|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
17-874 |
0e+00 |
|
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 1614.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 17 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 95
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 96 CFITKIIKVLRCVCffcskllvdsnnpkikdilikskgqprkrlthvyelckgkniceggeemdnkfgveqqeneedltk 175
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 176 ekghggcgryqprirrtglelyaewkhvnedsqekKILLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIVTVLPVPP 255
Cdd:cd02733 93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 256 LAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 335
Cdd:cd02733 138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 336 SIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPGAK 415
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 416 YIIRDNGDRIDLRFHPKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 495
Cdd:cd02733 298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 496 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKMPQP 575
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 576 AILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPddedsGPYKHISPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISY 655
Cdd:cd02733 458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 656 LEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 735
Cdd:cd02733 533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 736 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 815
Cdd:cd02733 613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 2064985138 816 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd02733 693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
16-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 979.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 16 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 94
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 95 VCFITKIIKVLRCVCFFCSKLLVDSNnpKIKDIL-----IKSKGQPRKRLT-HVYELCKGKNICEggeemdnkfgveqqe 168
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVCP--------------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 169 needltkekgHggCGRYQPRIRrtgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIV 248
Cdd:PRK08566 150 ----------H--CGEKQYKIK---FEKPTTFYEERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 327
Cdd:PRK08566 212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 328 QKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRG 407
Cdd:PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 408 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 485
Cdd:PRK08566 371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 486 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 565
Cdd:PRK08566 450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 566 STWDGKMPQPAILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPDDEDSGPYKhiSPGDTKVIVENGELIMGILCKKSLGT 645
Cdd:PRK08566 530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:PRK08566 608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:PRK08566 688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVRNSINQVV 885
Cdd:PRK08566 768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847
|
....*...
gi 2064985138 886 QLRYGEDG 893
Cdd:PRK08566 848 QFKYGEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
13-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 934.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 13 LRLIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKP 91
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 92 VFHVCFITKIIKVLRCVCFFCSKLlvdsnnpKIKDILIKskgQPRKRLthvyelckgkniceggEEMDNKFGVEQQENEE 171
Cdd:TIGR02390 79 VVHVGFAKEIYKILRATCRKCGRI-------TLTEEEIE---QYLEKI----------------NKLKEEGGDLASTLIE 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 172 DLTKEKGHGG----CGRYQPRIRrtglelYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEEDVILGMDPKFARPEWMI 247
Cdd:TIGR02390 133 KIVKEAAKRMkcphCGEEQKKIK------FEKPTYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMV 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 248 VTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAM 327
Cdd:TIGR02390 207 LTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPAR 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 328 QKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRG 407
Cdd:TIGR02390 287 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNG 366
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 408 NSQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSV 486
Cdd:TIGR02390 367 PDSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAV 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 487 TTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLS 566
Cdd:TIGR02390 447 CPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVA 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 567 TWDGKMPQPAILKPRPLWTGKQIFSLIIPGHIN-VIRTHSTHPDDEDSgpyKHISPGDTKVIVENGELIMGILCKKSLGT 645
Cdd:TIGR02390 526 GYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNfEGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGA 602
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:TIGR02390 603 EKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEP 682
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:TIGR02390 683 LPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTL 762
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVRNSINQVV 885
Cdd:TIGR02390 763 PHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLI 842
|
890
....*....|
gi 2064985138 886 QLRYGEDGLA 895
Cdd:TIGR02390 843 QFKYGEDGVD 852
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1056-1474 |
0e+00 |
|
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: 823.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1056 FRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTP 1135
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1136 SLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDVT--RISPWLLRIE 1213
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEdeevvdkMDDDVFLRCIESNMLTD 1293
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1294 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVS 1453
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 2064985138 1454 ENIMLGQLAPAGTGCFDLLLD 1474
Cdd:cd02584 390 ENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
828-1425 |
1.53e-178 |
|
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: 550.80 E-value: 1.53e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 828 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVRNSINQVVQLRYGEDGLAGENVEFQNLATV 907
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 908 KPSHKAFEKKFRFDCTNERALRRILQEDVVKDvqtnahvqgvlerefdrmkedrdtlrtifptgdskvvlpcnlarmiwn 987
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKE------------------------------------------------ 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 988 aqkifrintrtptdlnplrvvegvhelSKKLVIVNGDDPLSKQAQQNATLLFNIHLRSTLCSKRMTEEFRLSTEAFDWLL 1067
Cdd:pfam04998 113 ---------------------------ILVRDSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1068 GEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAAR 1147
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1148 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDF--------DVTRISPWLLRIELDRKHM 1219
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEvtneeeidPETGLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1220 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEDEEvvdKMDDDVFLRCIESNMLTDMTLQGI 1299
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDEL---FMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1300 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1378
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 2064985138 1379 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPL 1425
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
244-544 |
2.75e-171 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 522.08 E-value: 2.75e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 244 EWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNElpGL 323
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 324 PRAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQEL 403
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 404 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 482
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2064985138 483 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 544
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
13-352 |
1.50e-141 |
|
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: 442.11 E-value: 1.50e-141
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 13 LRLIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 90
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 91 PVFHVCFITKIIKVLRCVCFFCSKLLVDSNNPKIKDILIKSKGQ--PRKRLTHVYELCKGKNICEGGEEMDnkfgveqqe 168
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 169 needltkekghGGCGRYQPRIRRTGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIV 248
Cdd:pfam04997 150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 328
Cdd:pfam04997 217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
|
330 340
....*....|....*....|....
gi 2064985138 329 KSGRPLKSIKQRLKGKEGRVRGNL 352
Cdd:pfam04997 297 KSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
894-1077 |
3.78e-92 |
|
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: 296.72 E-value: 3.78e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 894 LAGENVEFQNLATVKPSHKAFEKKFRFDCTNERA--LRRILQEDVVKDVQTNAHVQGVLEREFDRMKEDRDTLRT-IFPT 970
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREiIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 971 GDSKVV-LPCNLARMIWNAQKIFRINTRTPTDLNPLRVVEGVHELSKKLVIVNGDDPLSKQAQQNATLLFNIHLRSTLCS 1049
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 2064985138 1050 KRMTEEFRLSTEAFDWLLGEIETKFNQS 1077
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1054-1477 |
1.04e-86 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 289.05 E-value: 1.04e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1054 EEFRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPK 1133
Cdd:PRK04309 31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1134 TPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaedqewvnvyyEMPDFDVTrispwllrIE 1213
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV----------------------DLANMTII--------IE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKFQEDEEVVDKmdddvflrciesnmLTD 1293
Cdd:PRK04309 161 LDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK--------------IRN 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1294 MTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:PRK04309 217 IKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAAR 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVS 1453
Cdd:PRK04309 279 NAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVT 358
|
410 420
....*....|....*....|....
gi 2064985138 1454 ENIMLGQLAPAGTGCFDLLLDAEK 1477
Cdd:PRK04309 359 ENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1058-1474 |
3.92e-84 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 281.17 E-value: 3.92e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1058 LSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSL 1137
Cdd:TIGR02389 20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1138 TVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaedqewvnvyyempdfDVTRISpwlLRIELDRK 1217
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VIIELDEE 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1218 HMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNaeklvlrIRIMNSDENKFQEDEEVVDKmdddvflrciesnmLTDMTLQ 1297
Cdd:TIGR02389 150 QLKERGITVDDVEKAIKKAKLGKVIEIDMDNN-------TITIKPGNPSLKELRKLKEK--------------IKNLHIK 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1298 GIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALE 1377
Cdd:TIGR02389 209 GIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAII 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1378 RELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVSENIM 1457
Cdd:TIGR02389 271 EEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENII 350
|
410
....*....|....*..
gi 2064985138 1458 LGQLAPAGTGCFDLLLD 1474
Cdd:TIGR02389 351 VGQPIPLGTGDVDLVMD 367
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
83-878 |
2.10e-61 |
|
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: 231.59 E-value: 2.10e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 83 FGHIELAKPVFHVCFITKIIKVLRcvcffcskLLVDSNNPKIKDIL-------IKSKGQPRKRLTHVYELCKGKNICEGG 155
Cdd:COG0086 92 MGHIELAMPVFHIWGLKSLPSRIG--------LLLDMSLRDLERVLyfesyvvIDPGDTPLEKGQLLTEDEYREILEEYG 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 156 EEMDNKFG---VEQQENEEDLTKEKGhggcgryqprirrtglELYAEWKHVNedSQEKKIllspervhEIFKRIsdeeDV 232
Cdd:COG0086 164 DEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK--------KLIKRL----KV 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 233 ILGMDPKFARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHV 312
Cdd:COG0086 214 VEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAV 293
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 313 ATMVDNELPGlpRAMQKSG-RPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEI 391
Cdd:COG0086 294 DALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL-----EL 366
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 392 VTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqigykverhmcdgdiVIFNRQPTLHK 464
Cdd:COG0086 367 FKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------------VLLNRAPTLHR 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 465 MSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIV 536
Cdd:COG0086 422 LGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPS 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 537 QDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKMPQPAILKPRPLWTGKQ------------IFSLIIP- 595
Cdd:COG0086 494 QDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgkivettvgryLVNEILPq 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 596 --GHINvirthsthpddedsgpykhispgdtKVIvengelimgilCKKSLGTsagsLVHISYLEMGHDITRLFYSNIQTV 673
Cdd:COG0086 569 evPFYN-------------------------QVI-----------NKKHIEV----IIRQMYRRCGLKETVIFLDRLKKL 608
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 674 VNNWLLIEGHSIGIGDSIADAKTyldiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfENQVNRILNDARDKTGSS 753
Cdd:COG0086 609 GFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTKASLETESF 677
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 754 AQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenSYLAGLTPT 832
Cdd:COG0086 678 LMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS---------------------NFREGLGVL 736
|
810 820 830 840
....*....|....*....|....*....|....*....|....*...
gi 2064985138 833 EFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYD-GTVR 878
Cdd:COG0086 737 EYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDcGTDR 784
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1513-1612 |
3.18e-13 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 67.93 E-value: 3.18e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1513 PAMTP-WNTGA--TPAYGAWSPSVGSGMTPGAAGFSPSA------------ASDASGFSPGYSPAWSP--TPGSPGSPGP 1575
Cdd:smart01104 1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRtpawggagsrtpAWGGAGPTGSRTPAWGGasAWGNKSSEGS 80
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 2064985138 1576 ASPYIPSPG---GAMSPNYSPTSPAYEPRSPGGYTPQSPG 1612
Cdd:smart01104 81 ASSWAAGPGgayGAPTPGYGGTPSAYGPATPGGGAMAGSA 120
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
762-1115 |
3.12e-12 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 72.34 E-value: 3.12e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 762 NNFKS---------MVVAGSKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 828
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 829 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD--GTVRnSInqVVQlryGEDGLAGENVEFQNlat 906
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEdcGTTR-GI--VVE---AMDDGDRVLIPLGD--- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 907 vkpshkafekkfrfdctneRALRRILQEDVVkdvqtnaHVQGvlerefdrmkedrdtlrtifptgdsKVVLPCNlarmiw 986
Cdd:PRK02597 238 -------------------RLLGRVLAEDVV-------DPEG-------------------------EVIAERN------ 260
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 987 naqkifrintrTPTDlnplrvvegvHELSKKL-------VIVNgdDPLSKQAQqnatllfnihlRStLCSKrmteefrls 1059
Cdd:PRK02597 261 -----------TAID----------PDLAKKIekagveeVMVR--SPLTCEAA-----------RS-VCRK--------- 296
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2064985138 1060 teAFDWllgeietkfnqSIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1115
Cdd:PRK02597 297 --CYGW-----------SLAHNhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| MISS |
pfam15822 |
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic ... |
1513-1611 |
1.02e-06 |
|
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic MAPK-interacting and spindle-stabilising protein-like proteins. MISS is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localization signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII spindle. MISS is the first example of a physiological MAPK-substrate that is stabilized in MII that specifically regulates MII spindle integrity during the CSF arrest.
