|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
795-1382 |
1.45e-155 |
|
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: 480.70 E-value: 1.45e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 795 GLTSPEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIVDYYRRV-SIDTRLVQQLYGEDGLDARQLETVRFETI 873
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVrNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 874 MLSDQELEDKFKYTGIQSPLFEEEFSRLKKDRDKYRQIFLnienfnfsqlltdvrqvpvnvasivknillsstsgvlpfd 953
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKL---------------------------------------- 120
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 954 eksilqkytmvktfcknlpyvfinnIQERLQTPIPVYLKRAASLMRILIRIELATVKTLNITCEQMSAILDLIRLQYTQS 1033
Cdd:pfam04998 121 -------------------------GRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLLCYGRLLYQQS 175
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1034 LINYGEAVGILAAQSVSEPLTQYMLDSHHRSVAGGTN-KSGIVRPQEIfsaKPVEAEQSSEMLLRLKNPEVETNKTYAQE 1112
Cdd:pfam04998 176 LINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNvTLGVPRLKEI---INVSKNIKSPSLTVYLFDEVGRELEKAKK 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1113 IANSIELITFERLILQWHLLYETYSSTKKNVMYPDFASDVEWMTDFLENHPLLQPPEDIANWCIRLELNKTTMILKSISL 1192
Cdd:pfam04998 253 VYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDPETGLLILVIRLLKILNKSIKKVVKS 332
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1193 ESIVNSLRAKHSNTYIMHSVENTASGIPIIIRIYLRESAFRRSTNTRMATDEKIAVNLVDKLLNSTIRGIPGIKNANVVK 1272
Cdd:pfam04998 333 EVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDELFMEEDPKLAILVASLLGNITLRGIPGIKRILVNE 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1273 LMRHRVDAQgklvrldniYAIKTNGTNIFGAMLDDN-IDPYTIVSSSIGDTMELYGIEAARQKIISEIRTVMGDKGP--N 1349
Cdd:pfam04998 413 DDKGKVEPD---------WVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQGIyiN 483
|
570 580 590
....*....|....*....|....*....|...
gi 1755167230 1350 HRHLLMYADLMTRTGQVTSLEKAGLNAREPSNV 1382
Cdd:pfam04998 484 DRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
7-861 |
5.54e-140 |
|
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: 451.32 E-value: 5.54e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 7 EIAAVQFNIAGDNDHKRQGVMEVTISNLF-EGTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQP 85
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYdEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 86 LFIAEIRRWLRVICLNCGAPIV---DLKRYEHLIR---------PKRLAE-----AASSqtegKQCYVCKVIHPKIIKDS 148
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLpeeEIEKYLERIRrlkekwpelVKRVIEkvkkkAKKR----KVCPHCGAPQYKIKLEK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 149 EdyFTFWVDQQGKIDKLYPQIIREIFSRVTYDTVVKLG-RSKNSHPEKLVLKAIQIPPISIRPGIRLGigSGPQSFHDIN 227
Cdd:cd02582 159 P--TTFYEEKEEGEVKLTPSEIRERLEKIPDEDLELLGiDPKTARPEWMVLTVLPVPPVTVRPSITLE--TGERSEDDLT 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 228 NVIQYIVRKNllipkdlqivrgQKIPLNVDRNL-QTIQQLYYNFLLDSVST---TATQGGTGKRGivMGARPAPSIMRRL 303
Cdd:cd02582 235 HKLVDIIRIN------------QRLKENIEAGApQLIIEDLWDLLQYHVTTyfdNEIPGIPPARH--RSGRPLKTLAQRL 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 304 PRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYK-- 381
Cdd:cd02582 301 KGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRpd 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 382 --QITQSVHDIEGLKQdfRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFD 459
Cdd:cd02582 381 grRIRLRYVNREELAE--RLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG---KTFRLNLAVCPPYNADFD 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 460 GDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKN-VMNKLHAMGLFQttqtDP 538
Cdd:cd02582 456 GDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEeALQLLSAAGYDG----LL 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 539 PCFANYSPTDLLDGKSVVSMLLKQTpINYQRAPTWYSEVYAPYMHYNKQDISTQIRNGELIEGVLDKKAVGAGSSGGIYH 618
Cdd:cd02582 532 PEPAILEPKPLWTGKQLFSLFLPKD-LNFEGKAKVCSGCSECKDEDCPNDGYVVIKNGKLLEGVIDKKAIGAEQPGSLLH 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 619 LISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADMLLTPEAHQEVQEIINELLLESEEINNRLLHGDIMPPIGLTTH 698
Cdd:cd02582 611 RIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLE 690
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 699 DFYEKLQLNAL-KFPDRILKPIMNSINPEtNGLFQMVATGAKGSNPNMIHIMAGIGQIEINTQRIQPQFSfGRTLVYYPR 777
Cdd:cd02582 691 ETLEMKIMQVLgKARDEAGKVASKYLDPF-NNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYR-NRTLPHFKP 768
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 778 FALEAQAYGFICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIVDYYRRVSiDTR--LVQQLY 855
Cdd:cd02582 769 GDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVR-DSRgnIIQFKY 847
|
....*.
gi 1755167230 856 GEDGLD 861
Cdd:cd02582 848 GEDGVD 853
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
5-1432 |
4.18e-139 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 461.42 E-value: 4.18e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 5 YAEIAAVQFNIAGDNDHKRQGVMEVTISNLF-EGTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVL 83
Cdd:PRK14977 6 VKAIDGIIFGLISPADARKIGFAEITAPEAYdEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPVI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 84 QPLFIAEIRRWLRVICLNCG---APIVDLKRYEHLIR-------------PKRLAEAASSQT-----EGKQCYVC-KVIH 141
Cdd:PRK14977 86 HIAFIDNIKDLLNSTCHKCAklkLPQEDLNVFKLIEEahaaardipekriDDEIIEEVRDQVkvyakKAKECPHCgAPQH 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 142 PKIIkdsEDYFTFWVDQQGKIDKLYPQIIREIFSRVTYDTVVKLG-RSKNSHPEKLVLKAIQIPPISIRPGIRLGigSGP 220
Cdd:PRK14977 166 ELEF---EEPTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELIGfDPKKARPEWAVLQAFLVPPLTARPSIILE--TGE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 221 QSFHDINNVIQYIVRKNllipKDLQIVRGQKIPLNVDRNLQTIQQLYYNFLLDSVST---TATQGGTGkrgivmgaRPAP 297
Cdd:PRK14977 241 RSEDDLTHILVDIIKAN----QKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAgipQAHHKGSG--------RPLK 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 298 SIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCS 377
Cdd:PRK14977 309 SLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGAN 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 378 RVYK--------QITQSVHDIEGLKQDFRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVS 449
Cdd:PRK14977 389 AIRKgdgtkirlDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPG---ATFRLHPA 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 450 ACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKNVMNKLHAMG 529
Cdd:PRK14977 466 VCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLA 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 530 LFqtTQTDPPCFANYSPTDLLDGKSVVSMLLKQTpINYQRAPTWY----SEVYAPYMhynKQDISTQIRNGELIEGVLDK 605
Cdd:PRK14977 546 GI--TDPLPEPAIKTKDGPAWTGKQLFSLFLPKD-FNFEGIAKWSagkaGEAKDPSC---LGDGYVLIKEGELISGVIDD 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 606 KAVGAGSSG--GIYHLISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADMLLTPEAHQEVQEIINEL------LLES 677
Cdd:PRK14977 620 NIIGALVEEpeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMkdevsdLIDQ 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 678 EEINNR--LLHGDIMPPIGLTTHDFYEKLQLNAL-KFPDRILKPIMNSINPETNGLFqMVATGAKGSNPNMIHIMAGIGQ 754
Cdd:PRK14977 700 RKITRKitIYKGKEELLRGMKEEEALEADIVNELdKARDKAGSSANDCIDADNAGKI-MAKTGARGSMANLAQIAGALGQ 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 755 IEINTqRIQPQFSFG--------RTLVYYPRFALEAQAYGFICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSSTGYAN 826
Cdd:PRK14977 779 QKRKT-RIGFVLTGGrlhegykdRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQ 857
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 827 RKAIFGLQSCIVDYYRRVSiDT--RLVQQLYGEDGLDARqletvrfetimlsdqeledkfkytgiqsplfeeefsrlKKD 904
Cdd:PRK14977 858 RRLANALEDIRLEYDETVR-DPhgHIIQFKFGEDGIDPQ--------------------------------------KLD 898
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 905 RDkyrqiflniENFNFSQLltdvrqvpvnvasIVKNILLSSTSGVLPFDEKSILQKYTmvKTFCKNLPYVFINNIQ-ERL 983
Cdd:PRK14977 899 HG---------EAFNLERI-------------IEKQKIEDRGKGASKDEIEELAKEYT--KTFNANLPKLLADAIHgAEL 954
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 984 QTpipvylkraaslmrilirielatvktlnitcEQMSAILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDSHHR 1063
Cdd:PRK14977 955 KE-------------------------------DELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHA 1003
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1064 SVAGGTNKS-GIVRPQEI--FSAKPVeaeqSSEMLLRLKNpEVETNKTYAQEIANSIELITFERLILQwhllYETYSSTK 1140
Cdd:PRK14977 1004 AGIKAMDVThGLERFIELvdARAKPS----TPTMDIYLDD-ECKEDIEKAIEIARNLKELKVRALIAD----SAIDNANE 1074
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1141 KNVMYPDfasdvewmTDFLENHpllqppedianwcirlelnkttmilkSISLESIVNSLRAKHSNTyimhSVENTASGIP 1220
Cdd:PRK14977 1075 IKLIKPD--------KRALENG--------------------------CIPMERFAEIEAALAKGK----KFEMELEDDL 1116
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1221 IIIRIYlrESAfrrSTNTRMATDEKIAvnlvDKLLNSTIRGIPGIKNANVVKLMRHRVDAqgklvrldniYAIKTNGTNI 1300
Cdd:PRK14977 1117 IILDLV--EAA---DRDKPLATLIAIR----NKILDKPVKGVPDIERAWVELVEKDGRDE----------WIIQTSGSNL 1177
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1301 FGAMLDDNIDPYTIVSSSIGDTMELYGIEAARQKIISEIRTVMGDKG--PNHRHLLMYADLMTRTG--QVTSLEKAGLN- 1375
Cdd:PRK14977 1178 AAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGleVDNRYIMLVADIMCSRGtiEAIGLQAAGVRh 1257
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....*....
