 KNltwgkaQLNMTSKSKV---PAKFWGPNAKEEDKVLVMDGELIHGIMDKSQFGASAFG-LVHSVYEIYSPEAAGMLLSI 790
Cdd:cd02582 554 PK------DLNFEGKAKVcsgCSECKDEDCPNDGYVVIKNGKLLEGVIDKKAIGAEQPGsLLHRIAKEYGNEVARRFLDS 627
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 791 LSRLFIKFLQSHGFTCRMDDLVLTKEGDQWRRELLdqgvglgDEAHLEFLGLADTAKTASPEVL-------SKEFKL--R 861
Cdd:cd02582 628 VTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEII-------KEAEKKVYELIEQYKNGELEPLpgrtleeTLEMKImqV 700
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 862 MNEViRDDnklagldnamkakvnklTSSITQKCLPdglirpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVP 941
Cdd:cd02582 701 LGKA-RDE-----------------AGKVASKYLD-------PFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERIN 755
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 942 LMVSGRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVHYDHTV 1021
Cdd:cd02582 756 RGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTV 835
|
1050 1060
....*....|....*....|....
gi 1954185479 1022 RDSDGSVLQFHYGEDSLDVIKAKH 1045
Cdd:cd02582 836 RDSRGNIIQFKYGEDGVDPAKSDH 859
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
10-1045 |
2.51e-180 |
|
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: 563.57 E-value: 2.51e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 10 EVDYVSFSFYEPSEIRKISVKQIFNPILFDALGHPTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNP 89
Cdd:TIGR02390 3 KIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 90 MFFDNLYAILRAKCIYChqfriSRALMKKysaqltllqhglvneaqslnelvldfkkteakddetledrmeeqalslstv 169
Cdd:TIGR02390 83 GFAKEIYKILRATCRKC-----GRITLTE--------------------------------------------------- 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 170 edyiEHIDTFMKNALADEESRKYAAKdykvTVINEVRKSVMRdfmkqcihSKKCANCSgisppirrdgaAKLFQLALNKK 249
Cdd:TIGR02390 107 ----EEIEQYLEKINKLKEEGGDLAS----TLIEKIVKEAAK--------RMKCPHCG-----------EEQKKIKFEKP 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 250 dqaamdrlnnqtGSFEEIKgfTNGQRFLTPYEVRKHvqalFEKEGDITTLLFGArDPRV--PSFIkkatyhmfFIEVLAV 327
Cdd:TIGR02390 160 ------------TYFYEEG--KEGDVKLTPSEIRER----LEKIPDEDAELLGI-NPKVarPEWM--------VLTVLPV 212
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 328 APTRFRpPSVmgdkTFESpqnellsnilkGSHLVRDLSEELQAISDQepvdKKKLEATRNRFVDSII------GLQHAVN 401
Cdd:TIGR02390 213 PPVTVR-PSI----TLET-----------GERSEDDLTHKLVDIIRI----NQRLKENIEAGAPQLIiedlweLLQYHVA 272
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 402 SFIDSTKNPTQVAQGKNLPP--GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVT 479
Cdd:TIGR02390 273 TYFDNELPGIPPARHRSGRPlkTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVT 352
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 480 PHNIKEMRQAVINGPNKWPGATHVQNED-QSIdvlgDLSIESRIALANSLlapqsshtaqsgnnpyptrtqTINKKVFRH 558
Cdd:TIGR02390 353 PWNIDELREYVLNGPDSWPGANYVIRPDgRRI----KIRDENKEELAERL---------------------EPGWVVERH 407
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 559 LRNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDNQYLVP 638
Cdd:TIGR02390 408 LIDGDIVLFNRQPSLHRMSMMGHKVKVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTP 486
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 639 TSGNPLRGLIQDNVDSGVWMSSRDTFFTKEEYQQLLYGSLRPETDGtgggkirmlPPAIMKPQPLWTGKQVISTILKNlt 718
Cdd:TIGR02390 487 RYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPP---------EPAIEKPKEYWTGKQIFSAFLPE-- 555
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 719 wgkaQLNMTSKSKVPAKFWGPNAKE---EDKVLVMDGELIHGIMDKSQFGASAFGLVHSVYEIYSPEAAGMLLSILSRLF 795
Cdd:TIGR02390 556 ----DLNFEGRAKICSGSDACKKEEcphDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLF 631
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 796 IKFLQSHGFTCRMDDLVLTKEGDQWRRELLDQGVGLGDE-------AHLEFL---GLADTAKTASPEVLSKefklrmnev 865
Cdd:TIGR02390 632 IRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNlieryrnGELEPLpgrTVEETLEMKIMEVLGK--------- 702
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 866 IRDDnklagldnamkakvnklTSSITQKCLPdglirpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVS 945
Cdd:TIGR02390 703 ARDE-----------------AGEVAEKYLD-------PENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYR 758
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 946 GRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVHYDHTVRDSD 1025
Cdd:TIGR02390 759 NRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTR 838
|
1050 1060
....*....|....*....|
gi 1954185479 1026 GSVLQFHYGEDSLDVIKAKH 1045
Cdd:TIGR02390 839 GNLIQFKYGEDGVDPMKSDH 858
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
11-1641 |
3.84e-178 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 571.97 E-value: 3.84e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 11 VDYVSFSFYEPSEIRKISVKQIFNPILFDALGHPTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPM 90
Cdd:PRK14977 9 IDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPVIHIA 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 91 FFDNLYAILRAKCIYChqfrisralmkkysAQLTLLQhglvneaQSLNELVLDFKKTEAKDDETlEDRMEEQalslstve 170
Cdd:PRK14977 89 FIDNIKDLLNSTCHKC--------------AKLKLPQ-------EDLNVFKLIEEAHAAARDIP-EKRIDDE-------- 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 171 dyiehidtfmknaladeesrkyaakdykvtVINEVRKSVMRDFMKqcihSKKCANCsgisppirrdgAAKLFQLALNKkd 250
Cdd:PRK14977 139 ------------------------------IIEEVRDQVKVYAKK----AKECPHC-----------GAPQHELEFEE-- 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 251 qaamdrlnnqtgSFEEIKGFTNGQRFLTPYEVRKhvqaLFEKEGDITTLLFGArDPrvpsfiKKATYHMFFIEVLAVAPT 330
Cdd:PRK14977 172 ------------PTIFIEKTEIEEHRLLPIEIRD----IFEKIIDDDLELIGF-DP------KKARPEWAVLQAFLVPPL 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 331 RFRPPSVMgdKTFESPQNELlsnilkgSHLVRDLSEelqaiSDQEPVDKKKLEATRNRFVDSIIGLQHAVNSFIDSTKN- 409
Cdd:PRK14977 229 TARPSIIL--ETGERSEDDL-------THILVDIIK-----ANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAg 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 410 -PTQVAQGKNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMR 487
Cdd:PRK14977 295 iPQAHHKGSGRPlKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMK 374
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 488 QAVINGPNKWPGATHVQNEDQ---SIDVLGDLSIESRIALANSLlapqsshtaqsgnnpyptrtqTINKKVFRHLRNGDM 564
Cdd:PRK14977 375 ELVINGPDEFPGANAIRKGDGtkiRLDFLEDKGKDALREAAEQL---------------------EIGDIVERHLADGDI 433
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 565 LLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDNQYLVPTSGNPL 644
Cdd:PRK14977 434 VIFNRQPSLHKLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPI 512
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 645 RGLIQDNVDSGVWMSSRDTFFTKEEYQQLLygslrpetdgTGGGKIRMLP-PAI-MKPQPLWTGKQVISTIL-KNLTW-G 720
Cdd:PRK14977 513 IGALQDFITAAYLITKDDALFDKNEASNIA----------MLAGITDPLPePAIkTKDGPAWTGKQLFSLFLpKDFNFeG 582
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 721 KAQLNMTSKSKvpAKfwGPNAKEEDKVLVMDGELIHGIMDKSQFGASAFG---LVHSVYEIYSPEAAGMLLSILSRLFIK 797
Cdd:PRK14977 583 IAKWSAGKAGE--AK--DPSCLGDGYVLIKEGELISGVIDDNIIGALVEEpesLIDRIAKDYGEAVAIEFLNKILIIAKK 658
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 798 FLQSHGFTCRMDDLVLTKEGdqwRRELLDQGVGLGDEAHleflGLADTAKTASPEVLSKEfKLRMNEVIRDDNKL-AGLD 876
Cdd:PRK14977 659 EILHYGFSNGPGDLIIPDEA---KQEIEDDIQGMKDEVS----DLIDQRKITRKITIYKG-KEELLRGMKEEEALeADIV 730
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 877 NAMKAKVNKLTSSITqKCLPdglirpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVSGR--------S 948
Cdd:PRK14977 731 NELDKARDKAGSSAN-DCID-------ADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRlhegykdrA 802
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 949 LPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVHYDHTVRDSDGSV 1028
Cdd:PRK14977 803 LSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHI 882
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1029 LQFHYGEDSLDVIKAKHINQFsfsahNFEALSQKYHPKAALASLEIKQGEEYAKKALKkpgkydpalsVYNPgthlgvvs 1108
Cdd:PRK14977 883 IQFKFGEDGIDPQKLDHGEAF-----NLERIIEKQKIEDRGKGASKDEIEELAKEYTK----------TFNA-------- 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1109 eRFALAMKDYIQknpdgmpfekDSQLSKNTARyagltknKFKALMNLKYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTF 1188
Cdd:PRK14977 940 -NLPKLLADAIH----------GAELKEDELE-------AICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTF 1001
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1189 HFAGYGAANVTLGIPRLREIImTAARKIKTPTMLLPLlpetsakkasqfcksasrltlaqlvdnvvvrektsaktaDNNY 1268
Cdd:PRK14977 1002 HAAGIKAMDVTHGLERFIELV-DARAKPSTPTMDIYL---------------------------------------DDEC 1041
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1269 KRSKTYSIRVnlfeekeyneeyrvsAKRVKEVLATAFLKDleelirkdikdtkkiediskahkmdapgdedanedlgdaa 1348
Cdd:PRK14977 1042 KEDIEKAIEI---------------ARNLKELKVRALIAD---------------------------------------- 1066
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1349 akdgYASDDAedmdakTARKSaqnkpqasydepdeddIVPednEKSLEDEEEEFEQAILagaddeeEVpKRPSSKGGKLE 1428
Cdd:PRK14977 1067 ----SAIDNA------NEIKL----------------IKP---DKRALENGCIPMERFA-------EI-EAALAKGKKFE 1109
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1429 EQAvqkskyctrfkfddnNGAFCEIDMEFPADTKKIL-MISLIEKSCARVVVHEVKGISKcfEYINPTENDTSKR--LQT 1505