Pssm-ID: 318115 [Multi-domain] Cd Length: 238 Bit Score: 51.91 E-value: 1.02e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1513 PAMTPWNTGATPaygawsPSVGSGMTPGAAGFSPSAASDASGFSPGYsPAWSPTPGSPGSPGPASPYIPSPGGamsPNYS 1592
Cdd:pfam15822 31 PGSNPWNNPSAP------PAVPSGLPPSTAPSTVPFGPAPTGMYPSI-PLTGPSPGPPAPFPPSGPSCPPPGG---PYPA 100
|
90 100
....*....|....*....|
gi 2064985138 1593 PTSPAyePRSPGGY-TPQSP 1611
Cdd:pfam15822 101 PTVPG--PGPIGPYpTPNMP 118
|
|
| PHA03307 |
PHA03307 |
transcriptional regulator ICP4; Provisional |
1505-1603 |
2.16e-05 |
|
transcriptional regulator ICP4; Provisional
Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 49.78 E-value: 2.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1505 PSPMSGMSPAMTPwntgATPAYGAWSPSVGSGMtpgAAGFSPSAASDASGFSPGYSPAWSPTPGSPgsPGPASPyiPSPG 1584
Cdd:PHA03307 298 PSPSSPGSGPAPS----SPRASSSSSSSRESSS---SSTSSSSESSRGAAVSPGPSPSRSPSPSRP--PPPADP--SSPR 366
|
90
....*....|....*....
gi 2064985138 1585 GAMSPNYSPTSPAYEPRSP 1603
Cdd:PHA03307 367 KRPRPSRAPSSPAASAGRP 385
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
17-874 |
0e+00 |
|
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 1614.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 17 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 95
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 96 CFITKIIKVLRCVCffcskllvdsnnpkikdilikskgqprkrlthvyelckgkniceggeemdnkfgveqqeneedltk 175
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 176 ekghggcgryqprirrtglelyaewkhvnedsqekKILLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIVTVLPVPP 255
Cdd:cd02733 93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 256 LAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 335
Cdd:cd02733 138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 336 SIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPGAK 415
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 416 YIIRDNGDRIDLRFHPKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 495
Cdd:cd02733 298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 496 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKMPQP 575
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 576 AILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPddedsGPYKHISPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISY 655
Cdd:cd02733 458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 656 LEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 735
Cdd:cd02733 533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 736 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 815
Cdd:cd02733 613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 2064985138 816 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd02733 693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
16-893 |
0e+00 |
|
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 997.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 16 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 94
Cdd:cd02582 4 IKGIKFGLLSPEEIRKMSVVE--IITPDTyDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 95 VCFITKIIKVLRCVCFFCSKLLV-----DSNNPKIKDiLIKSKGQPRKRL-THVYELCKGKNICEggeemdnkfgveqqe 168
Cdd:cd02582 82 VGFAKHIYDLLRATCRSCGRILLpeeeiEKYLERIRR-LKEKWPELVKRViEKVKKKAKKRKVCP--------------- 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 169 needltkekgHggCGRYQPRIRrtgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIV 248
Cdd:cd02582 146 ----------H--CGAPQYKIK---LEKPTTFYEEKEEGEVK---LTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVL 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 328
Cdd:cd02582 208 TVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARH 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 329 KSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGN 408
Cdd:cd02582 288 RSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGP 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 409 SQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSV 486
Cdd:cd02582 368 DKWPGANYVIRPDGRRIRLRYVNR-EELaeRLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAV 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 487 TTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLS 566
Cdd:cd02582 447 CPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAG 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 567 tWDGKMPQPAILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPDDEDSGPYKHisPGDTKVIVENGELIMGILCKKSLGT- 645
Cdd:cd02582 527 -YDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEGKAKVCSGCSECKDEDC--PNDGYVVIKNGKLLEGVIDKKAIGAe 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:cd02582 604 QPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEP 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:cd02582 684 LPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTL 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVRNSINQVV 885
Cdd:cd02582 764 PHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNII 843
|
....*...
gi 2064985138 886 QLRYGEDG 893
Cdd:cd02582 844 QFKYGEDG 851
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
16-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 979.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 16 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 94
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 95 VCFITKIIKVLRCVCFFCSKLLVDSNnpKIKDIL-----IKSKGQPRKRLT-HVYELCKGKNICEggeemdnkfgveqqe 168
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVCP--------------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 169 needltkekgHggCGRYQPRIRrtgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIV 248
Cdd:PRK08566 150 ----------H--CGEKQYKIK---FEKPTTFYEERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 327
Cdd:PRK08566 212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 328 QKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRG 407
Cdd:PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 408 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 485
Cdd:PRK08566 371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 486 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 565
Cdd:PRK08566 450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 566 STWDGKMPQPAILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPDDEDSGPYKhiSPGDTKVIVENGELIMGILCKKSLGT 645
Cdd:PRK08566 530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:PRK08566 608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:PRK08566 688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVRNSINQVV 885
Cdd:PRK08566 768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847
|
....*...
gi 2064985138 886 QLRYGEDG 893
Cdd:PRK08566 848 QFKYGEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
13-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 934.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 13 LRLIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKP 91
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 92 VFHVCFITKIIKVLRCVCFFCSKLlvdsnnpKIKDILIKskgQPRKRLthvyelckgkniceggEEMDNKFGVEQQENEE 171
Cdd:TIGR02390 79 VVHVGFAKEIYKILRATCRKCGRI-------TLTEEEIE---QYLEKI----------------NKLKEEGGDLASTLIE 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 172 DLTKEKGHGG----CGRYQPRIRrtglelYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEEDVILGMDPKFARPEWMI 247
Cdd:TIGR02390 133 KIVKEAAKRMkcphCGEEQKKIK------FEKPTYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMV 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 248 VTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAM 327
Cdd:TIGR02390 207 LTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPAR 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 328 QKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRG 407
Cdd:TIGR02390 287 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNG 366
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 408 NSQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSV 486
Cdd:TIGR02390 367 PDSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAV 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 487 TTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLS 566
Cdd:TIGR02390 447 CPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVA 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 567 TWDGKMPQPAILKPRPLWTGKQIFSLIIPGHIN-VIRTHSTHPDDEDSgpyKHISPGDTKVIVENGELIMGILCKKSLGT 645
Cdd:TIGR02390 526 GYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNfEGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGA 602
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:TIGR02390 603 EKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEP 682
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:TIGR02390 683 LPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTL 762
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVRNSINQVV 885
Cdd:TIGR02390 763 PHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLI 842
|
890
....*....|
gi 2064985138 886 QLRYGEDGLA 895
Cdd:TIGR02390 843 QFKYGEDGVD 852
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
12-1479 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 916.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 12 PLRLIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 90
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAE--ITAPEAyDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 91 PVFHVCFITKIIKVLRCVCFFCSKLLVDSNNpkikdiliKSKGQPRKRLTHVYELCKGKNIcegGEEMDNKFGvEQQENE 170
Cdd:PRK14977 83 PVIHIAFIDNIKDLLNSTCHKCAKLKLPQED--------LNVFKLIEEAHAAARDIPEKRI---DDEIIEEVR-DQVKVY 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 171 EDLTKEKGHggCGRYQPRirrtgLELYAEWKHVNEDSQEKKILLsPERVHEIFKRISDEEDVILGMDPKFARPEWMIVTV 250
Cdd:PRK14977 151 AKKAKECPH--CGAPQHE-----LEFEEPTIFIEKTEIEEHRLL-PIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQA 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 251 LPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQK- 329
Cdd:PRK14977 223 FLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKg 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 330 SGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNS 409
Cdd:PRK14977 303 SGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPD 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 410 QYPGAKYIIRDNGDRIDLRFHPKPSDL-------HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 482
Cdd:PRK14977 383 EFPGANAIRKGDGTKIRLDFLEDKGKDalreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRL 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 483 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLL 562
Cdd:PRK14977 463 HPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIA 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 563 MfLSTWDGKMPQPAI-LKPRPLWTGKQIFSLIIPGHIN--VIRTHSTHPDDEDSGPYkhiSPGDTKVIVENGELIMGILC 639
Cdd:PRK14977 543 M-LAGITDPLPEPAIkTKDGPAWTGKQLFSLFLPKDFNfeGIAKWSAGKAGEAKDPS---CLGDGYVLIKEGELISGVID 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 640 KKSLGTSAG---SLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIE 716
Cdd:PRK14977 619 DNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLID 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 717 K--------AHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQ 788
Cdd:PRK14977 699 QrkitrkitIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQ 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 789 QNVE--------GKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQR 860
Cdd:PRK14977 779 QKRKtrigfvltGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQR 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 861 RLIKSMESVMVKYDGTVRNSINQVVQLRYGEDGlagenvefqnlatvkpshkafekkfrfdctneralrrilqedvvkdv 940
Cdd:PRK14977 859 RLANALEDIRLEYDETVRDPHGHIIQFKFGEDG----------------------------------------------- 891
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 941 qtnahvqgvlereFDRMKEDRDTlrtifptgdskvvlPCNLARMIWNAQKIFRINTRTPtdlnplrvvEGVHELSKKlvi 1020
Cdd:PRK14977 892 -------------IDPQKLDHGE--------------AFNLERIIEKQKIEDRGKGASK---------DEIEELAKE--- 932
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1021 vngddpLSKQAQQNATLLFNIHLRSTlcskrmteefRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQM 1100
Cdd:PRK14977 933 ------YTKTFNANLPKLLADAIHGA----------ELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQM 996
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1101 TLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIYYdPNPQ 1180
Cdd:PRK14977 997 TLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN-ANEI 1075