gi 1755167230 1376 --AREPSNVLLRMALSSPVQVLTDAAIDSAVNPIYGIAAPTLMGSVPRIGTMYSDIIMD 1432
Cdd:PRK14977 1258 gfAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMD 1316
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
194-508 |
4.49e-93 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 302.52 E-value: 4.49e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 194 EKLVLKAIQIPPISIRPGIRLGIGSgpQSFHDINNVIQYIVRKNLLIPKDLQIvrgqKIPLNVDRNLQTIQQLYYNFLLD 273
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGR--FAEDDLTHLLRDIIKRNNRLKRLLEL----GAPSIIIRNEKRLLQEAVDTLID 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 274 SvstTATQGGTGKRGivmgaRPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAET 353
Cdd:smart00663 75 N---EGLPRANQKSG-----RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEI 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 354 VQHYNINRLMPYFLNGKrqyPGCSRVYKQITQSVHDIEGLKQDFRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRI 433
Cdd:smart00663 147 VTPLNIDKLRKLVRNGP---NGAKYIIRGKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRV 223
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1755167230 434 VVLENpkiSTFQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSF 508
Cdd:smart00663 224 RVLEG---KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
316-483 |
4.58e-77 |
|
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: 251.84 E-value: 4.58e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 316 GSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYkQITQSVHDIEGLKQ 395
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYII-RINGARRDLRYQKR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 396 --DFRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFDGDQMNLWVPWSVMS 473
Cdd:pfam00623 80 rlDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG---KTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 156
|
170
....*....|
gi 1755167230 474 RVEAELLCSV 483
Cdd:pfam00623 157 RAEAEELMLV 166
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1022-1432 |
8.06e-44 |
|
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: 165.07 E-value: 8.06e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1022 ILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDSHHrsVAGGTNKS---GIVRPQEIFS-AKPVeaeQSSEMLLR 1097
Cdd:cd02584 11 ILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFH--FAGVSAKNvtlGVPRLKEIINvAKNI---KTPSLTVY 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1098 LKnPEVETNKTYAQEIANSIELITFERLILQWHLLYEtysstkknvmyPDFAS-----DVEWMTDFLENHPLLQPPEDIA 1172
Cdd:cd02584 86 LE-PGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYD-----------PDPQNtvieeDKEFVESYFEFPDEDVEQDRLS 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1173 NWCIRLELNKTTMILKSISLESIVNSLRAKHSNT-YIMHSVENTASgipIIIRIYLRESafrRSTNTRMATDEKIAVNLV 1251
Cdd:cd02584 154 PWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDlNVIFSDDNAEK---LVIRIRIIND---DEEKEEDSEDDVFLKKIE 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1252 DKLLNSTI-RGIPGIKnanvVKLMR----HRVDAQGKLVRLDNIYAIKTNGTNIFGAMLDDNIDPYTIVSSSIGDTMELY 1326
Cdd:cd02584 228 SNMLSDMTlKGIEGIR----KVFIReenkKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVL 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1327 GIEAARQKIISEIRTVMGDKGP--NHRHLLMYADLMTRTGQVTSLEKAGLNaREPSNVLLRMALSSPVQVLTDAAIDSAV 1404
Cdd:cd02584 304 GIEAARKALLKELRNVISFDGSyvNYRHLALLCDVMTQRGHLMAITRHGIN-RQDTGPLMRCSFEETVDILLEAAAFGET 382
|
410 420
....*....|....*....|....*...
gi 1755167230 1405 NPIYGIAAPTLMGSVPRIGTMYSDIIMD 1432
Cdd:cd02584 383 DDLKGVSENIMLGQLAPIGTGCFDLLLD 410
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1007-1435 |
2.98e-39 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 151.15 E-value: 2.98e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1007 ATVKTLNITCEQMSAILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDS-HHRSVAGGTNKSGIVRPQEIFSAK- 1084
Cdd:PRK04309 28 EKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTfHYAGVAEINVTLGLPRLIEIVDARk 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1085 ----PVeaeqsseMLLRLKnPEVETNKTYAQEIANSIELITFErlilqwhllyetysstkknvmypDFASDVEWmtdfle 1160
Cdd:PRK04309 108 epstPM-------MTIYLK-DEYAYDREKAEEVARKIEATTLE-----------------------NLAKDISV------ 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1161 nhpllqppeDIANWCIRLELNKTTMILKSISLESIVNSLRakhSNTYIMHSVENTasgipiIIRIYLRE---SAFRRstn 1237
Cdd:PRK04309 151 ---------DLANMTIIIELDEEMLEDRGLTVDDVKEAIE---KKKGGEVEIEGN------TLIISPKEpsyRELRK--- 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1238 trmatdekiavnLVDKLLNSTIRGIPGIKNANVvklmRHRVDAqgklvrldniYAIKTNGTNIFGAMLDDNIDPYTIVSS 1317
Cdd:PRK04309 210 ------------LAEKIRNIKIKGIKGIKRVII----RKEGDE----------YVIYTEGSNLKEVLKVEGVDATRTTTN 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1318 SIGDTMELYGIEAARQKIISEIRTVMGDKG--PNHRHLLMYADLMTRTGQVTSLEKAGLNAREPSnVLLRMALSSPVQVL 1395
Cdd:PRK04309 264 NIHEIEEVLGIEAARNAIIEEIKNTLEEQGldVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKAS-VLARAAFEVTVKHL 342
|
410 420 430 440
....*....|....*....|....*....|....*....|
gi 1755167230 1396 TDAAIDSAVNPIYGIAAPTLMGSVPRIGTMYSDIIMDEKY 1435
Cdd:PRK04309 343 LDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
187-1084 |
2.56e-28 |
|
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: 124.39 E-value: 2.56e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 187 RSKNsHPEKLVLKAIQIPPISIRPGIRLGIGSGPQSfhDINNVIQYIVRKNLLIPKDLQIvrgqKIPLNVDRNLQTIQQL 266
Cdd:TIGR02386 211 DSGN-RPEWMVLDVIPVIPPELRPMVQLDGGRFATS--DLNDLYRRVINRNNRLKRLLEL----GAPEIIVRNEKRMLQE 283
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 267 YYNFLLDSvsttatqggtGKRG-IVMGA--RPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPIS 343
Cdd:TIGR02386 284 AVDALFDN----------GRRGkPVVGKnnRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKK 353
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 344 FARTLqvaetVQHYNINRLMpyflngKRQYPGCSRVYKQITQSVHDieglkqdfrlEVGDILYrDVVTGDVAFFNRQPSL 423
Cdd:TIGR02386 354 MALEL-----FKPFIIKRLI------DRELAANIKSAKKMIEQEDP----------EVWDVLE-DVIKEHPVLLNRAPTL 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 424 ERSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDS 503
Cdd:TIGR02386 412 HRLGIQAFEPVLVEGKAI---RLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDM 488
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 504 TVGSFLLTRTNTPM---GKNVMNKLHAMGLFQTTQTDppcfanyspTDLLDGKSVVSMLLKQTP---INYQRAPTWYsev 577
Cdd:TIGR02386 489 VLGLYYLTTEKPGAkgeGKIFSNVDEAIRAYDNGKVH---------LHALIGVRTSGEILETTVgrvIFNEILPEGF--- 556
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 578 yaPYMHYNKqdistqirngeliegVLDKKAVGAgssggIYHLISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADML 657
Cdd:TIGR02386 557 --PYINDNE---------------PLSKKEISS-----LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIV 614
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 658 LTPEAhqevQEIINELLLESEEINNRLLHGDImppiglTTHDFYEKLQLNALKFPDRILKPIMNSINPET---NGLFQMV 734
Cdd:TIGR02386 615 VPDEK----YEILKEADKEVAKIQKFYNKGLI------TDEERYRKVVSIWSETKDKVTDAMMKLLKKDTykfNPIFMMA 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 735 ATGAKGSNPNMIHImAGIGQIEINTqriqpqfsFGRTlVYYPrfaleaqaygfICNSYIAGLTSPEFIFGEMNGRFDLIN 814
Cdd:TIGR02386 685 DSGARGNISQFRQL-AGMRGLMAKP--------SGDI-IELP-----------IKSSFREGLTVLEYFISTHGARKGLAD 743
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 815 KALSTSSTGYANRKaifglqscIVDYYRRVSIDTRlvqqlygedglDARQLETVRFETIMLSDQEledkfkytgIQSPLF 894
Cdd:TIGR02386 744 TALKTADSGYLTRR--------LVDVAQDVVVREE-----------DCGTEEGIEVEAIVEGKDE---------IIESLK 795
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 895 EEEFSRLkkdrdkyrqiflnienfnfsqLLTDVRQvpvnvasivknillsstsgvlPFDEKSILQKYTMVKTfcknlpyv 974
Cdd:TIGR02386 796 DRIVGRY---------------------SAEDVYD---------------------PDTGKLIAEANTLITE-------- 825
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 975 finniqerlqtpipvylkraaslmRILIRIELATVKTLNI----TCEQMSAI------LDLIrlqyTQSLINYGEAVGIL 1044
Cdd:TIGR02386 826 ------------------------EIAEKIENSGIEKVKVrsvlTCESEHGVcqkcygRDLA----TGKLVEIGEAVGVI 877
|
890 900 910 920
....*....|....*....|....*....|....*....|...
gi 1755167230 1045 AAQSVSEPLTQYMLDSHHRSVAGGTNKS---GIVRPQEIFSAK 1084
Cdd:TIGR02386 878 AAQSIGEPGTQLTMRTFHTGGVAGASGDitqGLPRVKELFEAR 920
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
187-669 |
5.46e-16 |
|
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: 84.06 E-value: 5.46e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 187 RSKNSHPEKLVLKAI-QIPPiSIRPGIRLGIGSGPQSfhDIN----NVIQyivRKNLLiPKDLQIvrgqKIPLNVDRNLQ 261
Cdd:COG0086 218 RESGNRPEWMILDVLpVIPP-DLRPLVPLDGGRFATS--DLNdlyrRVIN---RNNRL-KRLLEL----KAPDIIVRNEK 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 262 TIQQLYYNFLLDSvsttatqggtGKRGIVM---GARPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEV 338
Cdd:COG0086 287 RMLQEAVDALFDN----------GRRGRAVtgaNKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQC 356
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 339 GYPISFArtlqvAETVQHYNINRLMPYFLngkrqypgcsrvykqitqsVHDIEGLK---QDFRLEVGDILyRDVVTGDVA 415
Cdd:COG0086 357 GLPKKMA-----LELFKPFIYRKLEERGL-------------------ATTIKSAKkmvEREEPEVWDIL-EEVIKEHPV 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 416 FFNRQPSLERSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGP 495
Cdd:COG0086 412 LLNRAPTLHRLGIQAFEPVLIEGKAI---QLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKP 488
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 496 VNGQVQDSTVGSFLLTRTNTPM---GK-------------NVMNKLHAMGLFQTTQTDPPCFANYSPTdllDGKSVVSML 559
Cdd:COG0086 489 IIVPSQDMVLGLYYLTREREGAkgeGMifadpeevlrayeNGAVDLHARIKVRITEDGEQVGKIVETT---VGRYLVNEI 565
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 560 LKQtpinyqraptwysEVyaPYmhYNKqdistqirngeliegVLDKKAVGAgssggIYHLISRRYGPQQALKMIFATQQL 639
Cdd:COG0086 566 LPQ-------------EV--PF--YNQ---------------VINKKHIEV-----IIRQMYRRCGLKETVIFLDRLKKL 608
|
490 500 510
....*....|....*....|....*....|....*..
gi 1755167230 640 ALNYVRNAGFTVSTADMLLTP-------EAHQEVQEI 669
Cdd:COG0086 609 GFKYATRAGISIGLDDMVVPKekqeifeEANKEVKEI 645
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
795-1382 |
1.45e-155 |
|
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: 480.70 E-value: 1.45e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 795 GLTSPEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIVDYYRRV-SIDTRLVQQLYGEDGLDARQLETVRFETI 873
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVrNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 874 MLSDQELEDKFKYTGIQSPLFEEEFSRLKKDRDKYRQIFLnienfnfsqlltdvrqvpvnvasivknillsstsgvlpfd 953
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKL---------------------------------------- 120
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 954 eksilqkytmvktfcknlpyvfinnIQERLQTPIPVYLKRAASLMRILIRIELATVKTLNITCEQMSAILDLIRLQYTQS 1033
Cdd:pfam04998 121 -------------------------GRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLLCYGRLLYQQS 175
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1034 LINYGEAVGILAAQSVSEPLTQYMLDSHHRSVAGGTN-KSGIVRPQEIfsaKPVEAEQSSEMLLRLKNPEVETNKTYAQE 1112
Cdd:pfam04998 176 LINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNvTLGVPRLKEI---INVSKNIKSPSLTVYLFDEVGRELEKAKK 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1113 IANSIELITFERLILQWHLLYETYSSTKKNVMYPDFASDVEWMTDFLENHPLLQPPEDIANWCIRLELNKTTMILKSISL 1192
Cdd:pfam04998 253 VYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDPETGLLILVIRLLKILNKSIKKVVKS 332
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1193 ESIVNSLRAKHSNTYIMHSVENTASGIPIIIRIYLRESAFRRSTNTRMATDEKIAVNLVDKLLNSTIRGIPGIKNANVVK 1272
Cdd:pfam04998 333 EVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDELFMEEDPKLAILVASLLGNITLRGIPGIKRILVNE 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1273 LMRHRVDAQgklvrldniYAIKTNGTNIFGAMLDDN-IDPYTIVSSSIGDTMELYGIEAARQKIISEIRTVMGDKGP--N 1349
Cdd:pfam04998 413 DDKGKVEPD---------WVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQGIyiN 483
|
570 580 590
....*....|....*....|....*....|...