Cdd:PRK14977 1110 MEL---------------EDDLIILDLVEAADRDKPLaTLIAIRNKILDKPVKGVPDIER--AWVELVEKDGRDEwiIQT 1172
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1506 EGVNLRGMWAFSDiIDVNYIDTNDIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEG------GY 1579
Cdd:PRK14977 1173 SGSNLAAVLEMKC-IDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGtieaigLQ 1251
|
1610 1620 1630 1640 1650 1660
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954185479 1580 KPFSRIGIGSNV-APFLKMSFESTCKFLTEATLHGDFDTLDSPSSRIVVGRVVEGGTGSFDVL 1641
Cdd:PRK14977 1252 AAGVRHGFAGEKdSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLL 1314
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
14-1045 |
5.60e-177 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 555.24 E-value: 5.60e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 14 VSFSFYEPSEIRKISVKQIFNPILFDALGHPTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFD 93
Cdd:PRK08566 12 IKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIHVGFAK 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 94 NLYAILRAKCIYChqfriSRALMKkysaqltllqhglvneaqslnelvldfkkteakDDEtledrmeeqalslstVEDYI 173
Cdd:PRK08566 92 LIYKLLRATCREC-----GRLKLT---------------------------------EEE---------------IEEYL 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 174 EHIDtfmknalaDEESRKYAAKDykvtVINEVRKsvmrdfmkQCIHSKKCANCSGISPPIRRDgaaKLFqlalnkkdqaa 253
Cdd:PRK08566 119 EKLE--------RLKEWGSLADD----LIKEVKK--------EAAKRMVCPHCGEKQYKIKFE---KPT----------- 164
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 254 mdrlnnqtgSFEEIKGftNGQRFLTPYEVRkhvqALFEKEGDITTLLFGArDPRV--PSFikkatyhmFFIEVLAVAPTR 331
Cdd:PRK08566 165 ---------TFYEERK--EGLVKLTPSDIR----ERLEKIPDEDLELLGI-NPEVarPEW--------MVLTVLPVPPVT 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 332 FRPpSVmgdkTFESPQnellsnilkgshlvR---DLSEELqaisdqepVDkkkLEATRNRFVDSIIG------------- 395
Cdd:PRK08566 221 VRP-SI----TLETGQ--------------RsedDLTHKL--------VD---IIRINQRLKENIEAgapqliiedlwel 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVAQ---GKNLPpGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKL 472
Cdd:PRK08566 271 LQYHVTTYFDNEIPGIPPARhrsGRPLK-TLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKEL 349
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 473 TYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNED-QSIDvlgdLSIESRIALANSLlapqsshtaqsgnnpyptrtqTI 551
Cdd:PRK08566 350 TVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDgRRIK----LTDKNKEELAEKL---------------------EP 404
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 552 NKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANT 631
Cdd:PRK08566 405 GWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLV 483
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 632 DNQYLVPTSGNPLRGLIQDNVdSGVWMSSRD-TFFTKEEYQQLLygslrpetdgtGGGKIRMLP---PAIMKPQPLWTGK 707
Cdd:PRK08566 484 QEHILSPRYGGPIIGGIQDHI-SGAYLLTRKsTLFTKEEALDLL-----------RAAGIDELPepePAIENGKPYWTGK 551
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 708 QVISTIL-KNLTW-GKAQLNmtSKSKVPAKFWGPNakeEDKVLVMDGELIHGIMDKSQFGASAFGLVHSVYEIYSPEAAG 785
Cdd:PRK08566 552 QIFSLFLpKDLNLeFKAKIC--SGCDECKKEDCEH---DAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERAR 626
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 786 MLLSILSRLFIKFLQSHGFTCRMDDLVLTKEGDQWRRELLDQGVGLGDE-------AHLEFL---GLADTAKTASPEVLS 855
Cdd:PRK08566 627 RFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEElieayenGELEPLpgrTLEETLEMKIMQVLG 706
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 856 KefklrmnevIRDDnklagldnamkakvnklTSSITQKCLPdglirpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQEL 935
Cdd:PRK08566 707 K---------ARDE-----------------AGEIAEKYLG-------LDNPAVIMARTGARGSMLNLTQMAACVGQQSV 753
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 936 EGRRVPLMVSGRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRV 1015
Cdd:PRK08566 754 RGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKV 833
|
1050 1060 1070
....*....|....*....|....*....|
gi 1954185479 1016 HYDHTVRDSDGSVLQFHYGEDSLDVIKAKH 1045
Cdd:PRK08566 834 EYDGTVRDTRGNIVQFKYGEDGVDPMKSDH 863
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
12-1018 |
1.82e-166 |
|
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: 522.48 E-value: 1.82e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 12 DYVSFSFYEPSEIRKISVKQIFNPILFDALGHPTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMF 91
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYENGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 92 FDNLYAILRakCIyChqfrisralmkkysaqltllqhglvneaqslnelvldfkkteakddetledrmeEQALSLSTVED 171
Cdd:cd02733 81 LTKILKILR--CV-C------------------------------------------------------KRELSAERVLE 103
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 172 YIEHIDtfmknalaDEESRkyaakdykvtvinevrksvmrdfmkqcihskkcancsgisppirrdgaaklfqlalnkkdq 251
Cdd:cd02733 104 IFKRIS--------DEDCR------------------------------------------------------------- 114
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 252 aamdrlnnqtgsfeeIKGFtngqrfltpyevrkhvqalfekegdittllfgarDPRV--PSFikkatyhmFFIEVLAVAP 329
Cdd:cd02733 115 ---------------ILGF----------------------------------DPKFsrPDW--------MILTVLPVPP 137
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 330 TRFRPpSVMGDKTFESpQNEL---LSNILK-------------GSHLVRDLSEELQAISdqepvdkkkleATrnrFVD-S 392
Cdd:cd02733 138 PAVRP-SVVMDGSARS-EDDLthkLADIIKannqlkrqeqngaPAHIIEEDEQLLQFHV-----------AT---YMDnE 201
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 393 IIGLQHAVNsfidstKNptqvaqGKNLPPgIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKL 472
Cdd:cd02733 202 IPGLPQATQ------KS------GRPLKS-IRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNL 268
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 473 TYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNEDqsidvlgdlsiESRIALAnslLAPQSShtaqsgnnpyptrTQTIN 552
Cdd:cd02733 269 TFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDD-----------GERIDLR---YLKKAS-------------DLHLQ 321
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 553 K--KVFRHLRNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIAN 630
Cdd:cd02733 322 YgyIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPY-STFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMM 400
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 631 TDNQYLVPTSGNPLRGLIQDNVdSGVW-MSSRDTFFTKEEYQQLLYGSlrPETDGtgggkiRMLPPAIMKPQPLWTGKQV 709
Cdd:cd02733 401 VPRQIVSPQSNKPVMGIVQDTL-LGVRkLTKRDTFLEKDQVMNLLMWL--PDWDG------KIPQPAILKPKPLWTGKQI 471
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 710 ISTILKNLTwgkaqlNMTSKSKVPAKFWGPNAKEEDKVLVMDGELIHGIMDKSQFGASAFGLVHSVYEIYSPEAAGMLLS 789
Cdd:cd02733 472 FSLIIPKIN------NLIRSSSHHDGDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIG 545
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 790 ILSRLFIKFLQSHGFTcrmddlvltkegdqwrrelldqgVGLGDEahleflgLADTAKTASPEVLSKEFKLRMNEVIRD- 868
Cdd:cd02733 546 NIQRVVNNWLLHNGFS-----------------------IGIGDT-------IADKETMKKIQETIKKAKRDVIKLIEKa 595
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 869 -DNKL---AGldNAMK----AKVNKL-------TSSITQKCLPDglirpfpKNDMQMMTVSGAKGSNVNATQISCLLGQQ 933
Cdd:cd02733 596 qNGELepqPG--KTLResfeNKVNRIlnkardkAGKSAQKSLSE-------DNNFKAMVTAGSKGSFINISQIIACVGQQ 666
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 934 ELEGRRVPLMVSGRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGL 1013
Cdd:cd02733 667 NVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDV 746
|
....*
gi 1954185479 1014 RVHYD 1018
Cdd:cd02733 747 MVKYD 751
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
21-1022 |
2.57e-157 |
|
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: 500.15 E-value: 2.57e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 21 PSEIRKISVKQIFNPILFDAL-GHPTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFDNLYAIL 99
Cdd:cd02583 3 PEDIIRLSEVEVTNRNLYDIEtRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIINIL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 100 RAKCIYChqfriSRALMKKysaqltllqhglvneaqslnelvldfkkteaKDDETLEDRMEEQALslstvedyiehidtf 179
Cdd:cd02583 83 QCICKTC-----SRVLLPE-------------------------------EEKRKFLKRLRRPNL--------------- 111
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 180 mknaladeESRKYAAKDYKVTvinevrksvmrdfmKQCIHSKKCANCSgisppirrdgaaklfqlaLNKKDQaamdrlnn 259
Cdd:cd02583 112 --------DNLQKKALKKKIL--------------EKCKKVRKCPHCG------------------LLKKAQ-------- 143
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 260 qtgsfEEikgftngqrfLTPYevrkHVQALFEK--EGDITTLLFGARDPRvPSfikkatyhMFFIEVLAVAPTRFRPpSV 337
Cdd:cd02583 144 -----ED----------LNPL----KVLNLFKNipPEDVELLLMNPLAGR-PE--------NLILTRIPVPPLCIRP-SV 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 338 MGDKTFESpqNEllsnilkgshlvRDLSEELQAISDQEPVDKKKLE--ATRNRFVDS--IIGLQHA--VNSfiDSTKNPT 411
Cdd:cd02583 195 VMDEKSGT--NE------------DDLTVKLSEIIFLNDVIKKHLEkgAKTQKIMEDwdFLQLQCAlyINS--ELPGLPL 258
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 412 QVAQGKNLPpGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMRQAVI 491
Cdd:cd02583 259 SMQPKKPIR-GFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVL 337
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 492 NGPNKWPGATHVQNEDQSidvlgdlsieSRIALANsllapqsshtaqsGNNPYPTRTQTINKKVFRHLRNGDMLLLNRQP 571