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1181 NTVVAEDQEWVNVYYEMPDFdvtrispwllrIELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeKLVlririm 1260
Cdd:PRK14977 1076 KLIKPDKRALENGCIPMERF-----------AEIEAALAKGKKFEMELEDDLIIL----------------DLV------ 1122
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1261 nsdenkfqedeEVVDKMDDDVFLRCIeSNMLTDMTLQGIEQISKVYMHLPQTDNKKkiiitedgefkalqEWILETDGVS 1340
Cdd:PRK14977 1123 -----------EAADRDKPLATLIAI-RNKILDKPVKGVPDIERAWVELVEKDGRD--------------EWIIQTSGSN 1176
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1341 LMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAI------TR 1414
Cdd:PRK14977 1177 LAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglqaagVR 1256
|
1450 1460 1470 1480 1490 1500
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2064985138 1415 HGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK 1479
Cdd:PRK14977 1257 HGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
24-878 |
0e+00 |
|
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 902.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 24 LSPDELKRMSVTEggIKYPE--TTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVCFITKI 101
Cdd:cd02583 1 LSPEDIIRLSEVE--VTNRNlyDIETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 102 IKVLRCVCFFCSKLLVDsnnPKIKDILIKSKGQPRKRLTH-------VYELCKGKNICEggeemdnkfgveqqeneedlt 174
Cdd:cd02583 79 INILQCICKTCSRVLLP---EEEKRKFLKRLRRPNLDNLQkkalkkkILEKCKKVRKCP--------------------- 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 175 kekgHggCGRYqprirrtglelyaewKHVNEDsqekkilLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIVTVLPVP 254
Cdd:cd02583 135 ----H--CGLL---------------KKAQED-------LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVP 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 255 PLAVRPAVVMQG-SARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSgRP 333
Cdd:cd02583 187 PLCIRPSVVMDEkSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPK-KP 265
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 334 LKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPG 413
Cdd:cd02583 266 IRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPG 345
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 414 AKYII-RDNGDRIDLRF-HPKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYN 491
Cdd:cd02583 346 ANFVIkRDGGKKKFLKYgNRRKIARELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYN 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 492 ADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwDGK 571
Cdd:cd02583 426 ADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYML--DGE 503
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 572 M----PQPAILKPRPLWTGKQIFSLII-PGHINVIRTHSTHPDDEDSGPYKHISPGDTKVIVENGELIMGILCKKSLGT- 645
Cdd:cd02583 504 IkidlPPPAILKPVELWTGKQIFSLLLrPNKKSPVLVNLEAKEKSYTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSg 583
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:cd02583 584 SKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLEL 663
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:cd02583 664 QPGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTL 743
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2064985138 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVR 878
Cdd:cd02583 744 PHFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1056-1474 |
0e+00 |
|
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: 823.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1056 FRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTP 1135
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1136 SLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDVT--RISPWLLRIE 1213
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEdeevvdkMDDDVFLRCIESNMLTD 1293
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1294 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVS 1453
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 2064985138 1454 ENIMLGQLAPAGTGCFDLLLD 1474
Cdd:cd02584 390 ENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
20-874 |
0e+00 |
|
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain] Cd Length: 779 Bit Score: 633.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 20 QFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVCFI 98
Cdd:cd01435 1 SFSFYSAEEIRKLSVKE--ITNPVTfDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFF 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 99 TKIIKVLRCVCFFCSKLlvdsnnpKIKDILIKskgqprkRLTHVYELCkgkniceggeemdnkfgveqqeneedltkEKG 178
Cdd:cd01435 79 DLLYKLLRGSCFYCHRF-------RISKWEVK-------LFVAKLKLL-----------------------------DKG 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 179 hggcgryqprirrtglelyaewkhvneDSQEKKILLSPervheifkrisdeedvilgmdpkfarPEWMIVTVLPVPPLAV 258
Cdd:cd01435 116 ---------------------------LLVEAAELDFG--------------------------YDMFFLDVLLVPPNRF 142
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 259 RPAVVMQGSArnqddLTHK----LADIVKINNQLR------RNEQSGAAAHVIAEDVKL---------LQFHVATMVDNE 319
Cdd:cd01435 143 RPPSFLGDKV-----FENPqnvlLSKILKDNQQIRdllasmRQAESQSKLDLISGKTNSeklinawlqLQSAVNELFDST 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 320 LPGLPRAMQKSGrplksIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDR 399
Cdd:cd01435 218 KAPKSGKKSPPG-----IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEE 292
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 400 LQELVRRGNSQYPGAKYIIRDNGDRIDLRFH--------------PKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKM 465
Cdd:cd01435 293 LRQAVINGPDVYPGANAIEDEDGRLILLSALseerrkalakllllLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKP 372
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 466 SMMGHRVRILPWS-TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 544
Cdd:cd01435 373 SIMAHKVRVLPGEkTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGV 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 545 KFTKRDVFLERGEVMNLLMF-LSTWDG-------KMPQPAILKPRPLWTGKQIFSLIIpghINVIRTHStHPDDEDS--- 613
Cdd:cd01435 453 LLTSRDTFFTREEYQQLVYAaLRPLFTsdkdgriKLLPPAILKPKPLWTGKQVISTIL---KNLIPGNA-PLLNLSGkkk 528
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 614 ------GPYKHISPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGI 687
Cdd:cd01435 529 tkkkvgGGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGI 608
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 688 GDSI----ADAKTyldiQNTIKKAKQDVIEVIEKAhnneleptpgntlrqtFENQVNRILNDARDKTGSSAQKSLSEYNN 763
Cdd:cd01435 609 EDLLltpkADEKR----RKILRKAKKLGLEAAAEF----------------LGLKLNKVTSSIIKACLPKGLLKPFPENN 668
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 764 FKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGRE 843
Cdd:cd01435 669 LQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGRE 748
|
890 900 910
....*....|....*....|....*....|.
gi 2064985138 844 GLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd01435 749 GLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
828-1425 |
1.53e-178 |
|
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: 550.80 E-value: 1.53e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 828 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDGTVRNSINQVVQLRYGEDGLAGENVEFQNLATV 907
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 908 KPSHKAFEKKFRFDCTNERALRRILQEDVVKDvqtnahvqgvlerefdrmkedrdtlrtifptgdskvvlpcnlarmiwn 987
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKE------------------------------------------------ 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 988 aqkifrintrtptdlnplrvvegvhelSKKLVIVNGDDPLSKQAQQNATLLFNIHLRSTLCSKRMTEEFRLSTEAFDWLL 1067
Cdd:pfam04998 113 ---------------------------ILVRDSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1068 GEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAAR 1147
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1148 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDF--------DVTRISPWLLRIELDRKHM 1219
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEvtneeeidPETGLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1220 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEDEEvvdKMDDDVFLRCIESNMLTDMTLQGI 1299
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDEL---FMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1300 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1378
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 2064985138 1379 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPL 1425
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
24-874 |
3.83e-178 |
|
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: 550.11 E-value: 3.83e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 24 LSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVCFITKI 101
Cdd:cd00399 1 MSPEEIRKWSVAK--VIKPETIDnrTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKV 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 102 IKVLRcvcffcskllvdsnnpkikdilikskgqprkrlthvyelckgkniceggeemdnkfgveqqeneedltkekghgg 181
Cdd:cd00399 79 PSFLG--------------------------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 182 cgryqprirrtglelyaewkhvnedsqekkillspervheifkrisdeedvilgmdpkfarPEWMIVTVLPVPPLAVRPA 261
Cdd:cd00399 84 -------------------------------------------------------------PEWMILTCLPVPPPCLRPS 102
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 262 VVmqgsarnqddlthkladivkinnqlrrneqsgaaahvIAEDVKLLQFHVATMVDNELPGLPRAMqKSGRPLKSIKQRL 341
Cdd:cd00399 103 VI-------------------------------------IEERWRLLQEHVDTYLDNGIAGQPQTQ-KSGRPLRSLAQRL 144
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 342 KGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMtfpeivtpfnidrlqelvrrgnsqypgakyiirdn 421
Cdd:cd00399 145 KGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 422 gdridlrfhpkpsdlhlqigykverhmcDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNL 501
Cdd:cd00399 190 ----------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNL 241
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 502 HLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKrdvflergevmnllmflstwdgkmpqpailkpr 581
Cdd:cd00399 242 HVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL--------------------------------- 288
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 582 plwtGKQIFSLIIPGhinvirthsthpddedsgpykhispgdtkvivengelimgilckkslgtsagSLVHISYLEMGHD 661
Cdd:cd00399 289 ----GKQIVSAALPG----------------------------------------------------GLLHTVTRELGPE 312
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 662 ITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNR 741
Cdd:cd00399 313 KAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILD 392
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 742 ILNDARDKTGSSAQKSL---SEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESR 818
Cdd:cd00399 393 FLNEARDKAGSAASVNLdlvSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAK 472
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 2064985138 819 GFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd00399 473 GFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
244-544 |
2.75e-171 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 522.08 E-value: 2.75e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 244 EWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNElpGL 323
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 324 PRAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQEL 403
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 404 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 482
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2064985138 483 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 544
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
13-352 |
1.50e-141 |
|
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: 442.11 E-value: 1.50e-141
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 13 LRLIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 90
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 91 PVFHVCFITKIIKVLRCVCFFCSKLLVDSNNPKIKDILIKSKGQ--PRKRLTHVYELCKGKNICEGGEEMDnkfgveqqe 168
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 169 needltkekghGGCGRYQPRIRRTGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEEDVILGMDPKFARPEWMIV 248
Cdd:pfam04997 150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 328
Cdd:pfam04997 217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
|
330 340
....*....|....*....|....