gi 1755167230 1350 HRHLLMYADLMTRTGQVTSLEKAGLNAREPSNV 1382
Cdd:pfam04998 484 DRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
7-861 |
5.54e-140 |
|
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: 451.32 E-value: 5.54e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 7 EIAAVQFNIAGDNDHKRQGVMEVTISNLF-EGTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQP 85
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYdEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 86 LFIAEIRRWLRVICLNCGAPIV---DLKRYEHLIR---------PKRLAE-----AASSqtegKQCYVCKVIHPKIIKDS 148
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLpeeEIEKYLERIRrlkekwpelVKRVIEkvkkkAKKR----KVCPHCGAPQYKIKLEK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 149 EdyFTFWVDQQGKIDKLYPQIIREIFSRVTYDTVVKLG-RSKNSHPEKLVLKAIQIPPISIRPGIRLGigSGPQSFHDIN 227
Cdd:cd02582 159 P--TTFYEEKEEGEVKLTPSEIRERLEKIPDEDLELLGiDPKTARPEWMVLTVLPVPPVTVRPSITLE--TGERSEDDLT 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 228 NVIQYIVRKNllipkdlqivrgQKIPLNVDRNL-QTIQQLYYNFLLDSVST---TATQGGTGKRGivMGARPAPSIMRRL 303
Cdd:cd02582 235 HKLVDIIRIN------------QRLKENIEAGApQLIIEDLWDLLQYHVTTyfdNEIPGIPPARH--RSGRPLKTLAQRL 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 304 PRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYK-- 381
Cdd:cd02582 301 KGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRpd 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 382 --QITQSVHDIEGLKQdfRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFD 459
Cdd:cd02582 381 grRIRLRYVNREELAE--RLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG---KTFRLNLAVCPPYNADFD 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 460 GDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKN-VMNKLHAMGLFQttqtDP 538
Cdd:cd02582 456 GDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEeALQLLSAAGYDG----LL 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 539 PCFANYSPTDLLDGKSVVSMLLKQTpINYQRAPTWYSEVYAPYMHYNKQDISTQIRNGELIEGVLDKKAVGAGSSGGIYH 618
Cdd:cd02582 532 PEPAILEPKPLWTGKQLFSLFLPKD-LNFEGKAKVCSGCSECKDEDCPNDGYVVIKNGKLLEGVIDKKAIGAEQPGSLLH 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 619 LISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADMLLTPEAHQEVQEIINELLLESEEINNRLLHGDIMPPIGLTTH 698
Cdd:cd02582 611 RIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLE 690
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 699 DFYEKLQLNAL-KFPDRILKPIMNSINPEtNGLFQMVATGAKGSNPNMIHIMAGIGQIEINTQRIQPQFSfGRTLVYYPR 777
Cdd:cd02582 691 ETLEMKIMQVLgKARDEAGKVASKYLDPF-NNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYR-NRTLPHFKP 768
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 778 FALEAQAYGFICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIVDYYRRVSiDTR--LVQQLY 855
Cdd:cd02582 769 GDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVR-DSRgnIIQFKY 847
|
....*.
gi 1755167230 856 GEDGLD 861
Cdd:cd02582 848 GEDGVD 853
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
5-1432 |
4.18e-139 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 461.42 E-value: 4.18e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 5 YAEIAAVQFNIAGDNDHKRQGVMEVTISNLF-EGTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVL 83
Cdd:PRK14977 6 VKAIDGIIFGLISPADARKIGFAEITAPEAYdEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPVI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 84 QPLFIAEIRRWLRVICLNCG---APIVDLKRYEHLIR-------------PKRLAEAASSQT-----EGKQCYVC-KVIH 141
Cdd:PRK14977 86 HIAFIDNIKDLLNSTCHKCAklkLPQEDLNVFKLIEEahaaardipekriDDEIIEEVRDQVkvyakKAKECPHCgAPQH 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 142 PKIIkdsEDYFTFWVDQQGKIDKLYPQIIREIFSRVTYDTVVKLG-RSKNSHPEKLVLKAIQIPPISIRPGIRLGigSGP 220
Cdd:PRK14977 166 ELEF---EEPTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELIGfDPKKARPEWAVLQAFLVPPLTARPSIILE--TGE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 221 QSFHDINNVIQYIVRKNllipKDLQIVRGQKIPLNVDRNLQTIQQLYYNFLLDSVST---TATQGGTGkrgivmgaRPAP 297
Cdd:PRK14977 241 RSEDDLTHILVDIIKAN----QKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAgipQAHHKGSG--------RPLK 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 298 SIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCS 377
Cdd:PRK14977 309 SLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGAN 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 378 RVYK--------QITQSVHDIEGLKQDFRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVS 449
Cdd:PRK14977 389 AIRKgdgtkirlDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPG---ATFRLHPA 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 450 ACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKNVMNKLHAMG 529
Cdd:PRK14977 466 VCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLA 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 530 LFqtTQTDPPCFANYSPTDLLDGKSVVSMLLKQTpINYQRAPTWY----SEVYAPYMhynKQDISTQIRNGELIEGVLDK 605
Cdd:PRK14977 546 GI--TDPLPEPAIKTKDGPAWTGKQLFSLFLPKD-FNFEGIAKWSagkaGEAKDPSC---LGDGYVLIKEGELISGVIDD 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 606 KAVGAGSSG--GIYHLISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADMLLTPEAHQEVQEIINEL------LLES 677
Cdd:PRK14977 620 NIIGALVEEpeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMkdevsdLIDQ 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 678 EEINNR--LLHGDIMPPIGLTTHDFYEKLQLNAL-KFPDRILKPIMNSINPETNGLFqMVATGAKGSNPNMIHIMAGIGQ 754
Cdd:PRK14977 700 RKITRKitIYKGKEELLRGMKEEEALEADIVNELdKARDKAGSSANDCIDADNAGKI-MAKTGARGSMANLAQIAGALGQ 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 755 IEINTqRIQPQFSFG--------RTLVYYPRFALEAQAYGFICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSSTGYAN 826
Cdd:PRK14977 779 QKRKT-RIGFVLTGGrlhegykdRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQ 857
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 827 RKAIFGLQSCIVDYYRRVSiDT--RLVQQLYGEDGLDARqletvrfetimlsdqeledkfkytgiqsplfeeefsrlKKD 904
Cdd:PRK14977 858 RRLANALEDIRLEYDETVR-DPhgHIIQFKFGEDGIDPQ--------------------------------------KLD 898
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 905 RDkyrqiflniENFNFSQLltdvrqvpvnvasIVKNILLSSTSGVLPFDEKSILQKYTmvKTFCKNLPYVFINNIQ-ERL 983
Cdd:PRK14977 899 HG---------EAFNLERI-------------IEKQKIEDRGKGASKDEIEELAKEYT--KTFNANLPKLLADAIHgAEL 954
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 984 QTpipvylkraaslmrilirielatvktlnitcEQMSAILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDSHHR 1063
Cdd:PRK14977 955 KE-------------------------------DELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHA 1003
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1064 SVAGGTNKS-GIVRPQEI--FSAKPVeaeqSSEMLLRLKNpEVETNKTYAQEIANSIELITFERLILQwhllYETYSSTK 1140
Cdd:PRK14977 1004 AGIKAMDVThGLERFIELvdARAKPS----TPTMDIYLDD-ECKEDIEKAIEIARNLKELKVRALIAD----SAIDNANE 1074
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1141 KNVMYPDfasdvewmTDFLENHpllqppedianwcirlelnkttmilkSISLESIVNSLRAKHSNTyimhSVENTASGIP 1220
Cdd:PRK14977 1075 IKLIKPD--------KRALENG--------------------------CIPMERFAEIEAALAKGK----KFEMELEDDL 1116
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1221 IIIRIYlrESAfrrSTNTRMATDEKIAvnlvDKLLNSTIRGIPGIKNANVVKLMRHRVDAqgklvrldniYAIKTNGTNI 1300
Cdd:PRK14977 1117 IILDLV--EAA---DRDKPLATLIAIR----NKILDKPVKGVPDIERAWVELVEKDGRDE----------WIIQTSGSNL 1177
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1301 FGAMLDDNIDPYTIVSSSIGDTMELYGIEAARQKIISEIRTVMGDKG--PNHRHLLMYADLMTRTG--QVTSLEKAGLN- 1375
Cdd:PRK14977 1178 AAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGleVDNRYIMLVADIMCSRGtiEAIGLQAAGVRh 1257
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....*....
gi 1755167230 1376 --AREPSNVLLRMALSSPVQVLTDAAIDSAVNPIYGIAAPTLMGSVPRIGTMYSDIIMD 1432
Cdd:PRK14977 1258 gfAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMD 1316
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
10-840 |
2.40e-134 |
|
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: 432.73 E-value: 2.40e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 10 AVQFNIAGDNDHKRQGVMEVTISNLFE-GTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQPLFI 88
Cdd:cd02733 2 RVQFGILSPDEIRAMSVAEIEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGFL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 89 AEIRRWLRviclncgapivdlkryehlirpkrlaeaassqtegkqCyVCKVIhpkiikdsedyftfwvdqqgkidkLYPQ 168
Cdd:cd02733 82 TKILKILR-------------------------------------C-VCKRE------------------------LSAE 99
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 169 IIREIFSRVTYDTVVKLGRS-KNSHPEKLVLKAIQIPPISIRPGIRLGIGSGPQSfhDINNVIQYIVRKNLLIPKDLQIV 247
Cdd:cd02733 100 RVLEIFKRISDEDCRILGFDpKFSRPDWMILTVLPVPPPAVRPSVVMDGSARSED--DLTHKLADIIKANNQLKRQEQNG 177
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 248 RGQKIplnVDRNLQTIQQLYYNFLLDSVST--TATQGGTgkrgivmgaRPAPSIMRRLPRKEGRIRKSLLGSQVWSISRS 325
Cdd:cd02733 178 APAHI---IEEDEQLLQFHVATYMDNEIPGlpQATQKSG---------RPLKSIRQRLKGKEGRIRGNLMGKRVDFSART 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 326 TICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYKQITQSVhDIEGLKQ--DFRLEVGD 403
Cdd:cd02733 246 VITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGERI-DLRYLKKasDLHLQYGY 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 404 ILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSV 483
Cdd:cd02733 325 IVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPY---STFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMV 401
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 484 RNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGK-NVMNKLHAMGLFqTTQTDPPCFANysPTDLLDGKSVVSMLLKQ 562
Cdd:cd02733 402 PRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKdQVMNLLMWLPDW-DGKIPQPAILK--PKPLWTGKQIFSLIIPK 478
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 563 TpINYQRAPTWYSEVYAPYMHYNKQDIstqIRNGELIEGVLDKKAVGAgSSGGIYHLISRRYGPQQALKMIFATQQLALN 642
Cdd:cd02733 479 I-NNLIRSSSHHDGDKKWISPGDTKVI---IENGELLSGILCKKTVGA-SSGGLIHVIWLEYGPEAARDFIGNIQRVVNN 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 643 YVRNAGFTVSTADMLLTPEAHQEVQEIINELLLESEEINNRLLHGDIMPPIGLTTHDFYE---KLQLNALKfpDRILKPI 719
Cdd:cd02733 554 WLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFEnkvNRILNKAR--DKAGKSA 631
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 720 MNSINpETNGLFQMVATGAKGSNPNMIHIMAGIGQIEINTQRIqpQFSF-GRTLVYYPRFALEAQAYGFICNSYIAGLTS 798
Cdd:cd02733 632 QKSLS-EDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRI--PFGFrRRTLPHFIKDDYGPESRGFVENSYLRGLTP 708
|
810 820 830 840
....*....|....*....|....*....|....*....|..