Cdd:cd02583 338 NGPDVHPGANFVIKRDGG----------KKKFLKY-------------GNRRKIARELKIGDIVERHLEDGDIVLFNRQP 394
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 572 TLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDNQYLVPTSGNPLRGLIQDN 651
Cdd:cd02583 395 SLHRLSIMAHRAKVMPW-RTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDF 473
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 652 VDSGVWMSSRDTFFTKEEYQQLL-YGSLrpetdgtGGGKIRMLPPAIMKPQPLWTGKQVISTILKNLTWGKAQLNMTSKS 730
Cdd:cd02583 474 LTASYLLTSKDVFFDRAQFCQLCsYMLD-------GEIKIDLPPPAILKPVELWTGKQIFSLLLRPNKKSPVLVNLEAKE 546
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 731 KV---PAKFWGPNakeEDKVLVMDGELIHGIMDKSQFGA-SAFGLVHSVYEIYSPEAAGMLLSILSRLFIKFLQSHGFTC 806
Cdd:cd02583 547 KSytkKSPDMCPN---DGYVVIRNSELLCGRLDKSTLGSgSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSI 623
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 807 RMDDLVLTKEGDQWRRELLDQGVGLGDEahleflgladtaktaspevLSKEFKlrmnevirdDNKL---AGLDNA--MKA 881
Cdd:cd02583 624 GIDDVTPSKELLKKKEELVDNGYAKCDE-------------------YIKQYK---------KGKLelqPGCTAEqtLEA 675
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 882 KVNKLTSSITQKC-------LPdglirpfPKNDMQMMTVSGAKGSNVNATQ-ISClLGQQELEGRRVPLMVSGRSLPSFR 953
Cdd:cd02583 676 KISGELSKIREDAgkaclkeLH-------KSNSPLIMALCGSKGSNINISQmIAC-VGQQIISGKRIPNGFEDRTLPHFP 747
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1954185479 954 PFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVHYDHTVR 1022
Cdd:cd02583 748 RNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1156-1641 |
2.31e-145 |
|
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: 448.56 E-value: 2.31e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1156 KYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIIMTAARKIKTPTMLLPLLPETSAKKAS 1235
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1236 QFCKSASRLTLAQLVDNVVVREktsaktadnnykrsktysirvnlfeekeyneeyrvsakrVKEVLATAFLKDLEELirk 1315
Cdd:cd02735 81 TLKKRLSRVTLSDVVEKVEVTE---------------------------------------ILKTIERVFKKLLGKW--- 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1316 dikdtkkiediskahkmdapgdedanedlgdaaakdgyasddaedmdaktarksaqnkpqasydepdeddivpedneksl 1395
Cdd:cd02735 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1396 edeeeefeqailagaddeeevpkrpsskggkleeqavqkskyctrfkfddnngafCEIDMEFPADTKKILMISLIEKSCA 1475
Cdd:cd02735 119 -------------------------------------------------------CEVTIKLPLSSPKLLLLSIVEKLAR 143
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1476 RVVVHEVKGISKCFEYINPTENDTSKRLQTEGVNLRGMWAFSDIIDVNYIDTNDIAAILNTYGVEAARNAIIKEVASVFA 1555
Cdd:cd02735 144 KAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFK 223
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1556 VYGIVVDRRHLTLIADYMTFEGGYKPFSRIGIGSNVAPFLKMSFESTCKFLTEATLHGDFDTLDSPSSRIVVGRVVEGGT 1635
Cdd:cd02735 224 VYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGT 303
|
....*.
gi 1954185479 1636 GSFDVL 1641
Cdd:cd02735 304 GLFDLL 309
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
308-1018 |
4.93e-119 |
|
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: 385.63 E-value: 4.93e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 308 VPSFIKkatYHMFFIEVLAVAPTRFRPPSVMgdktfespqnellsnilkgshlvrdlseelqaisdqepvdkkkLEATRN 387
Cdd:cd00399 78 VPSFLG---PEWMILTCLPVPPPCLRPSVII-------------------------------------------EERWRL 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 388 rfvdsiigLQHAVNSFIDSTKNPTQVAQGKNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPP 466
Cdd:cd00399 112 --------LQEHVDTYLDNGIAGQPQTQKSGRPlRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPK 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 467 VFATKLtypepvtphnikemrqavingpnkwpgathvqnedqsidvlgdlsiesrialansllapqsshtaqsgnnpypt 546
Cdd:cd00399 184 SIALTL-------------------------------------------------------------------------- 189
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 547 rtqtinkkvfrhlrNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAS 626
Cdd:cd00399 190 --------------DGDPVLFNRQPSLHKLSIMAHRVRVLPG-STFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEAR 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 627 FIANTDNQYLVPTSGNPLRGLIQDNVDSGVWMSsrdtfftkeeyqqllygslrpetdgtgggkirmlppaimkpqplwTG 706
Cdd:cd00399 255 ELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLT---------------------------------------------LG 289
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 707 KQVISTILKNltwgkaqlnmtskskvpakfwgpnakeedkvlvmdgelihgimdksqfgasafGLVHSVYEIYSPEAAGM 786
Cdd:cd00399 290 KQIVSAALPG-----------------------------------------------------GLLHTVTRELGPEKAAK 316
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 787 LLSILSRLFIKFLQSHGFTCRMDDLVLTKEGDQWRRELLDqgvglgdEAHLEFLgladtaktaspEVLsKEFKLRMNEVI 866
Cdd:cd00399 317 LLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIE-------EAKKKVD-----------EVE-EAFQAGLLTAQ 377
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 867 RDDNKLAGLDNAMKAKVNKLTSSITQKCLP-DGLIRPFpkNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVS 945
Cdd:cd00399 378 EGMTLEESLEDNILDFLNEARDKAGSAASVnLDLVSKF--NSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFS 455
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1954185479 946 GRSLPSFRPFDTSARAGGFVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVHYD 1018
Cdd:cd00399 456 DRTLPHFSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
972-1587 |
9.36e-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: 384.40 E-value: 9.36e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 972 GIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVHYDHTVRDSDGSVLQFHYGEDSLDVIKAKHINQFSF 1051
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1052 SAHNFEALSQKYhpkaaLASLEIKQGEEYAKKALKKPGKYDPALSVYNPGTHLGVVSERFALAMKDYIQKNpdgmPFEKD 1131
Cdd:pfam04998 81 EFSDLKLEDKFK-----NDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSKEAQERATLLFELLLKSGLE----SKRVR 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1132 SQLSKNTARYagltkNKFKALMNLKYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIIMT 1211
Cdd:pfam04998 152 SELTCNSKAF-----VCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINV 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1212 AArKIKTPTMLLPLLPETSAK--KASQFCKSASRLTLAQLVDNVvvrektsAKTADNNYKRSKTYSIRVNLFEEKEYNEE 1289
Cdd:pfam04998 227 SK-NIKSPSLTVYLFDEVGREleKAKKVYGAIEKVTLGSVVESG-------EILYDPDPFNTPIISDVKGVVKFFDIIDE 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1290 YRVSAKRVKEVLATAFLKDLEELIRKDIKDTKKIEDIskahkmdapgdedanedlgdaaakdgyasddaedmdaktarks 1369
Cdd:pfam04998 299 VTNEEEIDPETGLLILVIRLLKILNKSIKKVVKSEVI------------------------------------------- 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1370 aqNKPQASYDEPDEDDIVPEDNEKSLEDEeeefeqailagaddeeevpKRPSSKGGKLEEqavqkskyctrfkfddnnga 1449
Cdd:pfam04998 336 --PRSIRNKVDEGRDIAIGEITAFIIKIS-------------------KKIRQDTGGLRR-------------------- 374
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1450 fceidMEFPADTKKILMISLIEKSCARVVVHEVKGISKCfeYINPTEN---DTSKRLQTEGVNLRGMWAFSDIIDVNYID 1526
Cdd:pfam04998 375 -----VDELFMEEDPKLAILVASLLGNITLRGIPGIKRI--LVNEDDKgkvEPDWVLETEGVNLLRVLLVPGFVDAGRIL 447
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1954185479 1527 TNDIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIGI 1587
Cdd:pfam04998 448 SNDIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGI 508
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
319-650 |
1.33e-109 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 349.90 E-value: 1.33e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 319 MFFIEVLAVAPTRFRPPSVMGDKTF-ESPQNELLSNILKGSHLVRDLseelqaisdqepvdkKKLEATRNRFVDSIIGLQ 397
Cdd:smart00663 2 WMILTVLPVPPPCLRPSVQLDGGRFaEDDLTHLLRDIIKRNNRLKRL---------------LELGAPSIIIRNEKRLLQ 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 398 HAVNSFIDSTKNPTQVAQGKNLPPGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEP 477
Cdd:smart00663 67 EAVDTLIDNEGLPRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEI 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 478 VTPHNIKEMRQAVINGPnkwPGATHVQNEDQSidvlgDLSIESRIALANSLLapqsshtaqsgnnpyptrtqtINKKVFR 557
Cdd:smart00663 147 VTPLNIDKLRKLVRNGP---NGAKYIIRGKKT-----NLKLAKKSKIANHLK---------------------IGDIVER 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 558 HLRNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDNQYLV 637
Cdd:smart00663 198 HVIDGDVVLFNRQPTLHRMSIQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILS 276
|
330
....*....|...
gi 1954185479 638 PTSGNPLRGLIQD 650
Cdd:smart00663 277 PKNGKPIIGPIQD 289
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
440-631 |
1.78e-78 |
|
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: 256.08 E-value: 1.78e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 440 GKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMRQAVINGPNKWPGATHVQNEDQSIDVLGDLSIE 519
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 520 SRIALAnsllapqsshtaqsgnnpyptrtqtINKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANC 599
Cdd:pfam00623 81 LDKELE-------------------------IGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG-KTFRLNLSVT 134
|
170 180 190
....*....|....*....|....*....|..