gi 2064985138 329 KSGRPLKSIKQRLKGKEGRVRGNL 352
Cdd:pfam04997 297 KSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
55-878 |
4.85e-99 |
|
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: 337.45 E-value: 4.85e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 55 LMDPRQGVIERTGRCQTC-AGNMTECPGHFGHIELAKPVFHVCFITKIIKVLRCVCffcskllvdsnnPKIKDILIKSKG 133
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKIC------------PGCKSIKQKKKK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 134 QPRKRLTHVYelckgkniceggeeMDNKFGVEQQEnEEDLTKekghggcgryqprirrtglelyaewkhvnedsqekkil 213
Cdd:cd10506 88 PPRETLPPDY--------------WDFIPKDGQQE-ESCVTK-------------------------------------- 114
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 214 LSPERVHEIFKRISDEedvilgMDPKFA-----RPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQL 288
Cdd:cd10506 115 NLPILSLAQVKKILKE------IDPKLIakglpRQEGLFLKCLPVPPNCHRVTEFTHGFSTGSRLIFDERTRAYKKLVDF 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 289 RRNEQSGAAAHviaedvkllqfhvatmvdnelpglpramqKSGrpLKSIKQrlkgkegrvrgNLMGKRVDFSARTVITPD 368
Cdd:cd10506 189 IGTANESAASK-----------------------------KSG--LKWMKD-----------LLLGKRSGHSFRSVVVGD 226
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 369 PNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGnsqyPGAKYII--RDNGDRIDLRFHPKpsdlhLQIGYKVER 446
Cdd:cd10506 227 PYLELNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLT----LLLKGVIgvRRNGRLVGVRSHNT-----LQIGDVIHR 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 447 HMCDGDIVIFNRQPTLHKMSMMGHRVRILPW-STFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVT 525
Cdd:cd10506 298 PLVDGDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLIS 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 526 PQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTwdgKMPQPAILK--PR--PLWTGKQIFSLIIPghinvi 601
Cdd:cd10506 378 SQSGQNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKspPSngPLWTGKQLFQMLLP------ 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 602 rthsthPDDEDSGPykhispgDTKVIVENGELIMGiLCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIE 681
Cdd:cd10506 449 ------TDLDYSFP-------SNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMR 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 682 GHSIGIGD------SIADAKTYLDIQNTIKKAKQ----DVIEV----IEKAHNNELEPTPGNTLRQTFENQVN-RILNDA 746
Cdd:cd10506 515 GFSVSLSDlylssdSYSRQKMIEEISLGLREAEIacniKQLLVdsrkDFLSGSGEENDVSSDVERVIYERQKSaALSQAS 594
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 747 RDK-------TGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKrIPFGFKH---------RTLPHFIK 810
Cdd:cd10506 595 VSAfkqvfrdIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVK-LSYRIPRqlscaawnsQKSPRVIE 673
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2064985138 811 DDY-----GPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDtavKTAET-GYIQRRLIKSMESVMVKYDGTVR 878
Cdd:cd10506 674 KDGsecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
354-519 |
1.56e-97 |
|
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: 311.16 E-value: 1.56e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 354 GKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKP 433
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 434 SDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEI 513
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 2064985138 514 QELAMV 519
Cdd:pfam00623 161 EELMLV 166
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
894-1077 |
3.78e-92 |
|
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: 296.72 E-value: 3.78e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 894 LAGENVEFQNLATVKPSHKAFEKKFRFDCTNERA--LRRILQEDVVKDVQTNAHVQGVLEREFDRMKEDRDTLRT-IFPT 970
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREiIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 971 GDSKVV-LPCNLARMIWNAQKIFRINTRTPTDLNPLRVVEGVHELSKKLVIVNGDDPLSKQAQQNATLLFNIHLRSTLCS 1049
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 2064985138 1050 KRMTEEFRLSTEAFDWLLGEIETKFNQS 1077
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1052-1475 |
2.32e-88 |
|
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: 293.00 E-value: 2.32e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1052 MTEEFRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKR 1131
Cdd:cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1132 PKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpNPQNTVVaedqewvnvyyempdfdvtrispwllR 1211
Cdd:cd06528 90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI----DLFNMRI--------------------------T 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1212 IELDRKHMTDRKLTMEQIAEKINAGFGDDlncIFNDDNAEKLVLRIrimnsDENKFQEDEEVVDKmdddvflrciesnmL 1291
Cdd:cd06528 140 IELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKA-----EEPSIKELRKLAEK--------------I 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1292 TDMTLQGIEQISKVymhlpqtdnkkkIIITEDGefkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEA 1371
Cdd:cd06528 198 LNTKIKGIKGIKRV------------IVRKEED------EYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEA 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1372 VRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKG 1451
Cdd:cd06528 260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRG 339
|
410 420
....*....|....*....|....
gi 2064985138 1452 VSENIMLGQLAPAGTGCFDLLLDA 1475
Cdd:cd06528 340 VIENIIVGQPIPLGTGDVELTMDP 363
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1054-1477 |
1.04e-86 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 289.05 E-value: 1.04e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1054 EEFRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPK 1133
Cdd:PRK04309 31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1134 TPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaedqewvnvyyEMPDFDVTrispwllrIE 1213
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV----------------------DLANMTII--------IE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKFQEDEEVVDKmdddvflrciesnmLTD 1293
Cdd:PRK04309 161 LDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK--------------IRN 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1294 MTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:PRK04309 217 IKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAAR 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVS 1453
Cdd:PRK04309 279 NAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVT 358
|
410 420
....*....|....*....|....
gi 2064985138 1454 ENIMLGQLAPAGTGCFDLLLDAEK 1477
Cdd:PRK04309 359 ENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1058-1474 |
3.92e-84 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 281.17 E-value: 3.92e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1058 LSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSL 1137
Cdd:TIGR02389 20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1138 TVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaedqewvnvyyempdfDVTRISpwlLRIELDRK 1217
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VIIELDEE 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1218 HMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNaeklvlrIRIMNSDENKFQEDEEVVDKmdddvflrciesnmLTDMTLQ 1297
Cdd:TIGR02389 150 QLKERGITVDDVEKAIKKAKLGKVIEIDMDNN-------TITIKPGNPSLKELRKLKEK--------------IKNLHIK 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1298 GIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALE 1377
Cdd:TIGR02389 209 GIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAII 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1378 RELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVSENIM 1457
Cdd:TIGR02389 271 EEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENII 350
|
410
....*....|....*..
gi 2064985138 1458 LGQLAPAGTGCFDLLLD 1474
Cdd:TIGR02389 351 VGQPIPLGTGDVDLVMD 367
|
|
| RNA_pol_Rpb1_7 |
pfam04990 |
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1162-1297 |
1.33e-76 |
|
RNA polymerase Rpb1, domain 7; 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 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).
Pssm-ID: 461510 [Multi-domain] Cd Length: 136 Bit Score: 249.76 E-value: 1.33e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1162 TTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDV---TRISPWLLRIELDRKHMTDRKLTMEQIAEKINAGFG 1238
Cdd:pfam04990 1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDVedlDRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 2064985138 1239 DDLNCIFNDDNAEKLVLRIRIMNSDENKfqeDEEVVDKMDDDVFLRCIESNMLTDMTLQ 1297
Cdd:pfam04990 81 NDLFVIFSDDNAEKLVIRIRIINDEKEK---DEEQEDKAEDDVFLKRLEANMLDSLTLR 136
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
18-1133 |
6.50e-75 |
|
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: 273.85 E-value: 6.50e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 18 RVQFGVLSPDELKRMSvtEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 75
Cdd:TIGR02386 1 AIKISIASPDTIRNWS--YGEVKKPETInyRTLKPEKDGLFCEKifgptkdwecycgkykkiryKGVV-----CERCGVE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 76 MTECP---GHFGHIELAKPVFHVCF-------ITKII----KVLRCVCFFCSKLLVDSNNPKIKDILIKSKGQPRKRLTh 141
Cdd:TIGR02386 74 VTESKvrrERMGHIELAAPVAHIWYfkglpsrIGLLLditaKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLK- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 142 vyELCKGKNICEGGEemdnkfGVEQQENEEDLTKEkghggcgryqprIRRTGLELyaewKHVNEDSQEKKILLSPERVhE 221
Cdd:TIGR02386 153 --RYGDGFRAGMGAE------AIKELLEKIDLDKE------------IEELKIQL----RESKSDQKRKKLLKRLEIV-E 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 222 IFKRISdeedvilgmdpkfARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVI 301
Cdd:TIGR02386 208 AFKDSG-------------NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIV 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 302 AEDVKLLQFHVATMVDNELPGLPrAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRS 381
Cdd:TIGR02386 275 RNEKRMLQEAVDALFDNGRRGKP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKK 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 382 IAAnmtfpEIVTPFNIDRLQELvrrgnsqypGAKYIIRDNGDRIdLRFHPKPSDLhlqIGYKVERHMcdgdiVIFNRQPT 461
Cdd:TIGR02386 354 MAL-----ELFKPFIIKRLIDR---------ELAANIKSAKKMI-EQEDPEVWDV---LEDVIKEHP-----VLLNRAPT 410
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 462 LHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDT-- 539
Cdd:TIGR02386 411 LHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMvl 490
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 540 ----LTAVRKFTKRD--VFLERGEVM----NLLMFLSTWDGKMPQPAILKPRPlwtGKQIFSLIIPghinvirthsthpd 609
Cdd:TIGR02386 491 glyyLTTEKPGAKGEgkIFSNVDEAIraydNGKVHLHALIGVRTSGEILETTV---GRVIFNEILP-------------- 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 610 deDSGPYKHIS-PGDTKVIvengelimgilckkslgtsaGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIG 688
Cdd:TIGR02386 554 --EGFPYINDNePLSKKEI--------------------SSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISAS 611
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 689 DSIadakTYLDIQNTIKKAKQDVIEVIEKAHNNELepTPGNTLRQTFEnqvnrILNDARDKTGSSAQKSLS----EYNNF 764
Cdd:TIGR02386 612 DIV----VPDEKYEILKEADKEVAKIQKFYNKGLI--TDEERYRKVVS-----IWSETKDKVTDAMMKLLKkdtyKFNPI 680
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 765 KSMVVAGSKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenSYLAGLTPTEFFFHAMGGRE 843
Cdd:TIGR02386 681 FMMADSGARGNISQFRQLAGMRGlMAKPSGDIIELPIKS---------------------SFREGLTVLEYFISTHGARK 739
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 844 GLIDTAVKTAETGYIQRRLIKSMESVMVKYD--GTVRnsinqvvqlrygedglaGENVEfqnlATVKPSHKAFEKkfrfd 921
Cdd:TIGR02386 740 GLADTALKTADSGYLTRRLVDVAQDVVVREEdcGTEE-----------------GIEVE----AIVEGKDEIIES----- 793
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 922 cTNERALRRILQEDVVkdvqtnahvqgvlerefdrmkeDRDTLRTIFPTGDskvVLPCNLARMIWNAqKIFRINTRTPTD 1001
Cdd:TIGR02386 794 -LKDRIVGRYSAEDVY----------------------DPDTGKLIAEANT---LITEEIAEKIENS-GIEKVKVRSVLT 846
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1002 LNPLRvveGVhelskklvivngddplskqaqqnatllfnihlrstlCSKRMTEEfrLSTEAfdwllgEIETkfnqsiahp 1081
Cdd:TIGR02386 847 CESEH---GV------------------------------------CQKCYGRD--LATGK------LVEI--------- 870
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....