gi 1755167230 799 PEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIVDY 840
Cdd:cd02733 709 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKY 750
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
7-861 |
3.88e-120 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 398.07 E-value: 3.88e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 7 EIAAVQFNIAGDNDHKRQGVMEVTISNLF-EGTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQP 85
Cdd:PRK08566 8 RIGSIKFGLLSPEEIRKMSVTKIITADTYdDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIHV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 86 LFIAEIRRWLRVICLNCGAPIVD-------LKRYEHLIR----PKRLAEAASSQT-EGKQCYVCKVIHPKIIKDSEdyFT 153
Cdd:PRK08566 88 GFAKLIYKLLRATCRECGRLKLTeeeieeyLEKLERLKEwgslADDLIKEVKKEAaKRMVCPHCGEKQYKIKFEKP--TT 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 154 FWVDQQGKIDKLYPQIIREIFSRVTYDTVVKLG-RSKNSHPEKLVLKAIQIPPISIRPGIRLGigSGPQSFHDINNVIQY 232
Cdd:PRK08566 166 FYEERKEGLVKLTPSDIRERLEKIPDEDLELLGiNPEVARPEWMVLTVLPVPPVTVRPSITLE--TGQRSEDDLTHKLVD 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 233 IVRKNllipKDLQIVRGQKIPLNVDRNLQTIQQLYYNFLLD-SVSttatqggtgkrGIV----MGARPAPSIMRRLPRKE 307
Cdd:PRK08566 244 IIRIN----QRLKENIEAGAPQLIIEDLWELLQYHVTTYFDnEIP-----------GIPparhRSGRPLKTLAQRLKGKE 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 308 GRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYK----QI 383
Cdd:PRK08566 309 GRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRpdgrRI 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 384 TQSVHDIEGLKQdfRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFDGDQM 463
Cdd:PRK08566 389 KLTDKNKEELAE--KLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG---KTFRLNLAVCPPYNADFDGDEM 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 464 NLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKN-VMNKLHAMGLfqtTQTDPPCFA 542
Cdd:PRK08566 464 NLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEeALDLLRAAGI---DELPEPEPA 540
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 543 NYSPTDLLDGKSVVSMLLKQTpINYQRAPTWYSEVYAPYMHYNKQDISTQIRNGELIEGVLDKKAVGAGsSGGIYHLISR 622
Cdd:PRK08566 541 IENGKPYWTGKQIFSLFLPKD-LNLEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGAE-QGSILDRIVK 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 623 RYGPQQALKMIFATQQLALNYVRNAGFTVSTADMLLTPEAHQEVQEIINELLLESEEINNRLLHGDIMPPIGLTTHDFYE 702
Cdd:PRK08566 619 EYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLE 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 703 KLQLNAL-KFPDRILKPIMNSINPEtNGLFQMVATGAKGSNPNMIHIMAGIGQIEINTQRIQPQFSfGRTLVYYPRFALE 781
Cdd:PRK08566 699 MKIMQVLgKARDEAGEIAEKYLGLD-NPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYR-DRTLPHFKPGDLG 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 782 AQAYGFICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIVDYYRRVSiDTR--LVQQLYGEDG 859
Cdd:PRK08566 777 AEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVR-DTRgnIVQFKYGEDG 855
|
..
gi 1755167230 860 LD 861
Cdd:PRK08566 856 VD 857
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
23-828 |
2.23e-102 |
|
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: 346.46 E-value: 2.23e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 23 RQGVMEVTISNLF--EGTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQPLFIAEIRRWLRVICL 100
Cdd:cd02583 8 RLSEVEVTNRNLYdiETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIINILQCICK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 101 NCGAPIVDLKRYEH----LIRP-----------KRLAEAASSQtegKQCYVCKvihpKIIKDSEDyftfwvdqqgkidkL 165
Cdd:cd02583 88 TCSRVLLPEEEKRKflkrLRRPnldnlqkkalkKKILEKCKKV---RKCPHCG----LLKKAQED--------------L 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 166 YPQIIREIFSRVTYDTVVKLGRSKNS-HPEKLVLKAIQIPPISIRPGIRLGIGSGpQSFHDINNVIQYIVRKNLLIPKDL 244
Cdd:cd02583 147 NPLKVLNLFKNIPPEDVELLLMNPLAgRPENLILTRIPVPPLCIRPSVVMDEKSG-TNEDDLTVKLSEIIFLNDVIKKHL 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 245 QivRGQKIPLNVDrNLQTIQ---QLYYNFLLDSVSTTATQGgtgkrgivmgaRPAPSIMRRLPRKEGRIRKSLLGSQVWS 321
Cdd:cd02583 226 E--KGAKTQKIME-DWDFLQlqcALYINSELPGLPLSMQPK-----------KPIRGFCQRLKGKQGRFRGNLSGKRVDF 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 322 ISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYKQitqsvhdiEGLKQDF---- 397
Cdd:cd02583 292 SGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFVIKR--------DGGKKKFlkyg 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 398 -------RLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFDGDQMNLWVPWS 470
Cdd:cd02583 364 nrrkiarELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPW---RTFRFNECVCTPYNADFDGDEMNLHVPQT 440
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 471 VMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKNVMNKLHAMGLFQTTQTDPPCFANYSPTDLL 550
Cdd:cd02583 441 EEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYMLDGEIKIDLPPPAILKPVELW 520
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 551 DGKSVVSMLLK-----QTPINYqRAPTWYSEVYAPYMHYNkqDISTQIRNGELIEGVLDKKAVGAGSSGGIYHLISRRYG 625
Cdd:cd02583 521 TGKQIFSLLLRpnkksPVLVNL-EAKEKSYTKKSPDMCPN--DGYVVIRNSELLCGRLDKSTLGSGSKNSLFYVLLRDYG 597
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 626 PQQALKMIFATQQLALNYVRNAGFTVSTADMLLTPEAHQEVQEIINELLLESEEINNRLLHGDIMPPIGLTTHDFYE-KL 704
Cdd:cd02583 598 PEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAEQTLEaKI 677
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 705 Q--LNALKfpDRILKPIMNSINPeTNGLFQMVATGAKGSNPNMIHIMAGIGQIEINTQRIQPQFSfGRTLVYYPRFALEA 782
Cdd:cd02583 678 SgeLSKIR--EDAGKACLKELHK-SNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFE-DRTLPHFPRNSKTP 753
|
810 820 830 840
....*....|....*....|....*....|....*....|....*.
gi 1755167230 783 QAYGFICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSSTGYANRK 828
Cdd:cd02583 754 AAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRR 799
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
194-508 |
4.49e-93 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 302.52 E-value: 4.49e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 194 EKLVLKAIQIPPISIRPGIRLGIGSgpQSFHDINNVIQYIVRKNLLIPKDLQIvrgqKIPLNVDRNLQTIQQLYYNFLLD 273
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGR--FAEDDLTHLLRDIIKRNNRLKRLLEL----GAPSIIIRNEKRLLQEAVDTLID 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 274 SvstTATQGGTGKRGivmgaRPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAET 353
Cdd:smart00663 75 N---EGLPRANQKSG-----RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEI 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 354 VQHYNINRLMPYFLNGKrqyPGCSRVYKQITQSVHDIEGLKQDFRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRI 433
Cdd:smart00663 147 VTPLNIDKLRKLVRNGP---NGAKYIIRGKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRV 223
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1755167230 434 VVLENpkiSTFQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSF 508
Cdd:smart00663 224 RVLEG---KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
12-840 |
2.21e-92 |
|
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: 317.20 E-value: 2.21e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 12 QFNIAGDNDHKRQGVMEVTISNLFEGTL-PAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQPLFIAE 90
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGhPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 91 IRRWLRVICLNCgapivdlkryEHLIRPKRLAEAassqtegkqcYVCK---VIHPKIIKDSEDYFTfwvdqqgkidklyp 167
Cdd:cd01435 81 LYKLLRGSCFYC----------HRFRISKWEVKL----------FVAKlklLDKGLLVEAAELDFG-------------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 168 qiireifsrvtydtvvklgrsknshPEKLVLKAIQIPPISIRPGIRLGIGS--GPQSFH-----DINNVIQYIVRKNLLi 240
Cdd:cd01435 127 -------------------------YDMFFLDVLLVPPNRFRPPSFLGDKVfeNPQNVLlskilKDNQQIRDLLASMRQ- 180
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 241 PKDLQIVRGQKIPLNVDRNLQTIQQL--YYNFLLDSvsTTATqggtgkrgiVMGARPAPSIMRRLPRKEGRIRKSLLGSQ 318
Cdd:cd01435 181 AESQSKLDLISGKTNSEKLINAWLQLqsAVNELFDS--TKAP---------KSGKKSPPGIKQLLEKKEGLFRMNMMGKR 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 319 VWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCS-------RVYKQITQSVHDIE 391
Cdd:cd01435 250 VNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINGPDVYPGANaiededgRLILLSALSEERRK 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 392 GLKQDFRLE--------VGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENPKisTFQMNVSACAWYNADFDGDQM 463
Cdd:cd01435 330 ALAKLLLLLssaklllnGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRVLPGEK--TLRLHYANCKSYNADFDGDEM 407
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 464 NLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKN-----VMNKLHAMGLFQTT---Q 535
Cdd:cd01435 408 NLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTFFTREeyqqlVYAALRPLFTSDKDgriK 487
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 536 TDPPCFanYSPTDLLDGKSVVSMLLK------QTPINYQRAPTWYSEVYAPYMHYNKQDISTQIRNGELIEGVLDKKAVG 609
Cdd:cd01435 488 LLPPAI--LKPKPLWTGKQVISTILKnlipgnAPLLNLSGKKKTKKKVGGGKWGGGSEESQVIIRNGELLTGVLDKSQFG 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 610 AgSSGGIYHLISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADMLLTPEAHQEVQEIINELLLESEEINNRLLhgdi 689
Cdd:cd01435 566 A-SAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEFL---- 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 690 mppiGLTTHDFYEKLQLNALkfPDRILKPImnsinPEtNGLFQMVATGAKGSNPNMIHIMAGIGQIEINTQRIQPQFSfG 769
Cdd:cd01435 641 ----GLKLNKVTSSIIKACL--PKGLLKPF-----PE-NNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVS-G 707
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1755167230 770 RTLVYYPRFALEAQAYGFICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIVDY 840
Cdd:cd01435 708 KTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNY 778
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
316-483 |
4.58e-77 |
|
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: 251.84 E-value: 4.58e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 316 GSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYkQITQSVHDIEGLKQ 395
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYII-RINGARRDLRYQKR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 396 --DFRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFDGDQMNLWVPWSVMS 473
Cdd:pfam00623 80 rlDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG---KTFRLNLSVTTPYNADFDGDEMNLHVPQSEEA 156
|
170
....*....|
gi 1755167230 474 RVEAELLCSV 483
Cdd:pfam00623 157 RAEAEELMLV 166
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
20-840 |
3.50e-61 |
|
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: 219.61 E-value: 3.50e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 20 DHKRQGVMEVTISNLF-EGTLPAE-GGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQPLFIAEIrrwlrv 97
Cdd:cd00399 5 EIRKWSVAKVIKPETIdNRTLKAErGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKV------ 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 98 iclncgapivdlkryehlirpkrlaeaassqtegkqcyvckvihPKIIKdsedyftfwvdqqgkidklypqiireifsrv 177
Cdd:cd00399 79 --------------------------------------------PSFLG------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 178 tydtvvklgrsknshPEKLVLKAIQIPPISIRPGIrlgigsgpqsfhdinnviqyivrknllipkdlqIVRGQKiplnvd 257
Cdd:cd00399 84 ---------------PEWMILTCLPVPPPCLRPSV---------------------------------IIEERW------ 109
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 258 RNLQTIQQLYYNflldsvSTTATQGGTGKRGivmgaRPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDE 337
Cdd:cd00399 110 RLLQEHVDTYLD------NGIAGQPQTQKSG-----RPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQ 178
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 338 VGYPISFARTLQvaetvqhyninrlmpyflngkrqypgcsrvykqitqsvhdieglkqdfrlevgdilyrdvvtGDVAFF 417
Cdd:cd00399 179 VGVPKSIALTLD--------------------------------------------------------------GDPVLF 196
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 418 NRQPSLERSSIGVHRIVVLENpkiSTFQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVN 497
Cdd:cd00399 197 NRQPSLHKLSIMAHRVRVLPG---STFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLI 273
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 498 GQVQDSTVGSFLLTRtntpmgknvmnklhamglfqttqtdppcfanysptdlldGKSVVSMLLKqtpinyqraptwysev 577
Cdd:cd00399 274 GLSQDTLLGAYLLTL---------------------------------------GKQIVSAALP---------------- 298
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 578 yapymhynkqdistqirngeliegvldkkavgagssGGIYHLISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADML 657
Cdd:cd00399 299 ------------------------------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVI 342
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 658 LTPEAHQEVQEIINELLLESEEINNRLLHGDIMPPIGLTTHDFYEKLQLNAL-KFPDRILKPIM--NSINPETNGLFQMV 734
Cdd:cd00399 343 DDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDFLnEARDKAGSAASvnLDLVSKFNSIYVMA 422
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 735 ATGAKGSNPNMIHIMAGIGQIEINTQRIQPQFSfGRTLVYYPRFALEAQAYGFICNSYIAGLTSPEFIFGEMNGRFDLIN 814
Cdd:cd00399 423 MSGAKGSFINIRQMSACVGQQSVEGKRIPRGFS-DRTLPHFSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVD 501
|
810 820
....*....|....*....|....*.