gi 1954185479 600 NTYNADFDGDEMNIHFPQNEIARAEASFIANT 631
Cdd:pfam00623 135 TPYNADFDGDEMNLHVPQSEEARAEAEELMLV 166
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1144-1641 |
2.74e-56 |
|
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: 201.66 E-value: 2.74e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1144 LTKNKFKALMN---LKYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIImTAARKIKTPT 1220
Cdd:cd02584 3 LNKEAFDWILGeieTRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII-NVAKNIKTPS 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1221 MLLPLLPEtSAKKASQFCKSASRL---TLAQLVDNVVVrektsaktadnNYKRSKTYSIR------VNLFEE--KEYNEE 1289
Cdd:cd02584 82 LTVYLEPG-FAKDEEKAKKIQSRLehtTLKDVTAATEI-----------YYDPDPQNTVIeedkefVESYFEfpDEDVEQ 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1290 YRVSAKRVKEVLataflkDLEELIRKDIkdtkKIEDISKAHKmdapgdedanEDLGDaaakdgyasddaedmdaktarks 1369
Cdd:cd02584 150 DRLSPWLLRIEL------DRKKMTDKKL----SMEQIAKKIK----------EEFKD----------------------- 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1370 aqnkpqasydepDEDDIVPEDNEKSLEDEEEEFEQAILAGADDEEEVPKRpsskggkleeqavqkskyctrfKFDDNNga 1449
Cdd:cd02584 187 ------------DLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLK----------------------KIESNM-- 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1450 FCEIDME-FPADTKKILMISLIekscaRVVVHEVKGISKCFEYInptendtskrLQTEGVNLRGMWAFSDiIDVNYIDTN 1528
Cdd:cd02584 231 LSDMTLKgIEGIRKVFIREENK-----KKVDIETGEFKKREEWV----------LETDGVNLREVLSHPG-VDPTRTTSN 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1529 DIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIGIG-SNVAPFLKMSFESTCKFLT 1607
Cdd:cd02584 295 DIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINrQDTGPLMRCSFEETVDILL 374
|
490 500 510
....*....|....*....|....*....|....
gi 1954185479 1608 EATLHGDFDTLDSPSSRIVVGRVVEGGTGSFDVL 1641
Cdd:cd02584 375 EAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLL 408
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1129-1641 |
6.80e-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: 187.46 E-value: 6.80e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1129 EKDSQLSKNTARYAGLTKNKFKALMNL---KYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRL 1205
Cdd:cd06528 1 PLLKEKLEEVLKEHGLTLSEAEEIIKEvlrEYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1206 REiIMTAARKIKTPTMLLPLLPetsakkasqfcksasrltlaqlvdnvvvrektsaktadnnykrsktysirvnlfeeke 1285
Cdd:cd06528 81 IE-IVDARKEPSTPTMTIYLEE---------------------------------------------------------- 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1286 yneEYRVSAKRVKEVlatafLKDLEELirkdikdtkKIEDIskahkmdapgdedanedlgdaaakdgyASDDAEDMDAKT 1365
Cdd:cd06528 102 ---EYKYDREKAEEV-----ARKIEET---------TLENL---------------------------AEDISIDLFNMR 137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1366 ARKsaqnkpqasydEPDEDDIvpEDNeksledeeeefeqailaGADDEEEVPKRPSSKGGKLEEqavqkskyctrfkfdD 1445
Cdd:cd06528 138 ITI-----------ELDEEML--EDR-----------------GITVDDVLKAIEKLKKGKVGE---------------E 172
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1446 NNGafceIDMEFPADTKKILMISLIEKSCARVVVHEVKGISKCF------EYInptendtskrLQTEGVNLRGMWAFSDi 1519
Cdd:cd06528 173 GDV----TLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIvrkeedEYV----------IYTEGSNLKAVLKVEG- 237
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1520 IDVNYIDTNDIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIGIGSNVA-PFLKMS 1598
Cdd:cd06528 238 VDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPsVLARAA 317
|
490 500 510 520
....*....|....*....|....*....|....*....|...
gi 1954185479 1599 FESTCKFLTEATLHGDFDTLDSPSSRIVVGRVVEGGTGSFDVL 1641
Cdd:cd06528 318 FEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELT 360
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1156-1641 |
2.22e-47 |
|
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: 174.47 E-value: 2.22e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1156 KYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIImTAARKIKTPTMLLPLlpetsakkas 1235
Cdd:TIGR02389 35 EYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIV-DARKTPSTPSMTIYL---------- 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1236 qfcksasrltlaqlvdnvvvrektsaktadnnykrsktysirvnlfeEKEYNEEYRVSAKRVKEVLATaflkdleelirk 1315
Cdd:TIGR02389 104 -----------------------------------------------EDEYEKDREKAEEVAKKIEAT------------ 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1316 dikdtkKIEDISKahkmdapgdeDANEDLGDAAAKdgyASDDAEDMDAKTARKsaqnkpqasydepdeDDIvpedneksl 1395
Cdd:TIGR02389 125 ------KLEDVAK----------DISIDLADMTVI---IELDEEQLKERGITV---------------DDV--------- 161
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1396 edeeeefeqailagaddeeevpkrpsskggkleEQAVQKSKYCTRFKFDDNNGafcEIDMEFPADTKKILMisLIEKSCA 1475
Cdd:TIGR02389 162 ---------------------------------EKAIKKAKLGKVIEIDMDNN---TITIKPGNPSLKELR--KLKEKIK 203
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1476 RVVVHEVKGISKCF------EYInptendtskrLQTEGVNLRGMWAFSDiIDVNYIDTNDIAAILNTYGVEAARNAIIKE 1549
Cdd:TIGR02389 204 NLHIKGIKGIKRVVirkegdEYV----------IYTEGSNLKEVLKLEG-VDKTRTTTNDIHEIAEVLGIEAARNAIIEE 272
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1550 VASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIGI-GSNVAPFLKMSFESTCKFLTEATLHGDFDTLDSPSSRIVVG 1628
Cdd:TIGR02389 273 IKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGIsGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVG 352
|
490
....*....|...
gi 1954185479 1629 RVVEGGTGSFDVL 1641
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 ... |
424-1022 |
1.23e-46 |
|
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: 181.06 E-value: 1.23e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 424 RQALEKKEGL--FRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTYPEPVTPHNIKEMrqavingpnkwpgat 501
Cdd:cd10506 194 ESAASKKSGLkwMKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERL--------------- 258
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 502 hvqnedQSIDVLGDLSIESRIALANSLLAPQSSHTaqsgnnpyptrTQTINKKVFRHLRNGDMLLLNRQPTLHKPSIMAH 581
Cdd:cd10506 259 ------QEYCDLTLLLKGVIGVRRNGRLVGVRSHN-----------TLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIAL 321
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 582 KARILPGEKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDNQYLVPTSGNPLRGLIQDNVDSGVWMSSR 661
Cdd:cd10506 322 SVKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTER 401
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 662 DTFFTKEEYQQL-LYGSLRPetdgtgggkirmLPPAIMKPQ----PLWTGKQVISTILknltwgKAQLNMTSKSKVpakf 736
Cdd:cd10506 402 GVFLDKAQMQQLqMLCPSQL------------PPPAIIKSPpsngPLWTGKQLFQMLL------PTDLDYSFPSNL---- 459
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 737 wgpnakeedkVLVMDGELIHGiMDKSQFGASAFGLVHSVYEIYSPEAAGMLLSILSRLFIKFLQSHGFTCRMDDLVLTke 816
Cdd:cd10506 460 ----------VFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLS-- 526
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 817 GDQWRRELLDQGVGLG-DEA----HLEFLGLADTAKTASPEVLSKEFKLRMNEVIRDDNKLAGLDN----AMKAKVNKLT 887
Cdd:cd10506 527 SDSYSRQKMIEEISLGlREAeiacNIKQLLVDSRKDFLSGSGEENDVSSDVERVIYERQKSAALSQasvsAFKQVFRDIQ 606
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 888 SSITQKCLPDglirpfpkNDMQMMTVSGAKGSNVNATQISCLLGQQELEGR---RVPL-----MVSGRSLPSFRPFDTSA 959
Cdd:cd10506 607 NLVYKYASKD--------NSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVKlsyRIPRqlscaAWNSQKSPRVIEKDGSE 678
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 960 RAG-----GFVTGRFLTGIRPQEYYFHCMAGREGlidtAVKTSR--SGYLQRCLIKHLEGLRVHYDHTVR 1022
Cdd:cd10506 679 CTEsyipyGVVESSFLDGLNPLECFVHSITSRDS----SFSSNAdlPGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1136-1641 |
3.56e-46 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 171.57 E-value: 3.56e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1136 KNTARYAGLTKNKFKALMNL---KYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREiIMTA 1212
Cdd:PRK04309 27 REKLEERKLTEEEVEEIIEEvvrEYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIE-IVDA 105
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1213 ARKIKTPTMLLPLLPEtsakkasqfcksasrltlaqlvdnvvvrektsaktadnnYKRSktysirvnlfEEKEyneeyrv 1292
Cdd:PRK04309 106 RKEPSTPMMTIYLKDE---------------------------------------YAYD----------REKA------- 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1293 sakrvkevlataflkdlEELIRKdIKDTkKIEDISKahkmdapgdeDANEDLGDAAakdgyasddaedmdaktarksaqn 1372
Cdd:PRK04309 130 -----------------EEVARK-IEAT-TLENLAK----------DISVDLANMT------------------------ 156
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1373 kpqasydepdeddIVPEDNEKSLEDEeeefeqailaGADDEEEVPKRPSSKGGKLEEQAVQkskyctrfkfddnngafce 1452
Cdd:PRK04309 157 -------------IIIELDEEMLEDR----------GLTVDDVKEAIEKKKGGEVEIEGNT------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1453 idMEFPADTKKILMISLIEKSCARVVVHEVKGISKCF------EYInptendtskrLQTEGVNLRGMWAFsDIIDVNYID 1526
Cdd:PRK04309 195 --LIISPKEPSYRELRKLAEKIRNIKIKGIKGIKRVIirkegdEYV----------IYTEGSNLKEVLKV-EGVDATRTT 261
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1527 TNDIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIGI-GSNVAPFLKMSFESTCKF 1605
Cdd:PRK04309 262 TNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVsGEKASVLARAAFEVTVKH 341
|
490 500 510
....*....|....*....|....*....|....*.