gi 2064985138 1082 GEMVGALAAQSLGEPATQMTLNTFHYAGVSA--KNVTLGVPRLKELINiSKRPK 1133
Cdd:TIGR02386 871 GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPK 923
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1073-1469 |
3.66e-70 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 238.27 E-value: 3.66e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1073 KFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQaaRDAERA 1152
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLEND--RDEKSA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1153 KDILCRLEHTTLRKVTANTAIYYDPNpqntvvaedqewvNVYyempdfdvtrispwlLRIELDRKHMTDRKLTMEQIAEK 1232
Cdd:cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPD-------------DCY---------------ILIKLDKKIIEKLQLSKSNLYFL 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1233 INagfgddlncifnddnaeklvlririmnsdenkfqedeevvdkmdddvFLRciesNMLTDMTLQGIEQISKVYMHLPQT 1312
Cdd:cd02736 131 LQ-----------------------------------------------SLK----RKLPDVVVSGIPEVKRAVINKDKK 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1313 DNKKKIIItEDGEFKAlqewILETDGVslmrvlsekdvDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVN 1392
Cdd:cd02736 160 KGKYKLLV-EGYGLRA----VMNTPGV-----------IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSID 223
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2064985138 1393 YRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVSENIMLGQLAPAGTGCF 1469
Cdd:cd02736 224 PRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1051-1472 |
4.48e-70 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 245.49 E-value: 4.48e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1051 RMTEEFRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISK 1130
Cdd:PRK14897 151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1131 RPKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTantaiyydpnpqntvvaedqewvnvyyempDFdVTRISPWLL 1210
Cdd:PRK14897 231 KPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVA------------------------------DI-ITDIAEMSV 279
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1211 RIELDRKHMTDRKLTMEQIAEKInagfgddlncifnddnaEKLVLRIRIMNSDENKFQEDEEVVDKmdddvfLRCIESNm 1290
Cdd:PRK14897 280 VVELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDDGIIRLKPQQPSFKK------LYLLAEK- 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1291 LTDMTLQGIEQISKVymhlpqtdnkkkIIITEDGEfkalQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIE 1370
Cdd:PRK14897 336 VKSLTIKGIKGIKRA------------IARKENDE----RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIE 399
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1371 AVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGESDPMK 1450
Cdd:PRK14897 400 AARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLA 479
|
410 420
....*....|....*....|..
gi 2064985138 1451 GVSENIMLGQLAPAGTGCFDLL 1472
Cdd:PRK14897 480 GVAENIIVGQPITLGTGAVSLV 501
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
523-689 |
2.26e-62 |
|
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: 210.18 E-value: 2.26e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 523 IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwdgKMPQPAILKP-RPLWTGKQIFSLIIPGHINVI 601
Cdd:pfam04983 2 ILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 602 RTHSTHPDDEdsgpykhiSPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIE 681
Cdd:pfam04983 78 GKPKTNEEDL--------CENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKS 149
|
....*...
gi 2064985138 682 GHSIGIGD 689
Cdd:pfam04983 150 GFSIGIDD 157
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
83-878 |
2.10e-61 |
|
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: 231.59 E-value: 2.10e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 83 FGHIELAKPVFHVCFITKIIKVLRcvcffcskLLVDSNNPKIKDIL-------IKSKGQPRKRLTHVYELCKGKNICEGG 155
Cdd:COG0086 92 MGHIELAMPVFHIWGLKSLPSRIG--------LLLDMSLRDLERVLyfesyvvIDPGDTPLEKGQLLTEDEYREILEEYG 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 156 EEMDNKFG---VEQQENEEDLTKEKGhggcgryqprirrtglELYAEWKHVNedSQEKKIllspervhEIFKRIsdeeDV 232
Cdd:COG0086 164 DEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK--------KLIKRL----KV 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 233 ILGMDPKFARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHV 312
Cdd:COG0086 214 VEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAV 293
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 313 ATMVDNELPGlpRAMQKSG-RPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEI 391
Cdd:COG0086 294 DALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL-----EL 366
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 392 VTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqigykverhmcdgdiVIFNRQPTLHK 464
Cdd:COG0086 367 FKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------------VLLNRAPTLHR 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 465 MSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIV 536
Cdd:COG0086 422 LGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPS 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 537 QDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKMPQPAILKPRPLWTGKQ------------IFSLIIP- 595
Cdd:COG0086 494 QDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgkivettvgryLVNEILPq 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 596 --GHINvirthsthpddedsgpykhispgdtKVIvengelimgilCKKSLGTsagsLVHISYLEMGHDITRLFYSNIQTV 673
Cdd:COG0086 569 evPFYN-------------------------QVI-----------NKKHIEV----IIRQMYRRCGLKETVIFLDRLKKL 608
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 674 VNNWLLIEGHSIGIGDSIADAKTyldiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfENQVNRILNDARDKTGSS 753
Cdd:COG0086 609 GFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTKASLETESF 677
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 754 AQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenSYLAGLTPT 832
Cdd:COG0086 678 LMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS---------------------NFREGLGVL 736
|
810 820 830 840
....*....|....*....|....*....|....*....|....*...
gi 2064985138 833 EFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYD-GTVR 878
Cdd:COG0086 737 EYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDcGTDR 784
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
20-1114 |
4.34e-60 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 230.20 E-value: 4.34e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 20 QFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLM-------------------DPR-QGViertGRCQTCAGNMT 77
Cdd:PRK09603 1400 QLTLASPEKI--HSWSYGEVKKPETInyRTLKPERDGLFcmkifgptkdyeclcgkykKPRfKDI----GTCEKCGVAIT 1473
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 78 ECP---GHFGHIELAKPVFHVCFITKI---IKVLRCVcffcskllvdsnnpKIKDIlikskgqprKRLTHvYELCKGKNI 151
Cdd:PRK09603 1474 HSKvrrFRMGHIELATPVAHIWYVNSLpsrIGTLLGV--------------KMKDL---------ERVLY-YEAYIVKEP 1529
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 152 CEG-----GEEMDNKFGVEQQENEEDLTKEKGHGG-CGRYQPRIRRTGLE----------LYAEWKHVNEDSQEKKILls 215
Cdd:PRK09603 1530 GEAaydneGTKLVMKYDILNEEQYQNISRRYEDRGfVAQMGGEAIKDLLEeidlitllqsLKEEVKDTNSDAKKKKLI-- 1607
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 216 pervheifKRISDEEDVILGMDpkfaRPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSG 295
Cdd:PRK09603 1608 --------KRLKVVESFLNSGN----RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELG 1675
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 296 AAAHVIAEDVKLLQFHVATMVDNelpGLPRAMQKSG--RPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQI 373
Cdd:PRK09603 1676 APEIIVRNEKRMLQEAVDVLFDN---GRSTNAVKGAnkRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKM 1752
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 374 DQVGVPRSIAANMTFPEIvtpfnidrLQELVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqigYKVERHMCDGD 452
Cdd:PRK09603 1753 DECGLPKNMALELFKPHL--------LSKLEERGYaTTLKQAKRMIEQKSNEV----------------WECLQEITEGY 1808
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 453 IVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPV 532
Cdd:PRK09603 1809 PVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAV 1888
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 533 MGIVQDTLTAVRKFT--KRDVFLER---GEVMNLLMFLST--WDGKMPQPAILKPRPLWT--GKQIFSLIIPGHINVirt 603
Cdd:PRK09603 1889 AIPSQDMVLGLYYLSleKSGVKGEHklfSSVNEIITAIDTkeLDIHAKIRVLDQGNIIATsaGRMIIKSILPDFIPT--- 1965
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 604 hsthpddedsgpykhispgdtkvivengELIMGILCKKSLGTsagsLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGH 683
Cdd:PRK09603 1966 ----------------------------DLWNRPMKKKDIGV----LVDYVHKVGGIGITATFLDNLKTLGFRYATKAGI 2013
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 684 SIgigdSIADAKTYLDIQNTIKKAKQDVIEViekahnnELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSE--- 760
Cdd:PRK09603 2014 SI----SMEDIITPKDKQKMVEKAKVEVKKI-------QQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKdke 2082
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 761 -YNNFKSMVVAGSKGSKINISQVIAVVGqqnVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFFFHAM 839
Cdd:PRK09603 2083 gFNSIYMMADSGARGSAAQIRQLSAMRG---LMTK--PDGSIIET----------PIISNFKE-----GLNVLEYFNSTH 2142
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 840 GGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYdgtvrnsinqvvqlrygEDGLAGENVEFQNLATVKPSHKAFEkkfr 919
Cdd:PRK09603 2143 GARKGLADTALKTANAGYLTRKLIDVSQNVKVVS-----------------DDCGTHEGIEITDIAVGSELIEPLE---- 2201
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 920 fdctnERALRRILQEDVVkDVQTNAHV--QGVLerefdrmkEDRDTLRTIFPTGDSKVVLpcnlarmiwnaqkifrintR 997
Cdd:PRK09603 2202 -----ERIFGRVLLEDVI-DPITNEILlyADTL--------IDEEGAKKVVEAGIKSITI-------------------R 2248
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 998 TptdlnplrvvegvhelskklvivngddPLSKQAQQNatllfnihlrstLCSKrmteefrlsteAFDWLLGEietkfnQS 1077
Cdd:PRK09603 2249 T---------------------------PVTCKAPKG------------VCAK-----------CYGLNLGE------GK 2272
|
1130 1140 1150
....*....|....*....|....*....|....*..
gi 2064985138 1078 IAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKN 1114
Cdd:PRK09603 2273 MSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
242-872 |
2.44e-58 |
|
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: 215.08 E-value: 2.44e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 242 RPEWMIVTVLPVPPLAVRPAVVMQG-----SARNqdDLTHKladIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMV 316
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGgrfatSDLN--DLYRR---VINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALI 212
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 317 DNELPGLPrAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVTPFN 396
Cdd:cd01609 213 DNGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMAL-----ELFKPFV 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 397 IdrlQELVRRGNSQYP-GAKYIIRDNGDRIdlrfhpkpsdlhlqigYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRIL 475
Cdd:cd01609 287 I---RELIERGLAPNIkSAKKMIERKDPEV----------------WDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLI 347
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 476 PWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDtltavrkftkrdvfler 555
Cdd:cd01609 348 EGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQD----------------- 410
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 556 gevMNLLMFLSTWDGKMPQPA-ILKPRPlwtGKQIFSLIIPghinvirthsthpddedsgpykhispgdtkvivENGELI 634
Cdd:cd01609 411 ---MVLGLYYLTKERKGDKGEgIIETTV---GRVIFNEILP---------------------------------EGLPFI 451
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 635 MGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGD-SIADAKtyldiQNTIKKAKQDVIE 713
Cdd:cd01609 452 NKTLKKKVL----KKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDiVVPPEK-----KEIIKEAEEKVKE 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 714 vIEKAHNNeleptpGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEY--NNFKSMVVAGSKGSKINISQVIAVVG-QQN 790
Cdd:cd01609 523 -IEKQYEK------GLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDpfNPIYMMADSGARGSKSQIRQLAGMRGlMAK 595
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 791 VEGKRIPfgfkhrtLPhfIKDdygpesrgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVM 870
Cdd:cd01609 596 PSGKIIE-------LP--IKS------------NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVI 654
|
..