gi 1755167230 815 KALSTSSTGYANRKAIFGLQSCIVDY 840
Cdd:cd00399 502 TAVKTAESGYLQRRLVKALEDLVVHY 527
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
47-801 |
5.85e-50 |
|
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: 190.69 E-value: 5.85e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 47 DARMGTTDHHYKCITC-SHQRKQCMGHPGILQMHAPVLQPLFIAEIRRWLRVICLNCGAPIVDLKRYEHLIRPkrlaeaa 125
Cdd:cd10506 22 NPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKICPGCKSIKQKKKKPPRETLP------- 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 126 ssqtegkqcyvckvihpkiikdsEDYFTFWVD----QQGKIDKLYPQIIREIFSRVTYDTVVKLGRSKNSHPEKLVLKAI 201
Cdd:cd10506 95 -----------------------PDYWDFIPKdgqqEESCVTKNLPILSLAQVKKILKEIDPKLIAKGLPRQEGLFLKCL 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 202 QIPPISIRpgirlgIGSGPQSFHDinnviqyivrknllipkdlqivrGQKIPLnvDRNLQTIQQLYyNFLLDSVSTTATQ 281
Cdd:cd10506 152 PVPPNCHR------VTEFTHGFST-----------------------GSRLIF--DERTRAYKKLV-DFIGTANESAASK 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 282 GGTGKRgivmgarpapsimrrlprkegrIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINR 361
Cdd:cd10506 200 KSGLKW----------------------MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRER 257
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 362 LMPYF-----LNGKRQYPGCSRvykqitqsvhdIEGLKQDFRLEVGDILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVL 436
Cdd:cd10506 258 LQEYCdltllLKGVIGVRRNGR-----------LVGVRSHNTLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSVKVL 326
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 437 enPKISTFQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTRTNTP 516
Cdd:cd10506 327 --PTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGVF 404
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 517 MGKNVMNKLHAMGLFQTtqTDPPCF-ANYSPTDLLDGKSVVSMLLkqtpinyqraPTWYSEVYAPYMHYnkqdistqIRN 595
Cdd:cd10506 405 LDKAQMQQLQMLCPSQL--PPPAIIkSPPSNGPLWTGKQLFQMLL----------PTDLDYSFPSNLVF--------ISD 464
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 596 GELIEGvLDKKAVGAGSSGGIYHLIsRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADMLLTP--EAHQEVQEIINEL 673
Cdd:cd10506 465 GELISS-SGGSSWLRDSEGNLFSIL-VKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSSdsYSRQKMIEEISLG 542
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 674 LLESEEINNRLL-----HGDIM---PPIGLTTHDF----YEK----LQLNALK------FPDrILKPIMNSINPEtNGLF 731
Cdd:cd10506 543 LREAEIACNIKQllvdsRKDFLsgsGEENDVSSDVerviYERqksaALSQASVsafkqvFRD-IQNLVYKYASKD-NSLL 620
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 732 QMVATGAKGSNPNMIHIMAGIGqieinTQRIQPQFSFGRTLVYYPRfALEAQ------------------AYGFICNSYI 793
Cdd:cd10506 621 AMIKAGSKGSLLKLVQQSGCLG-----LQLSLVKLSYRIPRQLSCA-AWNSQksprviekdgsectesyiPYGVVESSFL 694
|
....*...
gi 1755167230 794 AGLTSPEF 801
Cdd:cd10506 695 DGLNPLEC 702
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1022-1432 |
8.06e-44 |
|
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: 165.07 E-value: 8.06e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1022 ILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDSHHrsVAGGTNKS---GIVRPQEIFS-AKPVeaeQSSEMLLR 1097
Cdd:cd02584 11 ILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFH--FAGVSAKNvtlGVPRLKEIINvAKNI---KTPSLTVY 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1098 LKnPEVETNKTYAQEIANSIELITFERLILQWHLLYEtysstkknvmyPDFAS-----DVEWMTDFLENHPLLQPPEDIA 1172
Cdd:cd02584 86 LE-PGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYD-----------PDPQNtvieeDKEFVESYFEFPDEDVEQDRLS 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1173 NWCIRLELNKTTMILKSISLESIVNSLRAKHSNT-YIMHSVENTASgipIIIRIYLRESafrRSTNTRMATDEKIAVNLV 1251
Cdd:cd02584 154 PWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDlNVIFSDDNAEK---LVIRIRIIND---DEEKEEDSEDDVFLKKIE 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1252 DKLLNSTI-RGIPGIKnanvVKLMR----HRVDAQGKLVRLDNIYAIKTNGTNIFGAMLDDNIDPYTIVSSSIGDTMELY 1326
Cdd:cd02584 228 SNMLSDMTlKGIEGIR----KVFIReenkKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVL 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1327 GIEAARQKIISEIRTVMGDKGP--NHRHLLMYADLMTRTGQVTSLEKAGLNaREPSNVLLRMALSSPVQVLTDAAIDSAV 1404
Cdd:cd02584 304 GIEAARKALLKELRNVISFDGSyvNYRHLALLCDVMTQRGHLMAITRHGIN-RQDTGPLMRCSFEETVDILLEAAAFGET 382
|
410 420
....*....|....*....|....*...
gi 1755167230 1405 NPIYGIAAPTLMGSVPRIGTMYSDIIMD 1432
Cdd:cd02584 383 DDLKGVSENIMLGQLAPIGTGCFDLLLD 410
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1007-1435 |
2.98e-39 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 151.15 E-value: 2.98e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1007 ATVKTLNITCEQMSAILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDS-HHRSVAGGTNKSGIVRPQEIFSAK- 1084
Cdd:PRK04309 28 EKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTfHYAGVAEINVTLGLPRLIEIVDARk 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1085 ----PVeaeqsseMLLRLKnPEVETNKTYAQEIANSIELITFErlilqwhllyetysstkknvmypDFASDVEWmtdfle 1160
Cdd:PRK04309 108 epstPM-------MTIYLK-DEYAYDREKAEEVARKIEATTLE-----------------------NLAKDISV------ 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1161 nhpllqppeDIANWCIRLELNKTTMILKSISLESIVNSLRakhSNTYIMHSVENTasgipiIIRIYLRE---SAFRRstn 1237
Cdd:PRK04309 151 ---------DLANMTIIIELDEEMLEDRGLTVDDVKEAIE---KKKGGEVEIEGN------TLIISPKEpsyRELRK--- 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1238 trmatdekiavnLVDKLLNSTIRGIPGIKNANVvklmRHRVDAqgklvrldniYAIKTNGTNIFGAMLDDNIDPYTIVSS 1317
Cdd:PRK04309 210 ------------LAEKIRNIKIKGIKGIKRVII----RKEGDE----------YVIYTEGSNLKEVLKVEGVDATRTTTN 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1318 SIGDTMELYGIEAARQKIISEIRTVMGDKG--PNHRHLLMYADLMTRTGQVTSLEKAGLNAREPSnVLLRMALSSPVQVL 1395
Cdd:PRK04309 264 NIHEIEEVLGIEAARNAIIEEIKNTLEEQGldVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKAS-VLARAAFEVTVKHL 342
|
410 420 430 440
....*....|....*....|....*....|....*....|
gi 1755167230 1396 TDAAIDSAVNPIYGIAAPTLMGSVPRIGTMYSDIIMDEKY 1435
Cdd:PRK04309 343 LDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1001-1433 |
2.99e-39 |
|
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: 150.48 E-value: 2.99e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1001 LIRIELATVKTLNITCEQMSAILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDS-HHRSVAGGTNKSGIVRPQE 1079
Cdd:cd06528 3 LKEKLEEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTfHYAGVAEINVTLGLPRLIE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1080 IFSAK-----PVeaeqsseMLLRLKnPEVETNKTYAQEIANSIELITFERLIlqwhllyetysstkknvmypdfaSDVEW 1154
Cdd:cd06528 83 IVDARkepstPT-------MTIYLE-EEYKYDREKAEEVARKIEETTLENLA-----------------------EDISI 131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1155 mtdflenhpllqppeDIANWCIRLELNKTTMILKSISLESIVNSLRakhSNTYIMHSVENTASGIPIIIRIYlRESAFRR 1234
Cdd:cd06528 132 ---------------DLFNMRITIELDEEMLEDRGITVDDVLKAIE---KLKKGKVGEEGDVTLIVLKAEEP-SIKELRK 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1235 stntrmatdekiavnLVDKLLNSTIRGIPGIKNANVVKLmrhrvdaqgklvrlDNIYAIKTNGTNIFGAMLDDNIDPYTI 1314
Cdd:cd06528 193 ---------------LAEKILNTKIKGIKGIKRVIVRKE--------------EDEYVIYTEGSNLKAVLKVEGVDPTRT 243
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1315 VSSSIGDTMELYGIEAARQKIISEIRTVMGDKG--PNHRHLLMYADLMTRTGQVTSLEKAGLNAREPSnVLLRMALSSPV 1392
Cdd:cd06528 244 TTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGldVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPS-VLARAAFEVTV 322
|
410 420 430 440
....*....|....*....|....*....|....*....|.
gi 1755167230 1393 QVLTDAAIDSAVNPIYGIAAPTLMGSVPRIGTMYSDIIMDE 1433
Cdd:cd06528 323 KHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMDP 363
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
7-314 |
6.12e-34 |
|
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: 133.57 E-value: 6.12e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 7 EIAAVQFNIAGDNDHKRQGVMEVTISNLFE--GTLPAEGGIYDARMGTTDHHYKCITCSHQRKQCMGHPGILQMHAPVLQ 84
Cdd:pfam04997 3 KIKEIQFGIASPEEIRKWSVGEVTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 85 PLFIAEIRRWLRVICLNCGAPIVD---------LKRYEHLIRPKRLAEAASS--------QTEGKQCYVCKVIHPKIIKD 147
Cdd:pfam04997 83 IGFFKKTLKILECVCKYCSKLLLDpgkpklfnkDKKRLGLENLKMGAKAILElckkkdlcEHCGGKNGVCGSQQPVSRKE 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 148 SEDYFTFW-VDQQGKID-KLYPQIIREIFSRVTYDTVVKLG-RSKNSHPEKLVLKAIQIPPISIRPGIRLGIGSGPQSfh 224
Cdd:pfam04997 163 GLKLKAAIkKSKEEEEKeILNPEKVLKIFKRISDEDVEILGfNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAED-- 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 225 DINNVIQYIVRKNLLIPKDLQivrgQKIPLNVDRNLQTIQQLYYNFLLDSVST---TATQGGTgkrgivmgaRPAPSIMR 301
Cdd:pfam04997 241 DLTHKLRDIIKRNNRLKKLLE----LGAPSHIIREEWRLLQEHVATLFDNEIPglpPALQKSK---------RPLKSISQ 307
|
330
....*....|...