gi 1954185479 1606 LTEATLHGDFDTLDSPSSRIVVGRVVEGGTGSFDVL 1641
Cdd:PRK04309 342 LLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELT 377
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1156-1638 |
4.47e-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: 156.99 E-value: 4.47e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1156 KYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIImTAARKIKTPTMLLPLLPETSAKKAS 1235
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEII-NASKNISTPIITAKLENDRDEKSAR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1236 QFCKSASRLTLAQLVDNVVVrektsaktadnNYKRSKTYsIRVNLfeekeyneeyrvsakrvkevlataflkdleelirk 1315
Cdd:cd02736 80 IVKGRIEKTYLGEVASYIEE-----------VYSPDDCY-ILIKL----------------------------------- 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1316 dikDTKKIEDIskahkmdapgdedanedlgdaaakdgyasddaedmdaktarksaqnkpqasydepdeddivpedneksl 1395
Cdd:cd02736 113 ---DKKIIEKL--------------------------------------------------------------------- 120
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1396 edeeeefeqailagaddeeevpkrpsskggKLEEQAVQkskyctrfkFDDNNgafceidmefpadtkkiLMISLiekscA 1475
Cdd:cd02736 121 ------------------------------QLSKSNLY---------FLLQS-----------------LKRKL-----P 139
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1476 RVVVHEVKGISKCFeyINPTENDTSKRLQTEGVNLRGMWAFSDIIDVNyIDTNDIAAILNTYGVEAARNAIIKEVASVFA 1555
Cdd:cd02736 140 DVVVSGIPEVKRAV--INKDKKKGKYKLLVEGYGLRAVMNTPGVIGTR-TTSNHIMEVEKVLGIEAARSTIINEIQYTMK 216
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1556 VYGIVVDRRHLTLIADYMTFEGGYKPFSRIGIGSNVAPFLKM-SFESTCKFLTEATLHGDFDTLDSPSSRIVVGRVVEGG 1634
Cdd:cd02736 217 SHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLaSFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIG 296
|
....
gi 1954185479 1635 TGSF 1638
Cdd:cd02736 297 TGLF 300
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
396-1208 |
1.91e-40 |
|
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: 164.07 E-value: 1.91e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVaQGKNLPP--GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLT 473
Cdd:TIGR02386 281 LQEAVDALFDNGRRGKPV-VGKNNRPlkSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELF 359
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 474 YP-------EPVTPHNIKEMRQAVINGPNK-WpgathvqnedqsiDVLgDLSIESRialansllapqsshtaqsgnnpyP 545
Cdd:TIGR02386 360 KPfiikrliDRELAANIKSAKKMIEQEDPEvW-------------DVL-EDVIKEH-----------------------P 402
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 546 trtqtinkkvfrhlrngdmLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEA 625
Cdd:TIGR02386 403 -------------------VLLNRAPTLHRLGIQAFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEA 462
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 626 SFIANTDNQYLVPTSGNPLRGLIQDNVdSGVWmssrdtFFTKEEYQQLlygslrpetdgtGGGKI-RMLPPAIMKPQplw 704
Cdd:TIGR02386 463 RALMLASNNILNPKDGKPIVTPSQDMV-LGLY------YLTTEKPGAK------------GEGKIfSNVDEAIRAYD--- 520
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 705 TGKQVISTILKNL--------TWGKAQLNMTSKSKVPakFWGPNAKEEDKVLvmdGELIhgimdksqfgasafglvHSVY 776
Cdd:TIGR02386 521 NGKVHLHALIGVRtsgeiletTVGRVIFNEILPEGFP--YINDNEPLSKKEI---SSLI-----------------DLLY 578
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 777 EIYSPEAAGMLLSILSRLFIKFLQSHGFTCRMDDLVLTKEgdqwRRELLDQgvglgdeahleflgladtaktASPEVLSK 856
Cdd:TIGR02386 579 EVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDE----KYEILKE---------------------ADKEVAKI 633
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 857 EFKLRMNEVIRDDNKLAGLDNAMKAKvNKLTSSItQKCLPDgliRPFPKNDMQMMTVSGAKGSNVNATQISCLLGqqele 936
Cdd:TIGR02386 634 QKFYNKGLITDEERYRKVVSIWSETK-DKVTDAM-MKLLKK---DTYKFNPIFMMADSGARGNISQFRQLAGMRG----- 703
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 937 grrvpLMV--SGRSLPsfRPFDTSARAGGFVTgrfltgirpqEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKhleglr 1014
Cdd:TIGR02386 704 -----LMAkpSGDIIE--LPIKSSFREGLTVL----------EYFISTHGARKGLADTALKTADSGYLTRRLVD------ 760
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1015 VHYDHTVRDSDgsvlqfhygedsldvikakhinqfsfsahnfealsqkYHPKAALASLEIKQGEEYAKKALKKP--GKYd 1092
Cdd:TIGR02386 761 VAQDVVVREED-------------------------------------CGTEEGIEVEAIVEGKDEIIESLKDRivGRY- 802
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1093 PALSVYNPGTHlGVVSERFALAMKDYIQKnpdgmpFEkDSQLSKNTARYAgLTKNKFKAL------MNLKYLHsLVEPGE 1166
Cdd:TIGR02386 803 SAEDVYDPDTG-KLIAEANTLITEEIAEK------IE-NSGIEKVKVRSV-LTCESEHGVcqkcygRDLATGK-LVEIGE 872
|
810 820 830 840
....*....|....*....|....*....|....*....|....
gi 1954185479 1167 AVGLLAAQSVGEPSTQMTLNTFHFAGYGAA--NVTLGIPRLREI 1208
Cdd:TIGR02386 873 AVGVIAAQSIGEPGTQLTMRTFHTGGVAGAsgDITQGLPRVKEL 916
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
634-811 |
2.36e-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: 2.36e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 634 QYLVPTSGNPLRGLIQDNVDSGVWMSSRDTFFTKEEYQQLLYGslrpetdgtgggKIRMLPPAIMKP-QPLWTGKQVIST 712
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMY------------GIVLPHPAILKPiKPLWTGKQTFSR 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 713 ILKNltwgkaQLNMTSKSKVPAKFWGPNakeEDKVLVMDGELIHGIMDKSQFGASAFGLVHSVYEIYSPEAAGMLLSILS 792
Cdd:pfam04983 69 LLPN------EINPKGKPKTNEEDLCEN---DSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQ 139
|
170
....*....|....*....
gi 1954185479 793 RLFIKFLQSHGFTCRMDDL 811
Cdd:pfam04983 140 KLGFRYLTKSGFSIGIDDI 158
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1144-1641 |
1.43e-38 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 152.27 E-value: 1.43e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1144 LTKNKFKALM---NLKYLHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIiMTAARKIKTPT 1220
Cdd:PRK14897 158 LSDDEYEEILrriREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEI-VDARKKPSTPT 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1221 MLLPLlpetsakkasqfcksasrltlaqlvdnvvvrektsaktadnnykrsktysirvnlfeekeyNEEYRVSAKRVKEV 1300
Cdd:PRK14897 237 MTIYL-------------------------------------------------------------KKDYREDEEKVREV 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1301 lataflkdleelirkdikdTKKIEDISKAhkmdapgdedaneDLGDAaakdgyaSDDAEDMDAKTarksaqnkpqasydE 1380
Cdd:PRK14897 256 -------------------AKKIENTTLI-------------DVADI-------ITDIAEMSVVV--------------E 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1381 PDEDDIvpedNEKSLEDeeeefeqailagaddEEEVPKRPSSKGGKLEEQAVQkskyctrfkfddnngafceIDMEFPAD 1460
Cdd:PRK14897 283 LDEEKM----KERLIEY---------------DDILAAISKLTFKTVEIDDGI-------------------IRLKPQQP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1461 TKKILMisLIEKSCARVVVHEVKGISKCfeyINPTENDTSK-RLQTEGVNLRgmwafsDIIDVNYID-----TNDIAAIL 1534
Cdd:PRK14897 325 SFKKLY--LLAEKVKSLTIKGIKGIKRA---IARKENDERRwVIYTQGSNLK------DVLEIDEVDptrtyTNDIIEIA 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1535 NTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIGIGSNVAPFL-KMSFESTCKFLTEATLHG 1613
Cdd:PRK14897 394 TVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLaRAAFEITGKHLLRAGILG 473
|
490 500
....*....|....*....|....*...