gi 2064985138 871 VK 872
Cdd:cd01609 655 VT 656
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1098-1476 |
5.07e-56 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 211.68 E-value: 5.07e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1098 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydp 1177
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI---- 616
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1178 npqntvvaedqewvnvyyempdfDVTRISpwlLRIELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRI 1257
Cdd:PRK14898 617 -----------------------DLWTQS---IKVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYL 663
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1258 RImnsDENKFQEDEEVVDKmdddvflrciesnmLTDMTLQGIEQISKVYMHLPQTDNKkkiiitedgefkalQEWILETD 1337
Cdd:PRK14898 664 KP---KTPSYKALRKRIPK--------------IKNIVLKGIPGIERVLVKKEEHEND--------------EEYVLYTQ 712
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1338 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGI 1417
Cdd:PRK14898 713 GSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGV 792
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 2064985138 1418 NRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAE 1476
Cdd:PRK14898 793 AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDRE 851
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
18-1467 |
2.62e-54 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 211.02 E-value: 2.62e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 18 RVQFGVLSPDELKRMS------VTEGGIKYPETTEGGR--PKLGGLMDPRQGVIER------TGR-CQTCAGNMTECP-- 80
Cdd:PRK14844 1450 EVSISIASPESIKRMSygeiedVSTANYRTFKVEKGGLfcPKIFGPVNDDECLCGKykkrrhRGRiCEKCGVEVTSSKvr 1529
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 81 -GHFGHIELAKPVFHVCFITKIIKVLRCvcffcsklLVDSNNPKIKDILIKSKGQPRKRLTHVYElcKGKNICEGG-EEM 158
Cdd:PRK14844 1530 rERMGHIELASPVAHIWFLKSLPSRIGA--------LLDMSLRDIENILYSDNYIVIDPLVSPFE--KGEIISEKAyNEA 1599
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 159 DNKFGVEQ-------QENEEDLTKEKGHggcgryqpRIRRtglELYAEWKHVNEDSQEKKILlspervheifKRISDEED 231
Cdd:PRK14844 1600 KDSYGIDSfvamqgvEAIRELLTRLDLH--------EIRK---DLRLELESVASEIRRKKII----------KRLRIVEN 1658
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 232 VILGMDpkfaRPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFH 311
Cdd:PRK14844 1659 FIKSGN----RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEA 1734
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 312 VATMVDNELPGlpRAMQKSGRP--LKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfp 389
Cdd:PRK14844 1735 VDSLFDNSRRN--ALVNKAGAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMAL----- 1807
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 390 EIVTPFNIDRLQELVRRGNSQYpgAKYIIRDNgdridlrfHPKPSDLHLQIgykVERHMcdgdiVIFNRQPTLHKMSMMG 469
Cdd:PRK14844 1808 ELFKPFVYSKLKMYGMAPTIKF--ASKLIRAE--------KPEVWDMLEEV---IKEHP-----VLLNRAPTLHRLGIQA 1869
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 470 HRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT-- 547
Cdd:PRK14844 1870 FEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTlq 1949
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 548 --KRD---VFLERGEVMNLLMflstwDGKMpqpailkprplwtgkqifsliipgHINV-IRTHSTHPDDEDSGPYKHISP 621
Cdd:PRK14844 1950 epKEDdlpSFGAFCEVEHSLS-----DGTL------------------------HIHSsIKYRMEYINSSGETHYKTICT 2000
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 622 GDTKVIV-------EN--GELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGD-SI 691
Cdd:PRK14844 2001 TPGRLILwqifpkhENlgFDLINQVLTVKEI----TSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDmVI 2076
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 692 ADAK-TYLD-IQNTIKKAK---QDVIEVIEKAHNNELEptpgntlrqTFENQVNRILNDARDKTgsSAQKSLSEYNNFKS 766
Cdd:PRK14844 2077 PETKaTHVDhARGEIKKFSmqyQDGLITRSERYNKVID---------EWSKCTDMIANDMLKAI--SIYDGNSKYNSVYM 2145
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 767 MVVAGSKGSKiniSQVIAVVGQQNVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFFFHAMGGREGLI 846
Cdd:PRK14844 2146 MVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIISNFRE-----GLNVFEYFNSTHGARKGLA 2205
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 847 DTAVKTAETGYIQRRLIK-SMESVMVKYDGTVRNSInqVVQlrygedglagenvefqnlATVKPShkafekkfrfdcTNE 925
Cdd:PRK14844 2206 DTALKTANSGYLTRRLVDvSQNCIVTKHDCKTKNGL--VVR------------------ATVEGS------------TIV 2253
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 926 RALRRILQEDVVKDVQTNAHVQGVLEREFDRMKEDRdtlrtifptgdskvVLPCNLARMiwnaqKIFRINTRTPTDLNPl 1005
Cdd:PRK14844 2254 ASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDK--------------VKQINIAGL-----DVVKIRSPLTCEISP- 2313
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1006 rvveGVhelskklvivngddplskqaqqnatllfnihlrSTLCSKRmteefrlsteafDWLLGEIetkfnQSIahpGEMV 1085
Cdd:PRK14844 2314 ----GV---------------------------------CSLCYGR------------DLATGKI-----VSI---GEAV 2336
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1086 GALAAQSLGEPATQMTLNTFHYAGVsaknVTLGVPRLKELINISKRPKTPSLTVFLLGQAARDA-ERAKDILC------- 1157
Cdd:PRK14844 2337 GVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIViSRSCEVVLidslgse 2412
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1158 RLEHTtlrkVTANTAIYYDPNPQNTVVAEDQEW-------------VNVYYEMPD-FDVTR------------ISPWLL- 1210
Cdd:PRK14844 2413 KLKHS----VPYGAKLYVDEGGSVKIGDKVAEWdpytlpiitektgTVSYQDLKDgISITEvmdestgisskvVKDWKLy 2488
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1211 --------RIELdrkhMTDRKLTMeQIAEKINAGFGDDLNCIFNDDNAEK-----LVLRI---------------RIMNS 1262
Cdd:PRK14844 2489 sgganlrpRIVL----LDDNGKVM-TLASGVEACYFIPIGAVLNVQDGQKvhagdVITRTpresvktrditgglpRVIEL 2563
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1263 DENKFQEDEEVVDKMDDDVFLRCIESNMLTDMTLQGI-EQISKVYMHLpqtdNKKKIIITEDGEFkaLQEWILETDGvsl 1341
Cdd:PRK14844 2564 FEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVdEQISPVEYLV----SRSKHVIVNEGDF--VRKGDLLMDG--- 2634
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1342 mrvlsekdvDPvrttsnDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTM------TCRGHLMAITRH 1415
Cdd:PRK14844 2635 ---------DP------DLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMlqkveiTDPGDTMYLVGE 2699
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1416 GINR----------QDTG-------PLMK---------------CSFEETVDVLMEASSHGESDPMKGVSENIMLGQLAP 1463
Cdd:PRK14844 2700 SIDKlevdrendamSNSGkrpahylPILQgitrasletssfisaASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIP 2779
|
....
gi 2064985138 1464 AGTG 1467
Cdd:PRK14844 2780 AGTG 2783
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1073-1472 |
3.40e-54 |
|
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: 192.41 E-value: 3.40e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1073 KFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKE-LINISKRPKTPSLTV-FLLGQAARDAE 1150
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREiLMTASKNIKTPSMTLpLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1151 RAK---------DILCRLEHTTLRKVTANTAIyydpnPQNtvvaedQEWVNVYYEMPdfdvtrispwllrieLDRKhmtd 1221
Cdd:cd02735 81 TLKkrlsrvtlsDVVEKVEVTEILKTIERVFK-----KLL------GKWCEVTIKLP---------------LSSP---- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1222 rKLTMEQIAEKInagfgddlncifnddnAEKLVLRirimnsdenkfqedeEVvdkmdddvflrciesnmltdmtlQGIEQ 1301
Cdd:cd02735 131 -KLLLLSIVEKL----------------ARKAVIR---------------EI-----------------------PGITR 155
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1302 ISKVYmhlpqTDNKKKiiitedgefkalQEWILETDGVSL--MRVLSEKdVDPVRTTSNDIVEIFTVLGIEAVRKALERE 1379
Cdd:cd02735 156 CFVVE-----EDKGGK------------TKYLVITEGVNLaaLWKFSDI-LDVNRIYTNDIHAMLNTYGIEAARRAIVKE 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1380 LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGInRQDTGPLMKCSFEETVDVLMEASSHGESDPMKGVSENIMLG 1459
Cdd:cd02735 218 ISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVG 296
|
410
....*....|...
gi 2064985138 1460 QLAPAGTGCFDLL 1472
Cdd:cd02735 297 KPVNGGTGLFDLL 309
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
242-1130 |
4.25e-53 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 206.26 E-value: 4.25e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 242 RPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELP 321
Cdd:PRK14906 311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 322 GLPrAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVTPFNIDRLQ 401
Cdd:PRK14906 391 GRP-VTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMAL-----ELFKPFVMKRLV 464
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 402 ELVRRGNSQypGAKYIIrdngdridlrfhpkpsDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFR 481
Cdd:PRK14906 465 ELEYAANIK--AAKRAV----------------DRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIK 526
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 482 LNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT-KRDVFLERGEVmn 560
Cdd:PRK14906 527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDGFEGEGRT-- 604
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 561 llmFLSTWDGKMpqpAILKPRPLWTGKQIFsliipghINVIRTHSTHPDDEDSGPYKHISPGDTKVivenGELIMGILCK 640
Cdd:PRK14906 605 ---FADFDDALN---AYDARADLDLQAKIV-------VRLSRDMTVRGSYGDLEETKAGERIETTV----GRIIFNQVLP 667
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 641 KSLGtsagslvHISYLEMGHDITRLfysnIQTVVNNWLLIEGHSI---------------GIGDSIADAKTYLDIQNTIK 705
Cdd:PRK14906 668 EDYP-------YLNYKMVKKDIGRL----VNDCCNRYSTAEVEPIldgikktgfhyatraGLTVSVYDATIPDDKPEILA 736
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 706 KAKQDVIEVIEKAHNNELEPtpgntlrQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAV 785
Cdd:PRK14906 737 EADEKVAAIDEDYEDGFLSE-------RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGM 809
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 786 VG-QQNVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK 864
Cdd:PRK14906 810 RGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVD 868
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 865 SMESVMVKYdgtvrnsinqvvqlrygEDGLAGENVEFqnlATVKPSHKafekkfrfdcTNERALRRILQEDVVkDVQTNA 944
Cdd:PRK14906 869 VAQDVIVRE-----------------EDCGTDEGVTY---PLVKPKGD----------VDTNLIGRCLLEDVC-DPNGEV 917
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 945 HvqgvlerefdrmkedrdtlrtiFPTGDskvvlpcnlarmiwnaqkifrintrtptdlnplrvvegvhelskklvIVNGD 1024
Cdd:PRK14906 918 L----------------------LSAGD-----------------------------------------------YIESM 928
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1025 DPLSKQAQQNATllfNIHLRSTLCSKrmtEEFRLSTEAFDWLLgeietkfnqSIAHP---GEMVGALAAQSLGEPATQMT 1101
Cdd:PRK14906 929 DDLKRLVEAGVT---KVQIRTLMTCH---AEYGVCQKCYGWDL---------ATRRPvniGTAVGIIAAQSIGEPGTQLT 993
|
890 900
....*....|....*....|....*....