gi 1755167230 302 RLPRKEGRIRKSL 314
Cdd:pfam04997 308 RLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
486-656 |
3.65e-32 |
|
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: 123.12 E-value: 3.65e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 486 WFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKNVMNKLHAMGLFQTTqtdPPCFANYSPtdLLDGKSVVSMLLKQtPI 565
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGIVLPH---PAILKPIKP--LWTGKQTFSRLLPN-EI 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 566 NYQRAPTWYSEvyapymHYNKQDISTQIRNGELIEGVLDKKAVGaGSSGGIYHLISRRYGPQQALKMIFATQQLALNYVR 645
Cdd:pfam04983 75 NPKGKPKTNEE------DLCENDSYVLINNGELISGVIDKKTVG-KSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLT 147
|
170
....*....|.
gi 1755167230 646 NAGFTVSTADM 656
Cdd:pfam04983 148 KSGFSIGIDDI 158
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
187-1084 |
2.56e-28 |
|
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: 124.39 E-value: 2.56e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 187 RSKNsHPEKLVLKAIQIPPISIRPGIRLGIGSGPQSfhDINNVIQYIVRKNLLIPKDLQIvrgqKIPLNVDRNLQTIQQL 266
Cdd:TIGR02386 211 DSGN-RPEWMVLDVIPVIPPELRPMVQLDGGRFATS--DLNDLYRRVINRNNRLKRLLEL----GAPEIIVRNEKRMLQE 283
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 267 YYNFLLDSvsttatqggtGKRG-IVMGA--RPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPIS 343
Cdd:TIGR02386 284 AVDALFDN----------GRRGkPVVGKnnRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKK 353
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 344 FARTLqvaetVQHYNINRLMpyflngKRQYPGCSRVYKQITQSVHDieglkqdfrlEVGDILYrDVVTGDVAFFNRQPSL 423
Cdd:TIGR02386 354 MALEL-----FKPFIIKRLI------DRELAANIKSAKKMIEQEDP----------EVWDVLE-DVIKEHPVLLNRAPTL 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 424 ERSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDS 503
Cdd:TIGR02386 412 HRLGIQAFEPVLVEGKAI---RLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDM 488
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 504 TVGSFLLTRTNTPM---GKNVMNKLHAMGLFQTTQTDppcfanyspTDLLDGKSVVSMLLKQTP---INYQRAPTWYsev 577
Cdd:TIGR02386 489 VLGLYYLTTEKPGAkgeGKIFSNVDEAIRAYDNGKVH---------LHALIGVRTSGEILETTVgrvIFNEILPEGF--- 556
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 578 yaPYMHYNKqdistqirngeliegVLDKKAVGAgssggIYHLISRRYGPQQALKMIFATQQLALNYVRNAGFTVSTADML 657
Cdd:TIGR02386 557 --PYINDNE---------------PLSKKEISS-----LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIV 614
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 658 LTPEAhqevQEIINELLLESEEINNRLLHGDImppiglTTHDFYEKLQLNALKFPDRILKPIMNSINPET---NGLFQMV 734
Cdd:TIGR02386 615 VPDEK----YEILKEADKEVAKIQKFYNKGLI------TDEERYRKVVSIWSETKDKVTDAMMKLLKKDTykfNPIFMMA 684
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 735 ATGAKGSNPNMIHImAGIGQIEINTqriqpqfsFGRTlVYYPrfaleaqaygfICNSYIAGLTSPEFIFGEMNGRFDLIN 814
Cdd:TIGR02386 685 DSGARGNISQFRQL-AGMRGLMAKP--------SGDI-IELP-----------IKSSFREGLTVLEYFISTHGARKGLAD 743
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 815 KALSTSSTGYANRKaifglqscIVDYYRRVSIDTRlvqqlygedglDARQLETVRFETIMLSDQEledkfkytgIQSPLF 894
Cdd:TIGR02386 744 TALKTADSGYLTRR--------LVDVAQDVVVREE-----------DCGTEEGIEVEAIVEGKDE---------IIESLK 795
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 895 EEEFSRLkkdrdkyrqiflnienfnfsqLLTDVRQvpvnvasivknillsstsgvlPFDEKSILQKYTMVKTfcknlpyv 974
Cdd:TIGR02386 796 DRIVGRY---------------------SAEDVYD---------------------PDTGKLIAEANTLITE-------- 825
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 975 finniqerlqtpipvylkraaslmRILIRIELATVKTLNI----TCEQMSAI------LDLIrlqyTQSLINYGEAVGIL 1044
Cdd:TIGR02386 826 ------------------------EIAEKIENSGIEKVKVrsvlTCESEHGVcqkcygRDLA----TGKLVEIGEAVGVI 877
|
890 900 910 920
....*....|....*....|....*....|....*....|...
gi 1755167230 1045 AAQSVSEPLTQYMLDSHHRSVAGGTNKS---GIVRPQEIFSAK 1084
Cdd:TIGR02386 878 AAQSIGEPGTQLTMRTFHTGGVAGASGDitqGLPRVKELFEAR 920
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
978-1434 |
4.87e-28 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 120.30 E-value: 4.87e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 978 NIQERLQTPIPVYLKRAASLMRILIRIELATVKTLNITCEQMSAILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQY- 1056
Cdd:PRK14897 122 NSNEDVLKVIDDVKKLGFRLPPSVIEEIAKAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMt 201
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1057 MLDSHHRSVAGGTNKSGIVRPQEIFSAKPVEAEQSSEMLLRlknPEVETNKTYAQEIANSIElitferlilqwhllyety 1136
Cdd:PRK14897 202 MRTFHYAGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIYLK---KDYREDEEKVREVAKKIE------------------ 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1137 sstkkNVMYPDFAsDVEwmtdflenhpllqppEDIANWCIRLELNKTTMILKSISLESIVNSLRAKHSNTYIMHSVenta 1216
Cdd:PRK14897 261 -----NTTLIDVA-DII---------------TDIAEMSVVVELDEEKMKERLIEYDDILAAISKLTFKTVEIDDG---- 315
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1217 sgipiIIRIYLRESAFRRstntrmatdekiAVNLVDKLLNSTIRGIPGIKNAnvvklmrhrvdaqgkLVRLDN---IYAI 1293
Cdd:PRK14897 316 -----IIRLKPQQPSFKK------------LYLLAEKVKSLTIKGIKGIKRA---------------IARKENderRWVI 363
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1294 KTNGTNIFGAMLDDNIDPYTIVSSSIGDTMELYGIEAARQKIISEIRTVMGDKGPN--HRHLLMYADLMTRTGQVTSLEK 1371
Cdd:PRK14897 364 YTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNvdIRHIMLVADMMTFDGSVKAIGR 443
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1755167230 1372 AGLNAREPSnVLLRMALSSPVQVLTDAAIDSAVNPIYGIAAPTLMGSVPRIGTMYSDIIMDEK 1434
Cdd:PRK14897 444 HGISGEKSS-VLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGR 505
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
191-838 |
8.82e-24 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 110.10 E-value: 8.82e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 191 SHPEKLVLKAIQIPPISIRPGIRLGigSGPQSFHDINNVIQYIVRKNLLIPKDLQIVRGQKIPLNVDRNLQ-TIQQLYYN 269
Cdd:PRK14844 1664 NRPEWMILTTIPILPPDLRPLVSLE--SGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQeAVDSLFDN 1741
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 270 FLLDSVSTTAtqGGTGKRgivmgarpaPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLq 349
Cdd:PRK14844 1742 SRRNALVNKA--GAVGYK---------KSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALEL- 1809
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 350 vaetvqhyninrLMPYFLNGKRQYpGCSRVYKQITQsvhdiegLKQDFRLEVGDILyRDVVTGDVAFFNRQPSLERSSIG 429
Cdd:PRK14844 1810 ------------FKPFVYSKLKMY-GMAPTIKFASK-------LIRAEKPEVWDML-EEVIKEHPVLLNRAPTLHRLGIQ 1868
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 430 VHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFL 509
Cdd:PRK14844 1869 AFEPILIEGKAI---QLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYY 1945
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 510 LTrtntpmgknvmnklhamgLFQTTQTDPPCFANYSPTD--LLDGksvvsMLLKQTPINYQraptwysevyapyMHYNKQ 587
Cdd:PRK14844 1946 LT------------------LQEPKEDDLPSFGAFCEVEhsLSDG-----TLHIHSSIKYR-------------MEYINS 1989
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 588 DISTQIR---------------------NGELIEGVLDKKAVgagssGGIYHLISRRYGpqQALKMIFATQQLAL--NYV 644
Cdd:PRK14844 1990 SGETHYKticttpgrlilwqifpkhenlGFDLINQVLTVKEI-----TSIVDLVYRNCG--QSATVAFSDKLMVLgfEYA 2062
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 645 RNAGFTVSTADMLLTPEAHQEVQEIINELLLESEEINNRLlhgdimppigLTTHDFYEKLQLNALKFPDRILKPIMNSI- 723
Cdd:PRK14844 2063 TFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGL----------ITRSERYNKVIDEWSKCTDMIANDMLKAIs 2132
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 724 ----NPETNGLFQMVATGAKGSNPNMIHiMAGIgqieintqriqpqfsfgRTLVYYPRFALEAQAygfICNSYIAGLTSP 799
Cdd:PRK14844 2133 iydgNSKYNSVYMMVNSGARGSTSQMKQ-LAGM-----------------RGLMTKPSGEIIETP---IISNFREGLNVF 2191
|
650 660 670
....*....|....*....|....*....|....*....
gi 1755167230 800 EFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIV 838
Cdd:PRK14844 2192 EYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIV 2230
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1030-1424 |
1.23e-23 |
|
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: 103.43 E-value: 1.23e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1030 YTQSLINYGEAVGILAAQSVSEPLTQYMLDSHHRSVAGGTN-KSGIVRPQEIF---SAKPveaeQSSEMLLRLKNPeveT 1105
Cdd:cd02735 2 YMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNvTLGIPRLREILmtaSKNI----KTPSMTLPLKNG---K 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1106 NKTYAQEIANSIELITFerlilqwhllyetysstkknvmypdfaSDVewmtdflenhpllqppedianwcirlelnkttm 1185
Cdd:cd02735 75 SAERAETLKKRLSRVTL---------------------------SDV--------------------------------- 94
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1186 iLKSISLESIVNSLRAKhsntyIMHSVENTASgipIIIRIYLRESAFrrstntrmatdekIAVNLVDKLL-NSTIRGIPG 1264
Cdd:cd02735 95 -VEKVEVTEILKTIERV-----FKKLLGKWCE---VTIKLPLSSPKL-------------LLLSIVEKLArKAVIREIPG 152
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1265 IKNANVVKlmrhrvdaqgKLVRLDNIYAIKTNGTNIFGAMLDDN-IDPYTIVSSSIGDTMELYGIEAARQKIISEIRTVM 1343
Cdd:cd02735 153 ITRCFVVE----------EDKGGKTKYLVITEGVNLAALWKFSDiLDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVF 222
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1344 GDKG--PNHRHLLMYADLMTRTGQVTSLEKAGLnaREPSNVLLRMALSSPVQVLTDAAIDSAVNPIYGIAAPTLMGSVPR 1421
Cdd:cd02735 223 KVYGiaVDPRHLSLIADYMTFEGGYRPFNRIGM--ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVN 300
|
...