gi 1954185479 1614 DFDTLDSPSSRIVVGRVVEGGTGSFDVL 1641
Cdd:PRK14897 474 EVDKLAGVAENIIVGQPITLGTGAVSLV 501
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
396-1192 |
3.83e-34 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 144.30 E-value: 3.83e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVaQGKNLPP--GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLt 473
Cdd:PRK09603 1688 LQEAVDVLFDNGRSTNAV-KGANKRPlkSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALEL- 1765
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 474 ypepVTPHNIKEMRQAVIngpnkwpgATHVQNEDQSIDvlgdlsiesrialansllapqsshtaQSGNNPYptrtqtink 553
Cdd:PRK09603 1766 ----FKPHLLSKLEERGY--------ATTLKQAKRMIE--------------------------QKSNEVW--------- 1798
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 554 KVFRHLRNGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDN 633
Cdd:PRK09603 1799 ECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDG-KAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSM 1877
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 634 QYLVPTSGNPLRGLIQDNVdSGVWMSSRDTFFTKEEYQqlLYGSLRPETDGTGGG------KIRmlppAIMKPQPLWT-- 705
Cdd:PRK09603 1878 NILLPASGKAVAIPSQDMV-LGLYYLSLEKSGVKGEHK--LFSSVNEIITAIDTKeldihaKIR----VLDQGNIIATsa 1950
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 706 GKQVISTILKNLtwgkaqlnmtskskVPAKFWGPNAKEEDKvlvmdGELIHGIMDKSQFGASAfglvhsvyeiyspeaag 785
Cdd:PRK09603 1951 GRMIIKSILPDF--------------IPTDLWNRPMKKKDI-----GVLVDYVHKVGGIGITA----------------- 1994
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 786 MLLSILSRLFIKFLQSHGFTCRMDDLVLTKEgdqwRRELLDQGVGLGDEAHLEFlglaDTAKTASPEvlskefklRMNEV 865
Cdd:PRK09603 1995 TFLDNLKTLGFRYATKAGISISMEDIITPKD----KQKMVEKAKVEVKKIQQQY----DQGLLTDQE--------RYNKI 2058
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 866 IrddnklagldNAMKAKVNKLTSSITQKCLPD--GLirpfpkNDMQMMTVSGAKGSNVNATQISCLLGqqelegrrvpLM 943
Cdd:PRK09603 2059 I----------DTWTEVNDKMSKEMMTAIAKDkeGF------NSIYMMADSGARGSAAQIRQLSAMRG----------LM 2112
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 944 VSgrslPSFRPFDTSaraggfVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLRVhydhtVRD 1023
Cdd:PRK09603 2113 TK----PDGSIIETP------IISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKV-----VSD 2177
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1024 SDGSvlqfHYGEDSLDVikakhinqfSFSAHNFEALSQKYHPKAA------------LASLEIKQGEEYAKKALKKPGKy 1091
Cdd:PRK09603 2178 DCGT----HEGIEITDI---------AVGSELIEPLEERIFGRVLledvidpitneiLLYADTLIDEEGAKKVVEAGIK- 2243
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1092 dpALSVYNPGThlgvvserfalamkdyiQKNPDGMpfekdsqlsknTARYAGLTKNKFKalmnlkylhsLVEPGEAVGLL 1171
Cdd:PRK09603 2244 --SITIRTPVT-----------------CKAPKGV-----------CAKCYGLNLGEGK----------MSYPGEAVGVV 2283
|
810 820
....*....|....*....|.
gi 1954185479 1172 AAQSVGEPSTQMTLNTFHFAG 1192
Cdd:PRK09603 2284 AAQSIGEPGTQLTLRTFHVGG 2304
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
396-1225 |
8.93e-33 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 139.24 E-value: 8.93e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVAQGKNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTY 474
Cdd:PRK14906 377 LQEAVDSLFDNGRRGRPVTGPGNRPlKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFK 456
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 475 P-------EPVTPHNIKEMRQAVING-PNKWpgathvqnedqsiDVLGDLsIESRialansllapqsshtaqsgnnpypt 546
Cdd:PRK14906 457 PfvmkrlvELEYAANIKAAKRAVDRGaSYVW-------------DVLEEV-IQDH------------------------- 497
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 547 rtqtinkkvfrhlrngdMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAS 626
Cdd:PRK14906 498 -----------------PVLLNRAPTLHRLGIQAFEPVLVEG-KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEAR 559
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 627 FIANTDNQYLVPTSGNPLRGLIQDNVDSGVWMSS-RDTF------FTKEEYQQLLYGSlRPETDGTGGGKIRMlpPAIMK 699
Cdd:PRK14906 560 VLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTeRDGFegegrtFADFDDALNAYDA-RADLDLQAKIVVRL--SRDMT 636
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 700 PQPLW-------TGKQVISTIlknltwGKAQLNmtskskvpakfwgpnakeedKVLVMDGELIHGIMDKSQFGAsafgLV 772
Cdd:PRK14906 637 VRGSYgdleetkAGERIETTV------GRIIFN--------------------QVLPEDYPYLNYKMVKKDIGR----LV 686
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 773 HSVYEIYSPEAAGMLLSILSRLFIKFLQSHGFTCRMDDLVLTKEGDQWRRELLDQGVGLGDEAHLEFLgladtaktaSPE 852
Cdd:PRK14906 687 NDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFL---------SER 757
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 853 VLSKEFKLRMNEVirddNKLAGldNAMKAKVNKltssitqkclpdglirpfpKNDMQMMTVSGAKGsnvNATQIscllgq 932
Cdd:PRK14906 758 ERHKQVVDIWTEA----TEEVG--EAMLAGFDE-------------------DNPIYMMADSGARG---NIKQI------ 803
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 933 QELEGRRvPLMVSgrslPSFRPFDTSARAGgfvtgrFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKhleg 1012
Cdd:PRK14906 804 RQLAGMR-GLMAD----MKGEIIDLPIKAN------FREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVD---- 868
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1013 lrVHYDHTVRDSDgsvlqfhYGEDsldvikakhinqfsfsahnfealsqkyhpkaalasleikQGEEYAkkALKKPGKYD 1092
Cdd:PRK14906 869 --VAQDVIVREED-------CGTD---------------------------------------EGVTYP--LVKPKGDVD 898
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1093 PALSVYNPGTHLGVVSERFALAMKDYIqknpdgmpfEKDSQLSKNTAryAGLTKNKFKALMNLKYLHSL----------- 1161
Cdd:PRK14906 899 TNLIGRCLLEDVCDPNGEVLLSAGDYI---------ESMDDLKRLVE--AGVTKVQIRTLMTCHAEYGVcqkcygwdlat 967
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1954185479 1162 ---VEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREiiMTAARKIKTPTMLLPL 1225
Cdd:PRK14906 968 rrpVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAE--LFEARKPKGEAVLAEI 1032
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1525-1637 |
1.78e-31 |
|
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: 121.37 E-value: 1.78e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1525 IDTNDIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIG-IGSNVAPFLKMSFESTC 1603
Cdd:cd00630 45 LNAASIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGfRASKTSPLMRASFEKTT 124
|
90 100 110
....*....|....*....|....*....|....
gi 1954185479 1604 KFLTEATLHGDFDTLDSPSSRIVVGRVVEGGTGS 1637
Cdd:cd00630 125 KHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
396-1007 |
7.19e-28 |
|
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: 121.47 E-value: 7.19e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVAQGKNLPP-GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTY 474
Cdd:cd01609 204 LQEAVDALIDNGRRGKPVTGANNRPLkSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFK 283
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 475 P-------EPVTPHNIKEMRQAVINGPNK-WpgathvqnedqsiDVLGDLSIESRIalansllapqsshtaqsgnnpypt 546
Cdd:cd01609 284 PfvireliERGLAPNIKSAKKMIERKDPEvW-------------DILEEVIKGHPV------------------------ 326
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 547 rtqtinkkvfrhlrngdmlLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEAS 626
Cdd:cd01609 327 -------------------LLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEAR 386
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 627 FIANTDNQYLVPTSGNPLRGLIQDNVdSGVWmssrdtFFTKEeyqqllygslRPETDGTGggkirmlppaimkpqplwtg 706
Cdd:cd01609 387 VLMLSSNNILSPASGKPIVTPSQDMV-LGLY------YLTKE----------RKGDKGEG-------------------- 429
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 707 kqVISTilknlTWGKAQLNMTskskVPAKFwgpnakeedkvlvmdgELIHGIMDKSQFGAsafgLVHSVYEIYSPEAAGM 786
Cdd:cd01609 430 --IIET-----TVGRVIFNEI----LPEGL----------------PFINKTLKKKVLKK----LINECYDRYGLEETAE 478
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 787 LLSILSRLFIKFLQSHGFTCRMDDLVLTKEgdqwRRELLDQGvglgdeahleflgladtaktaspEVLSKEFKLRMNE-V 865
Cdd:cd01609 479 LLDDIKELGFKYATRSGISISIDDIVVPPE----KKEIIKEA-----------------------EEKVKEIEKQYEKgL 531
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 866 IRDDNKlagldnamKAKVNKLTSSITQKcLPDGL---IRPFPKNDMQMMTVSGAKGSNVNATQISCLLGqqelegrrvpL 942
Cdd:cd01609 532 LTEEER--------YNKVIEIWTEVTEK-VADAMmknLDKDPFNPIYMMADSGARGSKSQIRQLAGMRG----------L 592
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1954185479 943 MVSgrslPSFRPFDTSaraggfVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLI 1007
Cdd:cd01609 593 MAK----PSGKIIELP------IKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLV 647
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
396-1192 |
4.05e-25 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 114.72 E-value: 4.05e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQV--AQGKNLPPGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLT 473
Cdd:PRK14844 1731 LQEAVDSLFDNSRRNALVnkAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELF 1810
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 474 YPepvtphnikemrqavingpnkwpgathvqnedqsidvlgdlSIESRIALANslLAPQSSHTAQSGNNPYPTRTQTINK 553
Cdd:PRK14844 1811 KP-----------------------------------------FVYSKLKMYG--MAPTIKFASKLIRAEKPEVWDMLEE 1847
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 554 KVFRHlrngdMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDN 633
Cdd:PRK14844 1848 VIKEH-----PVLLNRAPTLHRLGIQAFEPILIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTN 1921
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 634 QYLVPTSGNPlrgliqdnvdsgVWMSSRDTFFTkeeyqqLLYGSLRPETD------GTGGGKIRMLPPAIMkpqplwtgk 707
Cdd:PRK14844 1922 NVLSPSNGRP------------IIVPSKDIVLG------IYYLTLQEPKEddlpsfGAFCEVEHSLSDGTL--------- 1974
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 708 QVISTILKNLTWGKAQLNMTSKS--KVPAK--FWGPNAKEEDkvlvMDGELIHGIMDKSQFGasafGLVHSVYEIYSPEA 783
Cdd:PRK14844 1975 HIHSSIKYRMEYINSSGETHYKTicTTPGRliLWQIFPKHEN----LGFDLINQVLTVKEIT----SIVDLVYRNCGQSA 2046
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 784 AGMLLSILSRLFIKFLQSHGFTCRMDDLVLTKEgdqwRRELLDQGVGLGDEAHLEFlglADTAKTASPevlskefklRMN 863
Cdd:PRK14844 2047 TVAFSDKLMVLGFEYATFSGVSFSRCDMVIPET----KATHVDHARGEIKKFSMQY---QDGLITRSE---------RYN 2110
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 864 EVIRDDNKLAGLdnamkaKVNKLTSSITqkcLPDGLIRpfpKNDMQMMTVSGAKGSNVNATQISCLLGqqelegrrvpLM 943
Cdd:PRK14844 2111 KVIDEWSKCTDM------IANDMLKAIS---IYDGNSK---YNSVYMMVNSGARGSTSQMKQLAGMRG----------LM 2168
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 944 VSgrslPSFRPFDTSaraggfVTGRFLTGIRPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIkhleglrvhydhtvrd 1023
Cdd:PRK14844 2169 TK----PSGEIIETP------IISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLV---------------- 2222
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1024 sdgsvlqfhygEDSLDVIKAKHinqfSFSAHNFEALSQKYHPKAALASLEikqgeeyaKKALKKPGKYDpalsVYNPGTh 1103
Cdd:PRK14844 2223 -----------DVSQNCIVTKH----DCKTKNGLVVRATVEGSTIVASLE--------SVVLGRTAAND----IYNPVT- 2274
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1104 lgvvserfalamKDYIQKNPDGMPFEKDSQLSkntarYAGLTKNKFKA---------LMNLKYLHSL-----VEPGEAVG 1169
Cdd:PRK14844 2275 ------------KELLVKAGELIDEDKVKQIN-----IAGLDVVKIRSpltceispgVCSLCYGRDLatgkiVSIGEAVG 2337
|
810 820
....*....|....*....|...