gi 2064985138 1102 LNTFHYAGVSAKNVTLGVPRLKELINISK 1130
Cdd:PRK14906 994 MRTFHSGGVAGDDITQGLPRVAELFEARK 1022
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
242-1135 |
1.10e-47 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 187.97 E-value: 1.10e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 242 RPEWMIVTVLPVPPLAVRPAVVMQG-----SARNqdDLTHKLadivkI--NNQLRRNEQSGAAAHVIAEDVKLLQFHVAT 314
Cdd:PRK00566 223 KPEWMILDVLPVIPPDLRPLVQLDGgrfatSDLN--DLYRRV-----InrNNRLKRLLELGAPEIIVRNEKRMLQEAVDA 295
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 315 MVDNELPGlpRAMQ-KSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVT 393
Cdd:PRK00566 296 LFDNGRRG--RPVTgPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL-----ELFK 368
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 394 PFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqigykverhmcdgdiVIFNRQP 460
Cdd:PRK00566 369 PFIMKKLVErglattiksakkMVEREDPEvWDVLEEVIKE---------HP----------------------VLLNRAP 417
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 461 TLHKMSMM--------GHRVRILPwstfrLnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPV 532
Cdd:PRK00566 418 TLHRLGIQafepvlieGKAIQLHP-----L---VCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPI 489
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 533 mgIV--QD------TLTAVRKFTKrdvflerGEVMnllMFLSTWD-----------------GKMPQPAILKPRPlwtGK 587
Cdd:PRK00566 490 --IVpsQDmvlglyYLTREREGAK-------GEGM---VFSSPEEalrayengevdlharikVRITSKKLVETTV---GR 554
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 588 QIFSLIIPGHInvirthsthpddedsgPYkhispgdtkvivENGELIMGilcKKSLgtsaGSLVHISYLEMGHDITRLFY 667
Cdd:PRK00566 555 VIFNEILPEGL----------------PF------------INVNKPLK---KKEI----SKIINEVYRRYGLKETVIFL 599
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 668 SNIQTVVNNWLLIEGHSIGIGD-SIADAKtyldiQNTIKKAKQDVIEvIEKAHNNELeptpgntlrQTFE---NQVNRIL 743
Cdd:PRK00566 600 DKIKDLGFKYATRSGISIGIDDiVIPPEK-----KEIIEEAEKEVAE-IEKQYRRGL---------ITDGeryNKVIDIW 664
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 744 NDARDKTGSSAQKSLSEYNN-FKS---MVVAGSKGSKINISQVIAVVG-QQNVEGKRIPfgfkhrtLPhfIKddygpesr 818
Cdd:PRK00566 665 SKATDEVAKAMMKNLSKDQEsFNPiymMADSGARGSASQIRQLAGMRGlMAKPSGEIIE-------TP--IK-------- 727
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 819 gfveNSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD--GTVRNsinqvVQLRYGEDGlaG 896
Cdd:PRK00566 728 ----SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDdcGTDRG-----IEVTAIIEG--G 796
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 897 ENVEfqNLAtvkpshkafekkfrfdctnERALRRILQEDVVkdvqtnahvqgvlerefdrmkeDRDTLRTIFPTGDskvv 976
Cdd:PRK00566 797 EVIE--PLE-------------------ERILGRVLAEDVV----------------------DPETGEVIVPAGT---- 829
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 977 lpcnlarMI--WNAQKIfrintrtptdlnplrVVEGVHElskklvivngddplskqaqqnatllfnIHLRSTL------- 1047
Cdd:PRK00566 830 -------LIdeEIADKI---------------EEAGIEE---------------------------VKIRSVLtcetrhg 860
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1048 -CSK---RMteefrLSTeafdwllgeietkfnQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVsakNVTLGVPRLK 1123
Cdd:PRK00566 861 vCAKcygRD-----LAT---------------GKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVA 917
|
970
....*....|..
gi 2064985138 1124 ELINiSKRPKTP 1135
Cdd:PRK00566 918 ELFE-ARKPKGP 928
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
715-821 |
3.64e-45 |
|
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: 158.68 E-value: 3.64e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 715 IEKA-HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEG 793
Cdd:pfam05000 1 ITDAeRYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 2064985138 794 KRIPFGFKHRTLPHFIKDDYGPESRGFV 821
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
84-512 |
1.85e-41 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 164.31 E-value: 1.85e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 84 GHIELAKPVFHV-------CFIT----KIIKVLRCVCFFCSKLLVDSNNpkiKDILIKSKGqprkrlTHVYELCKGKNIc 152
Cdd:CHL00018 105 GYIKLACPVTHVwylkrlpSYIAnlldKPLKELEGLVYCDFSFARPIAK---KPTFLRLRG------LFEYEIQSWKYS- 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 153 eggeemDNKFgVEQQENEEDLTKEKGHGGcgryqPRIRR--TGLEL-------YAEWKHVNEDSQ------EKKILLspe 217
Cdd:CHL00018 175 ------IPLF-FSTQGFDTFRNREISTGA-----GAIREqlADLDLriiidnsLVEWKELGEEGStgneweDRKIGR--- 239
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 218 RVHEIFKRISDEEDVILgmdpKFARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRR-NEQSGA 296
Cdd:CHL00018 240 RKDFLVRRIKLAKHFIR----TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDlLTTSRS 315
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 297 AAH-VIAEDVKLLQFHVATMVDNELPGLPraMQKS-GRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQID 374
Cdd:CHL00018 316 TPGeLVMCQKKLLQEAVDALLDNGIRGQP--MRDGhNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLH 393
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 375 QVGVPRSIAAnmtfpEIVTPFNIdrlQELVRRGNSQYPG-AKYIIRDNGdridlrfhpkpsdlhlQIGYKVERHMCDGDI 453
Cdd:CHL00018 394 QCGLPREIAI-----ELFQPFVI---RGLIRQHLASNIRaAKSKIREKE----------------PIVWEILQEVMQGHP 449
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2064985138 454 VIFNRQPTLHKMSMM--------GHRVRILPwstfrlnlSVTTPYNADFDGDEMNLHLPQSLETRAE 512
Cdd:CHL00018 450 VLLNRAPTLHRLGIQafqpilveGRAICLHP--------LVCKGFNADFDGDQMAVHVPLSLEAQAE 508
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
241-538 |
3.23e-41 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 163.00 E-value: 3.23e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 241 ARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNEL 320
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 321 PGlPRAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVTPFNIDRl 400
Cdd:PRK02625 320 RG-RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAI-----ELFQPFVIHR- 392
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 401 qeLVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqigYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST 479
Cdd:PRK02625 393 --LIRQGIvNNIKAAKKLIQRADPEV----------------WQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 2064985138 480 FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD 538
Cdd:PRK02625 455 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1359-1468 |
8.31e-37 |
|
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: 136.78 E-value: 8.31e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1359 DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLM 1438
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 2064985138 1439 EASSHGESDPMKGVSENIMLGQLAPAGTGC 1468
Cdd:cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1082-1129 |
5.75e-21 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 91.33 E-value: 5.75e-21
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 2064985138 1082 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1129
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1513-1612 |
3.18e-13 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 67.93 E-value: 3.18e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1513 PAMTP-WNTGA--TPAYGAWSPSVGSGMTPGAAGFSPSA------------ASDASGFSPGYSPAWSP--TPGSPGSPGP 1575
Cdd:smart01104 1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRtpawggagsrtpAWGGAGPTGSRTPAWGGasAWGNKSSEGS 80
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 2064985138 1576 ASPYIPSPG---GAMSPNYSPTSPAYEPRSPGGYTPQSPG 1612
Cdd:smart01104 81 ASSWAAGPGgayGAPTPGYGGTPSAYGPATPGGGAMAGSA 120
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
762-1115 |
3.12e-12 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 72.34 E-value: 3.12e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 762 NNFKS---------MVVAGSKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 828
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 829 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD--GTVRnSInqVVQlryGEDGLAGENVEFQNlat 906
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEdcGTTR-GI--VVE---AMDDGDRVLIPLGD--- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 907 vkpshkafekkfrfdctneRALRRILQEDVVkdvqtnaHVQGvlerefdrmkedrdtlrtifptgdsKVVLPCNlarmiw 986
Cdd:PRK02597 238 -------------------RLLGRVLAEDVV-------DPEG-------------------------EVIAERN------ 260
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 987 naqkifrintrTPTDlnplrvvegvHELSKKL-------VIVNgdDPLSKQAQqnatllfnihlRStLCSKrmteefrls 1059
Cdd:PRK02597 261 -----------TAID----------PDLAKKIekagveeVMVR--SPLTCEAA-----------RS-VCRK--------- 296
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2064985138 1060 teAFDWllgeietkfnqSIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1115
Cdd:PRK02597 297 --CYGW-----------SLAHNhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
762-1115 |
3.34e-12 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 72.19 E-value: 3.34e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 762 NNFKSMVVAGSKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFH 837
Cdd:TIGR02388 119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 838 AMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD--GTVRNsinqvVQLRYGEDGlaGENVEFQNlatvkpshkafe 915
Cdd:TIGR02388 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEdcGTERS-----IVVRAMTEG--DKKISLGD------------ 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 916 kkfrfdctneRALRRILQEDVVkdvqtnaHVQGVLerefdrmkedrdtlrtifptgdskvvlpcnlarmiwnaqkIFRIN 995
Cdd:TIGR02388 236 ----------RLLGRLVAEDVL-------HPEGEV----------------------------------------IVPKN 258
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 996 TRTPTDLNPLRVVEGVHElskklviVNGDDPLSKQAQQnatllfnihlrsTLCSKrmteefrlsteAFDWllgeietkfn 1075
Cdd:TIGR02388 259 TAIDPDLAKTIETAGISE-------VVVRSPLTCEAAR------------SVCRK-----------CYGW---------- 298
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 2064985138 1076 qSIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1115
Cdd:TIGR02388 299 -SLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1077-1125 |
7.01e-11 |
|
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: 63.70 E-value: 7.01e-11
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 2064985138 1077 SIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVsAKNVTLGVPRLKEL 1125
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEEL 48
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1495-1595 |
1.38e-10 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 60.61 E-value: 1.38e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1495 GPTGMFFGTVPSPmsGMSPAMTP-WN--TGATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSPAW-SPT 1566
Cdd:smart01104 21 TPGTAAGGAPTAR--GGSGSRTPaWGgaGSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGGAYgAPT 96
|
90 100
....*....|....*....|....*....