gi 1755167230 1422 IGT 1424
Cdd:cd02735 301 GGT 303
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
190-514 |
8.00e-21 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 98.67 E-value: 8.00e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 190 NSHPEKLVLKAIQIPPISIRPGIRLGIGSGPQSfhDINNVIQYIVRKNLlipkdlQIVRGQKI--PLNVDRNLQTIQQLY 267
Cdd:PRK02625 239 GSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATS--DLNDLYRRVINRNN------RLARLQEIlaPEIIVRNEKRMLQEA 310
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 268 YNFLLDSvsttatqggtGKRG-IVMGA--RPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISF 344
Cdd:PRK02625 311 VDALIDN----------GRRGrTVVGAnnRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEM 380
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 345 ArtlqvAETVQHYNINRLMpyflngkRQypgcsrvykQITQSVHDIEGLKQDFRLEVGDILyRDVVTGDVAFFNRQPSLE 424
Cdd:PRK02625 381 A-----IELFQPFVIHRLI-------RQ---------GIVNNIKAAKKLIQRADPEVWQVL-EEVIEGHPVLLNRAPTLH 438
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 425 RSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDST 504
Cdd:PRK02625 439 RLGIQAFEPILVEGRAI---QLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMV 515
|
330
....*....|
gi 1755167230 505 VGSFLLTRTN 514
Cdd:PRK02625 516 LGCYYLTAEN 525
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
193-1115 |
2.77e-20 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 98.46 E-value: 2.77e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 193 PEKLVLKAIQIPPISIRPGIRLGigSGPQSFHDINNVIQYIVRKNLLIPKDLQIVRGQKIPLNVDRNLQ-TIQQLYYNfl 271
Cdd:PRK09603 1623 PEWMMLTVLPVLPPDLRPLVALD--GGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQeAVDVLFDN-- 1698
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 272 ldSVSTTATQGGTgkrgivmgARPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFARTLqva 351
Cdd:PRK09603 1699 --GRSTNAVKGAN--------KRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALEL--- 1765
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 352 etvqhyninrLMPYFLnGKRQYPGCSRVYKQITQSVHDieglKQDfrlEVGDILyRDVVTGDVAFFNRQPSLERSSIGVH 431
Cdd:PRK09603 1766 ----------FKPHLL-SKLEERGYATTLKQAKRMIEQ----KSN---EVWECL-QEITEGYPVLLNRAPTLHKQSIQAF 1826
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 432 RIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLT 511
Cdd:PRK09603 1827 HPKLIDGKAI---QLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLS 1903
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 512 rtntpMGKNVMNKLHAmgLFQTTQTdppcFANYSPTDLLDGKSVVSMLLKQTPINYQRAPTWYSEV---YAPYMHYN--- 585
Cdd:PRK09603 1904 -----LEKSGVKGEHK--LFSSVNE----IITAIDTKELDIHAKIRVLDQGNIIATSAGRMIIKSIlpdFIPTDLWNrpm 1972
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 586 -KQDIstqirnGELIEGVLDKKAVGagssggiyhlISRRYgpqqalkmIFATQQLALNYVRNAGFTVSTADmLLTPEAHQ 664
Cdd:PRK09603 1973 kKKDI------GVLVDYVHKVGGIG----------ITATF--------LDNLKTLGFRYATKAGISISMED-IITPKDKQ 2027
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 665 EVqeiINELLLESEEINNRLLHGDimppigLTTHDFYEKLQLNALKFPDRILKPIMNSINPET---NGLFQMVATGAKGS 741
Cdd:PRK09603 2028 KM---VEKAKVEVKKIQQQYDQGL------LTDQERYNKIIDTWTEVNDKMSKEMMTAIAKDKegfNSIYMMADSGARGS 2098
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 742 NpnmihimagiGQIEintqriqpQFSFGRTLVYYPRFALEAQAygfICNSYIAGLTSPEFIFGEMNGRFDLINKALSTSS 821
Cdd:PRK09603 2099 A----------AQIR--------QLSAMRGLMTKPDGSIIETP---IISNFKEGLNVLEYFNSTHGARKGLADTALKTAN 2157
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 822 TGYANRKAIfglqscivdyyrRVSIDTRLVQQlygedglDARQLETVRFETIMLSDQELEdkfkytgiqsPLFEEEFSRL 901
Cdd:PRK09603 2158 AGYLTRKLI------------DVSQNVKVVSD-------DCGTHEGIEITDIAVGSELIE----------PLEERIFGRV 2208
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 902 kkdrdkyrqiflnienfnfsqLLTDVrqvpvnVASIVKNILLSstSGVLpFDEksilqkytmvkTFCKNLPYVFINNIQE 981
Cdd:PRK09603 2209 ---------------------LLEDV------IDPITNEILLY--ADTL-IDE-----------EGAKKVVEAGIKSITI 2247
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 982 RlqTPIPVYLKRAASlmrilirielATVKTLNITCEQMSaildlirlqytqsliNYGEAVGILAAQSVSEPLTQYMLDSH 1061
Cdd:PRK09603 2248 R--TPVTCKAPKGVC----------AKCYGLNLGEGKMS---------------YPGEAVGVVAAQSIGEPGTQLTLRTF 2300
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 1755167230 1062 HrsvAGGTNKsgivRPQEifsAKPVEAEQssEMLLRLKNPEVETNKTYAQEIAN 1115
Cdd:PRK09603 2301 H---VGGTAS----RSQD---EREIVASK--EGFVRFYNLRTYTNKEGKNIIAN 2342
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
187-1086 |
9.12e-20 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 96.48 E-value: 9.12e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 187 RSKNShPEKLVLKAIQIPPISIRPGIRLGIGSGPQSfhDINNVIQYIVRKNLLIPKDLQIVRGQKIPLNVDRNLQtiqql 266
Cdd:PRK14906 307 KSGND-PADMILDVIPVIPPDLRPMVQLDGGRFATS--DLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQ----- 378
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 267 yynfllDSVSTTATQGGTGKRGIVMGARPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPISFAr 346
Cdd:PRK14906 379 ------EAVDSLFDNGRRGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMA- 451
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 347 tlqvAETVQHYNINRL--MPYFLNGKrqypGCSRVYKQITQSVHDIeglkqdfrLEvgdilyrDVVTGDVAFFNRQPSLE 424
Cdd:PRK14906 452 ----LELFKPFVMKRLveLEYAANIK----AAKRAVDRGASYVWDV--------LE-------EVIQDHPVLLNRAPTLH 508
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 425 RSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDST 504
Cdd:PRK14906 509 RLGIQAFEPVLVEGKAI---KLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMI 585
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 505 VGSFLLT--RTNTPmGK--------NVMN--------KLHAMGLFQTTQtDPPCFANYSPTDLLDGKSVVSMLLKQTPIN 566
Cdd:PRK14906 586 IGVYYLTteRDGFE-GEgrtfadfdDALNaydaradlDLQAKIVVRLSR-DMTVRGSYGDLEETKAGERIETTVGRIIFN 663
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 567 yQRAPTWYsevyaPYMHY--NKQDIstqirnGELIEGVLDkkavgagssggiyhlisrRYGPQQALKMIFATQQLALNYV 644
Cdd:PRK14906 664 -QVLPEDY-----PYLNYkmVKKDI------GRLVNDCCN------------------RYSTAEVEPILDGIKKTGFHYA 713
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 645 RNAGFTVSTADMLLTPEAhqevQEIINELLLESEEINnrllhgdimppigltthDFYEKLQLNalkfPDRILKPIMNSIN 724
Cdd:PRK14906 714 TRAGLTVSVYDATIPDDK----PEILAEADEKVAAID-----------------EDYEDGFLS----ERERHKQVVDIWT 768
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 725 PETNGLFQMVATGAKGSNPnmIHIMAGIGQiEINTQRIQpQFSFGRTLVyyprfaleAQAYGFICNSYIA-----GLTSP 799
Cdd:PRK14906 769 EATEEVGEAMLAGFDEDNP--IYMMADSGA-RGNIKQIR-QLAGMRGLM--------ADMKGEIIDLPIKanfreGLSVL 836
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 800 EFIFGEMNGRFDLINKALSTSSTGYANRkaifglqscivdyyrrvsidtRLVqqlygedglDARQLETVRFETIMLSDqe 879
Cdd:PRK14906 837 EYFISTHGARKGLVDTALRTADSGYLTR---------------------RLV---------DVAQDVIVREEDCGTDE-- 884
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 880 ledkfkytGIQSPLFEEefsrlKKDRDkyrqiflniENFNFSQLLTDVRQVPVNVasivkniLLSSTSGVLPFDEKSILQ 959
Cdd:PRK14906 885 --------GVTYPLVKP-----KGDVD---------TNLIGRCLLEDVCDPNGEV-------LLSAGDYIESMDDLKRLV 935
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 960 kytmvktfcknlpyvfinniqerlqtpipvylkrAASLMRILIRiELATVKTLNITCEQMSAiLDLIrlqyTQSLINYGE 1039
Cdd:PRK14906 936 ----------------------------------EAGVTKVQIR-TLMTCHAEYGVCQKCYG-WDLA----TRRPVNIGT 975
|
890 900 910 920
....*....|....*....|....*....|....*....|....*....
gi 1755167230 1040 AVGILAAQSVSEPLTQY-MLDSHHRSVAGGTNKSGIVRPQEIFSA-KPV 1086
Cdd:PRK14906 976 AVGIIAAQSIGEPGTQLtMRTFHSGGVAGDDITQGLPRVAELFEArKPK 1024
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
176-838 |
2.61e-18 |
|
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: 91.04 E-value: 2.61e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 176 RVTYDTVVKLGRSKNsHPEKLVLKAIQIPPISIRPGIRLGIGSGPQSfhDINNViqY---IVRKNLLipKDLQ------- 245
Cdd:cd01609 123 RVIYFVVESFRKSGN-RPEWMILTVLPVIPPDLRPMVQLDGGRFATS--DLNDL--YrrvINRNNRL--KKLLelgapei 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 246 IVRGQKiplnvdRNLQtiqqlyynfllDSVSTTATQGGTGKRGIVMGARPAPSIMRRLPRKEGRIRKSLLGSQVWSISRS 325
Cdd:cd01609 196 IVRNEK------RMLQ-----------EAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRS 258
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 326 TICGNSDLHLDEVGYPISFArtlqvAETVQHYNINRLmpyflngkrqypgcsrVYKQITQSVHDIEGLKQDFRLEVGDIL 405
Cdd:cd01609 259 VIVVGPELKLHQCGLPKEMA-----LELFKPFVIREL----------------IERGLAPNIKSAKKMIERKDPEVWDIL 317
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 406 yRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRN 485
Cdd:cd01609 318 -EEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAI---QLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSN 393
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 486 WFISTKSSGPVNGQVQDSTVGSFLLTRTNTPMGKNvmnklhamGLFQTTQtdppcfanysptdlldGKSVVSMLLKQTPi 565
Cdd:cd01609 394 NILSPASGKPIVTPSQDMVLGLYYLTKERKGDKGE--------GIIETTV----------------GRVIFNEILPEGL- 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 566 nyqraptwysevyaPYmhYNKqdistqirngeliegVLDKKAvgagssggIYHLISR---RYGPQQALKMIFATQQLALN 642
Cdd:cd01609 449 --------------PF--INK---------------TLKKKV--------LKKLINEcydRYGLEETAELLDDIKELGFK 489
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 643 YVRNAGFTVSTADMLLTPEAhqevQEIINELLLESEEINNRLLHGdimppiGLTTHDFYEKLQLNALKFPDRILKPIMNS 722
Cdd:cd01609 490 YATRSGISISIDDIVVPPEK----KEIIKEAEEKVKEIEKQYEKG------LLTEEERYNKVIEIWTEVTEKVADAMMKN 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 723 INP-ETNGLFQMVATGAKGsNPNMIHIMAGI--------GQIeintqriqpqfsfgrtlVYYPrfaleaqaygfICNSYI 793
Cdd:cd01609 560 LDKdPFNPIYMMADSGARG-SKSQIRQLAGMrglmakpsGKI-----------------IELP-----------IKSNFR 610
|
650 660 670 680
....*....|....*....|....*....|....*....|....*
gi 1755167230 794 AGLTSPEFIFGEMNGRFDLINKALSTSSTGYANRKAIFGLQSCIV 838
Cdd:cd01609 611 EGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIV 655
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1317-1424 |
1.17e-17 |
|
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: 81.70 E-value: 1.17e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1317 SSIGDTMELYGIEAARQKIISEIRTVMGDKGP--NHRHLLMYADLMTRTGQVTSLEKAGLNArEPSNVLLRMALSSPVQV 1394
Cdd:cd00630 48 ASIHEMLEALGIEAARETIIREIQKVLASQGVsvDRRHIELIADVMTYSGGLRGVTRSGFRA-SKTSPLMRASFEKTTKH 126
|
90 100 110
....*....|....*....|....*....|
gi 1755167230 1395 LTDAAIDSAVNPIYGIAAPTLMGSVPRIGT 1424
Cdd:cd00630 127 LLDAAAAGEKDELEGVSENIILGRPAPLGT 156
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1170-1435 |
1.44e-16 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 85.72 E-value: 1.44e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1170 DIANWCIRLELNKTTMILKSISLESIVNSLRAKhsnTYIMHSVENTasgipiIIRIYLRESAFRRstntrmatdekiAVN 1249
Cdd:PRK14898 617 DLWTQSIKVELDEETLADRGLTIESVEEAIEKK---LGVKIDRKGT------VLYLKPKTPSYKA------------LRK 675
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1250 LVDKLLNSTIRGIPGIknaNVVKLMRHRVDAQGKlvrldniYAIKTNGTNiFGAMLD-DNIDPYTIVSSSIGDTMELYGI 1328
Cdd:PRK14898 676 RIPKIKNIVLKGIPGI---ERVLVKKEEHENDEE-------YVLYTQGSN-LREVFKiEGVDTSRTTTNNIIEIQEVLGI 744
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1329 EAARQKIISEIRTVMGDKG--PNHRHLLMYADLMTRTGQVTSLEKAGLnAREPSNVLLRMALSSPVQVLTDAAIDSAVNP 1406
Cdd:PRK14898 745 EAARNAIINEMMNTLEQQGleVDIRHLMLVADIMTADGEVKPIGRHGV-AGEKGSVLARAAFEETVKHLYDAAEHGEVDK 823
|
250 260
....*....|....*....|....*....