gi 1954185479 1170 LLAAQSVGEPSTQMTLNTFHFAG 1192
Cdd:PRK14844 2338 VIAAQSVGEPGTQLTMRTFHIGG 2360
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
877-965 |
2.14e-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: 96.28 E-value: 2.14e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 877 NAMKAKVNKLTSSITQKCLPdglirpfPKNDMQMMTVSGAKGSNVNATQISCLLGQQELEGRRVPLMVSGRSLPSFRPFD 956
Cdd:pfam05000 27 NNILNKARDPAGNIASKSLD-------PNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGKRIPFGFSGRTLPHFKKDD 99
|
....*....
gi 1954185479 957 TSARAGGFV 965
Cdd:pfam05000 100 EGPESRGFV 108
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1181-1640 |
1.62e-22 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 105.36 E-value: 1.62e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1181 TQMTLNTFHFAGYGAANVTLGIPRLREIImtAARKI-KTPTMLLPLLPE--TSAKKASQFCKSASRLTLAQLVDNVvvre 1257
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIV--DARKEpSTPIMTVHLKGEyaTDREKAEEVAKKIESLTLGDVATSI---- 614
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1258 ktsaktADNNYkrskTYSIRVNLFEEkeyneeyrvsakRVKEVLATAflKDLEELIRKDIKdtkkiediskahkmdapgd 1337
Cdd:PRK14898 615 ------AIDLW----TQSIKVELDEE------------TLADRGLTI--ESVEEAIEKKLG------------------- 651
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1338 edanedlgdaaakdgyasddaedmdAKTARKSAqnkpqasydepdeddivpedneksledeeeefeqAILAGaddeeevP 1417
Cdd:PRK14898 652 -------------------------VKIDRKGT----------------------------------VLYLK-------P 665
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1418 KRPSSKGgkleeqavqkskyctrfkfddnngafceidmefpadtkkilMISLIEKsCARVVVHEVKGISKCFEYINPTEN 1497
Cdd:PRK14898 666 KTPSYKA-----------------------------------------LRKRIPK-IKNIVLKGIPGIERVLVKKEEHEN 703
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1498 DTSKRLQTEGVNLRGMWAFsDIIDVNYIDTNDIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEG 1577
Cdd:PRK14898 704 DEEYVLYTQGSNLREVFKI-EGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADG 782
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1954185479 1578 GYKPFSRIGIGSNVAPFL-KMSFESTCKFLTEATLHGDFDTLDSPSSRIVVGRVVEGGTGSFDV 1640
Cdd:PRK14898 783 EVKPIGRHGVAGEKGSVLaRAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDL 846
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
396-1437 |
3.31e-22 |
|
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: 104.47 E-value: 3.31e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVAQGKNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTY 474
Cdd:COG0086 289 LQEAVDALFDNGRRGRAVTGANKRPlKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFK 368
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 475 P-------EPVTPHNIKEMRQAVingpnkwpgathVQNEDQSIDVLGDLSIEsrialansllapqsshtaqsgnnpYPtr 547
Cdd:COG0086 369 PfiyrkleERGLATTIKSAKKMV------------EREEPEVWDILEEVIKE------------------------HP-- 410
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 548 tqtinkkvfrhlrngdmLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASF 627
Cdd:COG0086 411 -----------------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARL 472
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 628 IANTDNQYLVPTSGNPLRGLIQDNVDSGVWMSSRD--------TFFTKEEYQQLLYgslrpetdgtgGGKIRMlpPAIMK 699
Cdd:COG0086 473 LMLSTNNILSPANGKPIIVPSQDMVLGLYYLTRERegakgegmIFADPEEVLRAYE-----------NGAVDL--HARIK 539
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 700 PQPLWTGKQVISTIlkNLTWGKAQLNMTSKSKVPakFWgpnakeeDKVlvmdgelihgiMDKSQFGAsafgLVHSVYEIY 779
Cdd:COG0086 540 VRITEDGEQVGKIV--ETTVGRYLVNEILPQEVP--FY-------NQV-----------INKKHIEV----IIRQMYRRC 593
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 780 SPEAAGMLLSILSRLFIKFLQSHGFTCRMDDLVLTKEgdqwRRELLdqgvglgDEAHleflgladtaktaspevlskefk 859
Cdd:COG0086 594 GLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKE----KQEIF-------EEAN----------------------- 639
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 860 lrmNEVIR-DDNKLAGLDNAmKAKVNKL------TSSITQKCLPDGLiRPFpkNDMQMMTVSGAKGSnvnATQIscllgq 932
Cdd:COG0086 640 ---KEVKEiEKQYAEGLITE-PERYNKVidgwtkASLETESFLMAAF-SSQ--NTTYMMADSGARGS---ADQL------ 703
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 933 QELEGRRvPLMV--SGR--SLP---SFrpfdtsaRAGgfvtgrflTGIRpqeYYFHCMAG-REGLIDTAVKTSRSGYLQR 1004
Cdd:COG0086 704 RQLAGMR-GLMAkpSGNiiETPigsNF-------REG--------LGVL---EYFISTHGaRKGLADTALKTADSGYLTR 764
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1005 CLIKhleglrVHYDHTVRDSDgsvlqfhYGEDSLDVIKAkhinqfsfsahnfealsqkyhpkaalasleIKQGEEyAKKA 1084
Cdd:COG0086 765 RLVD------VAQDVIVTEED-------CGTDRGITVTA------------------------------IKEGGE-VIEP 800
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1085 LKKP--GKYdPALSVYNPGTHLGVVSERFALAMKDYIQKNPDGMPFEKDSQLSKNTARYAGLTKnkfKALMNLKYLHsLV 1162
Cdd:COG0086 801 LKERilGRV-AAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAK---CYGRDLARGH-LV 875
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1163 EPGEAVGLLAAQSVGEPSTQMTLNTFH-------FAGYGAANVTLGIPRLREIIMTAARKIKTPTMLLPLLPETSAKKAS 1235
Cdd:COG0086 876 NIGEAVGVIAAQSIGEPGTQLTMRTFHiggaasrAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSELVIVDDGG 955
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1236 QFCKSASRLTLAQLVDNVVVREKTSAKTADNNYKRSKTYSIRVNLFEEKEYNEEYRVSAKRVKEVLATAFLKDLEELIRK 1315
Cdd:COG0086 956 RREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRG 1035
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1316 DIKDTKKIEdiskaHKMDAPGDEDANEDLGDAAAKDGYASDDAEDMDAKTARKSAQNKPQASYDEPDEDDIVPEDNEKSL 1395
Cdd:COG0086 1036 GGKLLIRAL-----KLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGLARVAAA 1110
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|..
gi 1954185479 1396 EDEEEEFEQAILAGADDEEEVPKRPSSKGGKLEEQAVQKSKY 1437
Cdd:COG0086 1111 AEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIE 1152
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
396-643 |
8.97e-22 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 102.29 E-value: 8.97e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTK--NPTQVAQGKNLPpGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLT 473
Cdd:CHL00018 328 LQEAVDALLDNGIrgQPMRDGHNKPYK-SFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELF 406
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 474 YPepvtphnikemrqAVINGpnkwpgathvqnedqsidvlgdlSIESRiaLANSLLApqsshtAQS---GNNPyptrtqt 550
Cdd:CHL00018 407 QP-------------FVIRG-----------------------LIRQH--LASNIRA------AKSkirEKEP------- 435
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 551 INKKVFRHLRNGDMLLLNRQPTLHKPSIMAHKArILPGEKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIAN 630
Cdd:CHL00018 436 IVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQP-ILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMF 514
|
250
....*....|...
gi 1954185479 631 TDNQYLVPTSGNP 643
Cdd:CHL00018 515 SHMNLLSPAIGDP 527
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
10-435 |
5.06e-21 |
|
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595 Cd Length: 320 Bit Score: 95.82 E-value: 5.06e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 10 EVDYVSFSFYEPSEIRKISVKQIFNPILFDALGH-PTKGGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYN 88
Cdd:pfam04997 3 KIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLkPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 89 PMFFDNLYAILRAKCIYChqfriSRALMKKYSAQltllqhglvneaqslnelvldfkkteakddetledrmeeqalslst 168
Cdd:pfam04997 83 IGFFKKTLKILECVCKYC-----SKLLLDPGKPK---------------------------------------------- 111
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 169 vedyiehIDTFMKNALADEESRKYAAKdykvtvINEVRKSVMRdfmkqCIHSK-KCANCSGISPPIRRDGaaklfqLALN 247
Cdd:pfam04997 112 -------LFNKDKKRLGLENLKMGAKA------ILELCKKKDL-----CEHCGgKNGVCGSQQPVSRKEG------LKLK 167
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 248 kkdqAAMDRLNNqtgsfEEIKgftngqRFLTPYEVRKhvqaLFEK--EGDITTLLFGARDPRVPSFIkkatyhmffIEVL 325
Cdd:pfam04997 168 ----AAIKKSKE-----EEEK------EILNPEKVLK----IFKRisDEDVEILGFNPSGSRPEWMI---------LTVL 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 326 AVAPTRFRPPSVMGDKTF-ESPQNELLSNILKGSHLVRDLSEELqaisdqepvdkkkleATRNRFVDSIIGLQHAVNSFI 404
Cdd:pfam04997 220 PVPPPCIRPSVQLDGGRRaEDDLTHKLRDIIKRNNRLKKLLELG---------------APSHIIREEWRLLQEHVATLF 284
|
410 420 430
....*....|....*....|....*....|....