gi 2064985138 1567 PGSPGSPGPASPyiPSPGGAMspNYSPTS 1595
Cdd:smart01104 97 PGYGGTPSAYGP--ATPGGGA--MAGSAS 121
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1082-1473 |
2.30e-09 |
|
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain] Cd Length: 381 Bit Score: 61.67 E-value: 2.30e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1082 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAknvtlgVPRLKELI--NISKRPKTPSLTVFLLGQAARDA------ERAK 1153
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESSP------LELLKEVLecRSKSKSKENDRRVILSLHLCKCDhgfeyeRAAL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1154 DILCRLEHTTLRKVTANTAIYYDPNPQntvvaedqewvnvyyEMPDFDVTRISPWLLRIELDRKHMTDRKLTmeqiaeKI 1233
Cdd:cd02737 75 EVKNHLERVTLEDLATTSMIKYSPQAT---------------EAIVGEIGDQLNTKKKGKKKAIFSTSLKIT------KF 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1234 NAGfgddlNCIFNDDNAEKLVLR---IRIMNSDENKfQEDEEVVDKMDDDVFlrciesNMLTDMTLQGIEQISKVYMhLP 1310
Cdd:cd02737 134 SPW-----VCHFHLDKECQKLSDgpcLTFSVSKEVS-KSSEELLDVLRDRII------PFLLETVIKGDERIKSVNI-LW 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1311 QTDNKKKIIITEDGEFKAlqEWILETdGVSLMRVLSEKD---------------VDPVRTTSNDIVEIFTVLGIEAVRKA 1375
Cdd:cd02737 201 EDSPSTSWVKSVGKSSRG--ELVLEV-TVEESCKKTRGNawnvvmdacipvmdlIDWERSMPYSIQQIKSVLGIDAAFEQ 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1376 LERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDT-----GPLMKCSFEETVDVLMEASSHGESDPMK 1450
Cdd:cd02737 278 FVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRslkisAPFTEACFSSPIKCFLKAAKKGASDSLS 357
|
410 420
....*....|....*....|....
gi 2064985138 1451 GVSENIMLGQLAPAGTGC-FDLLL 1473
Cdd:cd02737 358 GVLDACAWGKEAPVGTGSkFEILW 381
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
828-1110 |
1.00e-07 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 57.64 E-value: 1.00e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 828 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMV-KYD-GTVRnSInqvvqlrygedglagenvefqnla 905
Cdd:CHL00117 172 GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVrETDcGTTR-GI------------------------ 226
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 906 TVKPSHKAFEKKFrfdcTNERALRRILQEDVVKDVQTNAHvqgvlerefdrmkedRDTLRTIfptgdskvvlpcNLARMI 985
Cdd:CHL00117 227 SVSPRNGMMIERI----LIQTLIGRVLADDIYIGSRCIAT---------------RNQDIGI------------GLANRF 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 986 --WNAQKIFrinTRTPtdlnplrvvegvhelskklvivngddplskqaqqnatllFNIHLRSTLCSKRmteefrlsteaf 1063
Cdd:CHL00117 276 itFRAQPIS---IRSP---------------------------------------LTCRSTSWICQLC------------ 301
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|..
gi 2064985138 1064 dwllgeietkFNQSIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGV 1110
Cdd:CHL00117 302 ----------YGWSLAHGdlvelGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| MISS |
pfam15822 |
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic ... |
1513-1611 |
1.02e-06 |
|
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic MAPK-interacting and spindle-stabilising protein-like proteins. MISS is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localization signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII spindle. MISS is the first example of a physiological MAPK-substrate that is stabilized in MII that specifically regulates MII spindle integrity during the CSF arrest.
Pssm-ID: 318115 [Multi-domain] Cd Length: 238 Bit Score: 51.91 E-value: 1.02e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1513 PAMTPWNTGATPaygawsPSVGSGMTPGAAGFSPSAASDASGFSPGYsPAWSPTPGSPGSPGPASPYIPSPGGamsPNYS 1592
Cdd:pfam15822 31 PGSNPWNNPSAP------PAVPSGLPPSTAPSTVPFGPAPTGMYPSI-PLTGPSPGPPAPFPPSGPSCPPPGG---PYPA 100
|
90 100
....*....|....*....|
gi 2064985138 1593 PTSPAyePRSPGGY-TPQSP 1611
Cdd:pfam15822 101 PTVPG--PGPIGPYpTPNMP 118
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1429-1467 |
3.28e-06 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 52.31 E-value: 3.28e-06
10 20 30
....*....|....*....|....*....|....*....
gi 2064985138 1429 SFEETVDVLMEASSHGESDPMKGVSENIMLGQLAPAGTG 1467
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
|
|
| PHA03307 |
PHA03307 |
transcriptional regulator ICP4; Provisional |
1505-1603 |
2.16e-05 |
|
transcriptional regulator ICP4; Provisional
Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 49.78 E-value: 2.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1505 PSPMSGMSPAMTPwntgATPAYGAWSPSVGSGMtpgAAGFSPSAASDASGFSPGYSPAWSPTPGSPgsPGPASPyiPSPG 1584
Cdd:PHA03307 298 PSPSSPGSGPAPS----SPRASSSSSSSRESSS---SSTSSSSESSRGAAVSPGPSPSRSPSPSRP--PPPADP--SSPR 366
|
90
....*....|....*....
gi 2064985138 1585 GAMSPNYSPTSPAYEPRSP 1603
Cdd:PHA03307 367 KRPRPSRAPSSPAASAGRP 385
|
|
| Aft1_HRA |
pfam11786 |
Aft1 HRA domain; This domain is found in the transcription factor Aft1 which is required for a ... |
1495-1572 |
5.47e-05 |
|
Aft1 HRA domain; This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The HRA domain is involved in meiotic recombination. It has been shown to be necessary and sufficient to activate recombination.
Pssm-ID: 371723 Cd Length: 76 Bit Score: 43.29 E-value: 5.47e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2064985138 1495 GPTGMFFGTVPSPMSG-MSPAMTPWNTGATPAYGAWSPSVGSGMTPGAAGFSpsaasdaSGFSPGYSPAWSPTPgSPGS 1572
Cdd:pfam11786 1 DPTGFPWGATNSLRSGpLSPAMLAGPQGASQSDYFDTTSIRTGFTPNESSLR-------TGLTPGGGGSMFPAP-SPNT 71
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1429-1468 |
2.88e-04 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 46.09 E-value: 2.88e-04
10 20 30 40
....*....|....*....|....*....|....*....|
gi 2064985138 1429 SFEETVDVLMEASSHGESDPMKGVSENIMLGQLAPAGTGC 1468
Cdd:CHL00117 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1050-1102 |
6.90e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 44.88 E-value: 6.90e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 2064985138 1050 KRMTEEFRLSTEAFDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTL 1102
Cdd:PRK14898 25 EKLSKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| Caudal_act |
pfam04731 |
Caudal like protein activation region; This family consists of the amino termini of proteins ... |
1488-1599 |
1.04e-03 |
|
Caudal like protein activation region; This family consists of the amino termini of proteins belonging to the caudal-related homeobox protein family. This region is thought to mediate transcription activation. The level of activation caused by mouse Cdx2 is affected by phosphorylation at serine 60 via the mitogen-activated protein kinase pathway. Caudal family proteins are involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium, and are important in differentiation and maintenance of the intestinal epithelial lining. Caudal proteins always have a homeobox DNA binding domain (pfam00046).
Pssm-ID: 461413 [Multi-domain] Cd Length: 136 Bit Score: 41.27 E-value: 1.04e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1488 IPGISVAGPTGmffGTVPSPMSgmsPAMTPWNTGATPAYGAWSPSVGSGMTPGAAGFSPsaasdasgfsPGYSpawSPTP 1567
Cdd:pfam04731 33 VPGMDPHGQSL---GAWGSPYG---PPREDWNAYGPGPSSTVGTAPMNDASPGQIAYSP----------PDYS---SLHP 93
|
90 100 110
....*....|....*....|....*....|..
gi 2064985138 1568 GSPGSPGPASPYIPSPGGAMSPNYSPTSPaYE 1599
Cdd:pfam04731 94 PGPSSGLSLPPPLNSSLEQLSPSRQRRSP-YE 124
|
|
| PHA03247 |
PHA03247 |
large tegument protein UL36; Provisional |
1506-1612 |
1.67e-03 |
|
large tegument protein UL36; Provisional
Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 43.77 E-value: 1.67e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1506 SPMSGMSPAMTPWNTGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPA--WSPTPGSPGSPGPASPYIPSP 1583
Cdd:PHA03247 2753 GPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAavLAPAAALPPAASPAGPLPPPT 2832
|
90 100
....*....|....*....|....*....
gi 2064985138 1584 GGAMSPNYSPTSPAYEPRSPGGYTpqSPG 1612
Cdd:PHA03247 2833 SAQPTAPPPPPGPPPPSLPLGGSV--APG 2859
|
|
| PHA03247 |
PHA03247 |
large tegument protein UL36; Provisional |
1488-1660 |
5.88e-03 |
|
large tegument protein UL36; Provisional
Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 41.85 E-value: 5.88e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1488 IPGISVAGPTGMFFGTVPSPMSGMSPAMTPWNTGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGF-------SPGYS 1560
Cdd:PHA03247 2750 TPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAAlppaaspAGPLP 2829
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064985138 1561 PAWSPTPGSPGSP-GPASPYIP-----SPGG-------AMSPNYSPTSPAYEP-RSPGGYTPQSPGYSPTSPSYSPTSPL 1626
Cdd:PHA03247 2830 PPTSAQPTAPPPPpGPPPPSLPlggsvAPGGdvrrrppSRSPAAKPAAPARPPvRRLARPAVSRSTESFALPPDQPERPP 2909
|
170 180 190
....*....|....*....|....*....|....
gi 2064985138 1627 PPPAPTTAQRLLPTLPPHQATPQLLRLTHPHLPL 1660
Cdd:PHA03247 2910 QPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943
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