gi 1755167230 1407 IYGIAAPTLMGSVPRIGTMYSDIIMDEKY 1435
Cdd:PRK14898 824 LKGVIENVIVGKPIKLGTGCVDLRIDREY 852
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
687-788 |
1.71e-16 |
|
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: 76.63 E-value: 1.71e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 687 GDIMPPIGLTTHDFYEKLQLNALKFPDRILKPIMNSINPETNGLFQMVATGAKGSNPNMIHIMAGIGQIEINTQRIQPQF 766
Cdd:pfam05000 8 GKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGKRIPFGF 87
|
90 100
....*....|....*....|..
gi 1755167230 767 SfGRTLVYYPRFALEAQAYGFI 788
Cdd:pfam05000 88 S-GRTLPHFKKDDEGPESRGFV 108
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
187-669 |
5.46e-16 |
|
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: 84.06 E-value: 5.46e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 187 RSKNSHPEKLVLKAI-QIPPiSIRPGIRLGIGSGPQSfhDIN----NVIQyivRKNLLiPKDLQIvrgqKIPLNVDRNLQ 261
Cdd:COG0086 218 RESGNRPEWMILDVLpVIPP-DLRPLVPLDGGRFATS--DLNdlyrRVIN---RNNRL-KRLLEL----KAPDIIVRNEK 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 262 TIQQLYYNFLLDSvsttatqggtGKRGIVM---GARPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEV 338
Cdd:COG0086 287 RMLQEAVDALFDN----------GRRGRAVtgaNKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQC 356
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 339 GYPISFArtlqvAETVQHYNINRLMPYFLngkrqypgcsrvykqitqsVHDIEGLK---QDFRLEVGDILyRDVVTGDVA 415
Cdd:COG0086 357 GLPKKMA-----LELFKPFIYRKLEERGL-------------------ATTIKSAKkmvEREEPEVWDIL-EEVIKEHPV 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 416 FFNRQPSLERSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSVRNWFISTKSSGP 495
Cdd:COG0086 412 LLNRAPTLHRLGIQAFEPVLIEGKAI---QLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKP 488
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 496 VNGQVQDSTVGSFLLTRTNTPM---GK-------------NVMNKLHAMGLFQTTQTDPPCFANYSPTdllDGKSVVSML 559
Cdd:COG0086 489 IIVPSQDMVLGLYYLTREREGAkgeGMifadpeevlrayeNGAVDLHARIKVRITEDGEQVGKIVETT---VGRYLVNEI 565
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 560 LKQtpinyqraptwysEVyaPYmhYNKqdistqirngeliegVLDKKAVGAgssggIYHLISRRYGPQQALKMIFATQQL 639
Cdd:COG0086 566 LPQ-------------EV--PF--YNQ---------------VINKKHIEV-----IIRQMYRRCGLKETVIFLDRLKKL 608
|
490 500 510
....*....|....*....|....*....|....*..
gi 1755167230 640 ALNYVRNAGFTVSTADMLLTP-------EAHQEVQEI 669
Cdd:COG0086 609 GFKYATRAGISIGLDDMVVPKekqeifeEANKEVKEI 645
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1038-1424 |
1.01e-10 |
|
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain] Cd Length: 381 Bit Score: 65.52 E-value: 1.01e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1038 GEAVGILAAQSVSEPLTQYMLDSHHRSvaggtNKSGIVRPQEIF--SAKPVEAEQSSEMLLRLKNPEVETNKTY---AQE 1112
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSL-----ESSPLELLKEVLecRSKSKSKENDRRVILSLHLCKCDHGFEYeraALE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1113 IANSIELITFERLIlqwhllyeTYSSTKknvmypdfasDVEWMTDFLENHPLLQPPEDIANWCIRLELNKTTMILKSISL 1192
Cdd:cd02737 76 VKNHLERVTLEDLA--------TTSMIK----------YSPQATEAIVGEIGDQLNTKKKGKKKAIFSTSLKITKFSPWV 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1193 E-SIVNSLRAKHSNTYIMHSVENTASgipiiiriylresafrrSTNTRMATDeKIAVNLVDKLLNSTIRGIPGIKNANVV 1271
Cdd:cd02737 138 ChFHLDKECQKLSDGPCLTFSVSKEV-----------------SKSSEELLD-VLRDRIIPFLLETVIKGDERIKSVNIL 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1272 -----------KLMRHRvdaQGKLVRLDNIY-AIKTNGTNIFGAMLD------DNID-----PYtivssSIGDTMELYGI 1328
Cdd:cd02737 200 wedspstswvkSVGKSS---RGELVLEVTVEeSCKKTRGNAWNVVMDacipvmDLIDwersmPY-----SIQQIKSVLGI 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1329 EAARQKIISEIRTVMGDKGPN-HR-HLLMYADLMTRTGQVTSLEKAGLnaREPSNVL------LRMALSSPVQVLTDAAI 1400
Cdd:cd02737 272 DAAFEQFVQRLESAVSMTGKSvLReHLLLVADSMTYSGEFVGLNAKGY--KAQRRSLkisapfTEACFSSPIKCFLKAAK 349
|
410 420
....*....|....*....|....
gi 1755167230 1401 DSAVNPIYGIAAPTLMGSVPRIGT 1424
Cdd:cd02737 350 KGASDSLSGVLDACAWGKEAPVGT 373
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
189-544 |
1.78e-10 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 65.70 E-value: 1.78e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 189 KNSHPEKLVLKAIQIPPISIRPGIRLGigSGPQSFHDINNViqY---IVRKNLLIpkDLQIVRGqKIPLNVDRNLQTIQQ 265
Cdd:CHL00018 257 TNIEPEWMVLCLLPVLPPELRPIIQLD--GGKLMSSDLNEL--YrrvIYRNNTLT--DLLTTSR-STPGELVMCQKKLLQ 329
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 266 LYYNFLLDSvsttatqggtGKRGIVMGA---RPAPSIMRRLPRKEGRIRKSLLGSQVWSISRSTICGNSDLHLDEVGYPI 342
Cdd:CHL00018 330 EAVDALLDN----------GIRGQPMRDghnKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPR 399
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 343 SFArtlqvAETVQHYNINRLMpyflngKRQYPGCSRVYKQITQSVHDIeglkqdfrleVGDILyRDVVTGDVAFFNRQPS 422
Cdd:CHL00018 400 EIA-----IELFQPFVIRGLI------RQHLASNIRAAKSKIREKEPI----------VWEIL-QEVMQGHPVLLNRAPT 457
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 423 LERSSIGVHRIVVLENPKIstfQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLC-SVRNWFiSTKSSGPVNGQVQ 501
Cdd:CHL00018 458 LHRLGIQAFQPILVEGRAI---CLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMfSHMNLL-SPAIGDPISVPSQ 533
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1755167230 502 DSTVGSFLLTrTNTPMG--KNVMNKLHamglfQTTQTDPPCFANY 544
Cdd:CHL00018 534 DMLLGLYVLT-IGNRRGiyANRYNPCN-----RKNSTKEPYFSNS 572
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1038-1118 |
4.83e-09 |
|
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: 56.66 E-value: 4.83e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 1038 GEAVGILAAQSVSEPLTQYMLDS-HHRSVAGGTNKSGIVRPQEIFSAKpveaeqSSEMLLRLKNPEVeTNKTYAQEIANS 1116
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTfHFAGVASMNVTLGLPRLKEILNAA------SIHEMLEALGIEA-ARETIIREIQKV 73
|
..
gi 1755167230 1117 IE 1118
Cdd:cd00630 74 LA 75
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
860-1008 |
4.06e-08 |
|
RNA polymerase Rpb1, domain 6; 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 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511 Cd Length: 188 Bit Score: 54.81 E-value: 4.06e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 860 LDARQLETVRFETIMLSDQELEDKFKYTGIQSP------------------------LFEEEFSRLKKDRDKYRQIflni 915
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKsgflpgyleegvikeiagdpevqqLLDEEYEQLLEDRELLREI---- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 916 enfNFSQLLTDVRQVPVNVASIVKN------ILLSSTSGVLPFDeksILQKytmVKTFCKNLPYVFINN--IQERlQtpi 987
Cdd:pfam04992 77 ---IFPTGDSKVPQLPVNIQRIIQNaqkifhIDDRKPSDLHPIY---VIEG---VRELLDRLVVVRGDDplSKEA-Q--- 143
|
170 180
....*....|....*....|.
gi 1755167230 988 pvylKRAASLMRILIRIELAT 1008
Cdd:pfam04992 144 ----ENATLLFKILLRSRLAS 160
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1033-1086 |
8.30e-06 |
|
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: 48.29 E-value: 8.30e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1755167230 1033 SLINYGEAVGILAAQSVSEPLTQYMLDSHHrsvAGGTNK---SGIVRPQEIFSAKPV 1086
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFH---TGGVATditQGLPRVEELFEARKI 54
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
398-512 |
9.15e-05 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 47.37 E-value: 9.15e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1755167230 398 RLEVGDILYrDVVTGDVAFFNRQPSLERSSI---------G----VHRIVvlenpkistfqmnvsaCAWYNADFDGDQMN 464
Cdd:PRK00566 395 DPEVWDVLE-EVIKEHPVLLNRAPTLHRLGIqafepvlieGkaiqLHPLV----------------CTAFNADFDGDQMA 457
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1755167230 465 LWVPWSVMSRVEAELLCSVRNWFISTKSSGPVNGQVQDSTVGSFLLTR 512
Cdd:PRK00566 458 VHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTR 505
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1014-1055 |
2.63e-04 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 45.70 E-value: 2.63e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1755167230 1014 ITCEQMSAIldlIRLQYTQSLINY-----GEAVGILAAQSVSEPLTQ 1055
Cdd:CHL00117 289 LTCRSTSWI---CQLCYGWSLAHGdlvelGEAVGIIAGQSIGEPGTQ 332
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1031-1085 |
4.83e-04 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 44.67 E-value: 4.83e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1755167230 1031 TQSLINYGEAVGILAAQSVSEPLTQYMLDSHHrsvAGGTN-KSGIVRPQEIFSA-KP 1085
Cdd:PRK00566 872 TGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFH---TGGVDiTGGLPRVAELFEArKP 925
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1014-1080 |
5.52e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 44.50 E-value: 5.52e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1755167230 1014 ITCEQMSAILDLIRLQYTQSLINYGEAVGILAAQSVSEPLTQYMLDSHHRSVaggTNKSGIVRPQEI 1080
Cdd:PRK14898 33 VTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLPYDEKII---VKEGGETRVTEI 96
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1003-1055 |
1.36e-03 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 43.45 E-value: 1.36e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1755167230 1003 RIELATVKTLNI----TCEqmsAILDLIRLQYTQSL-----INYGEAVGILAAQSVSEPLTQ 1055
Cdd:PRK02597 270 KIEKAGVEEVMVrsplTCE---AARSVCRKCYGWSLahnhlVDLGEAVGIIAAQSIGEPGTQ 328
|
|
| |