gi 1954185479 405 DSTK---NPTQVAQGKNLpPGIRQALEKKEGLFR 435
Cdd:pfam04997 285 DNEIpglPPALQKSKRPL-KSISQRLKGKEGRFR 317
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1165-1212 |
5.69e-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: 91.33 E-value: 5.69e-21
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1954185479 1165 GEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANVTLGIPRLREIIMTA 1212
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
396-652 |
1.33e-20 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 98.28 E-value: 1.33e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVAQGKNLP-PGIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLTy 474
Cdd:PRK02625 307 LQEAVDALIDNGRRGRTVVGANNRPlKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELF- 385
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 475 pEPVTPHNIkeMRQAVINgpNKWPGATHVQNEDQSI-DVLGDLsIEsrialansllapqsshtaqsgnnpyptrtqtink 553
Cdd:PRK02625 386 -QPFVIHRL--IRQGIVN--NIKAAKKLIQRADPEVwQVLEEV-IE---------------------------------- 425
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 554 kvfrhlrnGDMLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAEASFIANTDN 633
Cdd:PRK02625 426 --------GHPVLLNRAPTLHRLGIQAFEPILVEG-RAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASN 496
|
250
....*....|....*....
gi 1954185479 634 QYLVPTSGNPLRGLIQDNV 652
Cdd:PRK02625 497 NILSPATGEPIVTPSQDMV 515
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
396-1222 |
3.81e-17 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 88.20 E-value: 3.81e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 396 LQHAVNSFIDSTKNPTQVAqGKNLPP--GIRQALEKKEGLFRKHMMGKRVNYAARSVISPDPFIETSEIGIPPVFATKLT 473
Cdd:PRK00566 289 LQEAVDALFDNGRRGRPVT-GPNNRPlkSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELF 367
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 474 YP-------EPVTPHNIKemrQAvingpNKWpgathVQNEDQSI-DVLgdlsiesrialansllapqsshtaqsgnnpyp 545
Cdd:PRK00566 368 KPfimkklvERGLATTIK---SA-----KKM-----VEREDPEVwDVL-------------------------------- 402
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 546 trtqtinKKVFR-HLrngdmLLLNRQPTLHKPSIMAHKARILPGeKTIRMHYANCNTYNADFDGDEMNIHFPQNEIARAE 624
Cdd:PRK00566 403 -------EEVIKeHP-----VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAE 469
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 625 ASFIANTDNQYLVPTSGNPlrgliqdnvdsgVWMSSRDT-----FFTKEeyqqllygslRPETDGTGG------------ 687
Cdd:PRK00566 470 ARVLMLSSNNILSPANGKP------------IIVPSQDMvlglyYLTRE----------REGAKGEGMvfsspeealray 527
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 688 --GKIRMLPPAIMKpqplWTGKQVISTilknlTWGKAQLNMTskskVPAKFwgpnakeedkvlvmDGELIHGIMDKSQFG 765
Cdd:PRK00566 528 enGEVDLHARIKVR----ITSKKLVET-----TVGRVIFNEI----LPEGL--------------PFINVNKPLKKKEIS 580
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 766 AsafgLVHSVYEIYSPEAAGMLLSILSRLFIKFLQSHGFTCRMDDLVLTKEgdqwRRELLDqgvglgdEAHLEFlgladt 845
Cdd:PRK00566 581 K----IINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPE----KKEIIE-------EAEKEV------ 639
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 846 aktaspEVLSKEFKL-------RMNEVI----RDDNKLAgldNAMKAKVNKltssitqkclpdgliRPFPKNDMQMMTVS 914
Cdd:PRK00566 640 ------AEIEKQYRRglitdgeRYNKVIdiwsKATDEVA---KAMMKNLSK---------------DQESFNPIYMMADS 695
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 915 GAKGsnvNATQISCLLGqqeLEGrrvpLMV--SGRSLPsfRPFDTSARAGgfvtgrfLTGIrpqEYYF--HcmaG-REGL 989
Cdd:PRK00566 696 GARG---SASQIRQLAG---MRG----LMAkpSGEIIE--TPIKSNFREG-------LTVL---EYFIstH---GaRKGL 750
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 990 IDTAVKTSRSGYLQRCLIKhleglrVHYDHTVRDSD-GSvlqfHYGEDSLDVIKAKHInqfsfsahnFEALSQK------ 1062
Cdd:PRK00566 751 ADTALKTADSGYLTRRLVD------VAQDVIVREDDcGT----DRGIEVTAIIEGGEV---------IEPLEERilgrvl 811
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1063 ----YHPKA----ALASLEIkqGEEYAKKALKKPGKYDPALSVYNPGTHLGVVSerfalamKDYiqknpdGMpfekdsql 1134
Cdd:PRK00566 812 aedvVDPETgeviVPAGTLI--DEEIADKIEEAGIEEVKIRSVLTCETRHGVCA-------KCY------GR-------- 868
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1135 skNTARyagltknkfkalmnlkylHSLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFagyGAANVTLGIPRLREIImtAAR 1214
Cdd:PRK00566 869 --DLAT------------------GKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHT---GGVDITGGLPRVAELF--EAR 923
|
....*...
gi 1954185479 1215 KIKTPTML 1222
Cdd:PRK00566 924 KPKGPAII 931
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
21-99 |
4.15e-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: 83.64 E-value: 4.15e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 21 PSEIRKISVKQIFNPILFDALGHPTK-GGLYDPALGPFQKTQICATCSQDHFNCPGHFGHIEIPIPAYNPMFFDNLYAIL 99
Cdd:cd00399 3 PEEIRKWSVAKVIKPETIDNRTLKAErGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPSFL 82
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1160-1216 |
2.86e-13 |
|
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: 70.25 E-value: 2.86e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1954185479 1160 SLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYgAANVTLGIPRLREIImtAARKI 1216
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEELF--EARKI 54
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
891-1198 |
2.10e-12 |
|
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: 72.58 E-value: 2.10e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 891 TQKCLPDGLIRPF----PKNDMQMMTVSGAKGsnvNATQISCLLGQQEL----EGRRVPLmvsgrslpsfrPFDTSARAG 962
Cdd:TIGR02388 100 TNEELKDEVVNNFrqtdPLNSVYMMAFSGARG---NMSQVRQLVGMRGLmanpQGEIIDL-----------PIKTNFREG 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 963 GFVTgrfltgirpqEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKhleglrVHYDHTVRDSDGSVlqfhygEDSLDVIK 1042
Cdd:TIGR02388 166 LTVT----------EYVISSYGARKGLVDTALRTADSGYLTRRLVD------VSQDVIVREEDCGT------ERSIVVRA 223
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1043 AKHINQ-FSFSAHNFEALSQK--YHPkaalasleikQGEEYAKKAlkkpGKYDPALSvynpgthlgvvSERFALAMKDYI 1119
Cdd:TIGR02388 224 MTEGDKkISLGDRLLGRLVAEdvLHP----------EGEVIVPKN----TAIDPDLA-----------KTIETAGISEVV 278
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1954185479 1120 QKNPdgMPFEKDSQLSKNTARYAgLTKNKfkalmnlkylhsLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAGYGAANV 1198
Cdd:TIGR02388 279 VRSP--LTCEAARSVCRKCYGWS-LAHAH------------LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
895-1192 |
2.10e-10 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 66.17 E-value: 2.10e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 895 LPDGLIRPFPKND----MQMMTVSGAKGsnvNATQISCLLGQQEL----EGRRVPLmvsgrslpsfrPFDTSARAGGFVT 966
Cdd:PRK02597 105 LKDEVVKNFRQNDplnsVYMMAFSGARG---NMSQVRQLVGMRGLmanpQGEIIDL-----------PIKTNFREGLTVT 170
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 967 grfltgirpqEYYFHCMAGREGLIDTAVKTSRSGYLQRCLIKhleglrVHYDHTVRDSD-----GSVLQfhyGEDSLDVI 1041
Cdd:PRK02597 171 ----------EYVISSYGARKGLVDTALRTADSGYLTRRLVD------VSQDVIVREEDcgttrGIVVE---AMDDGDRV 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1042 KAKhinqfsfsahnfeaLSQKYHPKAALASLEIKQGEEYAKKAlkkpGKYDPALSvynpgthlgvvsERFALAMKDYIQK 1121
Cdd:PRK02597 232 LIP--------------LGDRLLGRVLAEDVVDPEGEVIAERN----TAIDPDLA------------KKIEKAGVEEVMV 281
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1954185479 1122 NpdgmpfekdSQLSKNTAR------YA-GLTKNKfkalmnlkylhsLVEPGEAVGLLAAQSVGEPSTQMTLNTFHFAG 1192
Cdd:PRK02597 282 R---------SPLTCEAARsvcrkcYGwSLAHNH------------LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGG 338
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1160-1189 |
2.15e-09 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 62.65 E-value: 2.15e-09
10 20 30
....*....|....*....|....*....|
gi 1954185479 1160 SLVEPGEAVGLLAAQSVGEPSTQMTLNTFH 1189
Cdd:CHL00117 310 DLVELGEAVGIIAGQSIGEPGTQLTLRTFH 339
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1522-1641 |
2.18e-09 |
|
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: 61.28 E-value: 2.18e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1954185479 1522 VNYIDT-----NDIAAILNTYGVEAARNAIIKEVASVFAVYGIVVDRRHLTLIADYMTFEGGYKPFSRIGIG------SN 1590
Cdd:cd02737 249 MDLIDWersmpYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKaqrrslKI 328
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 1954185479 1591 VAPFLKMSFESTCKFLTEATLHGDFDTLDSPSSRIVVGRVVEGGTGS-FDVL 1641
Cdd:cd02737 329 SAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSkFEIL 380
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1156-1185 |
4.09e-06 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 51.82 E-value: 4.09e-06
10 20 30
....*....|....*....|....*....|
gi 1954185479 1156 KYLHSLVEPGEAVGLLAAQSVGEPSTQMTL 1185
Cdd:PRK14898 48 AYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
