|
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 ... |
15-868 |
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: 1612.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 15 KRVQFGILSPDEIRRMSVTEGGvqFAETME-GGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFHI 93
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIE--HPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 94 GFITKTIKILRCVCfycskmlvsphnpkikeivmksrgqprkrlayvydlckgkticeggedmdltkenqqpdpnkkpgh 173
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 174 ggcghyqpsirrtgldltaewkhqnedsqekKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLPVPPLAVR 253
Cdd:cd02733 93 -------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVR 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 254 PAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGKPLKAIKA 333
Cdd:cd02733 142 PSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQ 221
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 334 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIVR 413
Cdd:cd02733 222 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIR 301
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 414 DNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEM 493
Cdd:cd02733 302 DDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEM 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 494 NLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWDAKMPQPCILK 573
Cdd:cd02733 382 NLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQPAILK 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 574 PRPLWTGKQIFSLIIPGNVNMIRTHSTHPdeedeGPYKWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLHICFLELG 653
Cdd:cd02733 462 PKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYG 536
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 654 HDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLRQTFENKV 733
Cdd:cd02733 537 PEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKV 616
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 734 NRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDDYGPESRG 813
Cdd:cd02733 617 NRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRG 696
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*
gi 17530899 814 FVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYD 868
Cdd:cd02733 697 FVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
14-887 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 975.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 14 VKRVQFGILSPDEIRRMSVTEggVQFAETM-EGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFH 92
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTYdDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 93 IGFiTKTI-KILRCVCFYCSKMLVSPHnpKIKEIV-----MKSRGQPRKRLA-YVYDLCKGKTICeggedmdltkenqqp 165
Cdd:PRK08566 87 VGF-AKLIyKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------- 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 166 dpnkkPgHggCGHYQPSIRrtgLDLTAEWKHQNEDSQEKkivVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVL 245
Cdd:PRK08566 149 -----P-H--CGEKQYKIK---FEKPTTFYEERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVL 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 246 PVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSG 325
Cdd:PRK08566 215 PVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSG 294
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 326 KPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQY 405
Cdd:PRK08566 295 RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKH 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 406 PGAKYIVRDNGERIDLRFHPKSsDL--HLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSP 483
Cdd:PRK08566 375 PGANYVIRPDGRRIKLTDKNKE-ELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPP 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 484 YNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWD 563
Cdd:PRK08566 454 YNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDE 533
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 564 AKMPQPCILKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDEGPYKwiSPGDTKVMVEHGELIMGILCKKSLGTSAGS 643
Cdd:PRK08566 534 LPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGAEQGS 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 644 LLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGN 723
Cdd:PRK08566 612 ILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGR 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 724 TLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFI 803
Cdd:PRK08566 692 TLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFK 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 804 KDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRY 883
Cdd:PRK08566 772 PGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKY 851
|
....
gi 17530899 884 GEDG 887
Cdd:PRK08566 852 GEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
11-888 |
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: 927.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 11 LRQVKRVQFGILSPDEIRRMSVTEggVQFAETM-EGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKP 89
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVE--VVTADTYdDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 90 VFHIGFITKTIKILRCVCFYCSKMLVSP-----HNPKIKEIVMKSrGQPRKRLA-YVYDLCKGKTICeggedmdltkenq 163
Cdd:TIGR02390 79 VVHVGFAKEIYKILRATCRKCGRITLTEeeieqYLEKINKLKEEG-GDLASTLIeKIVKEAAKRMKC------------- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 164 qpdPNkkpghggCGHYQPSIRrtgLDLTAEWkHQNEDSQEKKIVVSAERvwEILKHITDEECFILGMDPKYARPDWMIVT 243
Cdd:TIGR02390 145 ---PH-------CGEEQKKIK---FEKPTYF-YEEGKEGDVKLTPSEIR--ERLEKIPDEDAELLGINPKVARPEWMVLT 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 244 VLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQK 323
Cdd:TIGR02390 209 VLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHR 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 324 SGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNS 403
Cdd:TIGR02390 289 SGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPD 368
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 404 QYPGAKYIVRDNGERIDLRFHPKSSDL-HLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTS 482
Cdd:TIGR02390 369 SWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCP 448
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 483 PYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLpTW 562
Cdd:TIGR02390 449 PYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVA-GY 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 563 DAKMPQPCILKPRPLWTGKQIFSLIIPGNVNMI------RTHSTHPDEEDegpykwisPGDTKVMVEHGELIMGILCKKS 636
Cdd:TIGR02390 528 FGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFEgrakicSGSDACKKEEC--------PHDAYVVIKNGKLLKGVIDKKA 599
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 637 LGTSAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNME 716
Cdd:TIGR02390 600 IGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGE 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 717 LEPTPGNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRK 796
Cdd:TIGR02390 680 LEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRN 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 797 RTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVG 876
Cdd:TIGR02390 760 RTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRG 839
|
890
....*....|..
gi 17530899 877 QLIQLRYGEDGL 888
Cdd:TIGR02390 840 NLIQFKYGEDGV 851
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1050-1468 |
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: 798.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1050 FRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 1129
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1130 SLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPT--RISPWLLRIE 1207
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1208 LDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDedeavdkMEDDMFLRCIEANMLSD 1287
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1288 MTLQGIEAIgkvYMHLPQTDSKKRiVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVR 1367
Cdd:cd02584 234 MTLKGIEGI---RKVFIREENKKK-VDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1368 KSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVS 1447
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 17530899 1448 ENIIMGQLPKMGTGCFDLLLD 1468
Cdd:cd02584 390 ENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
822-1419 |
1.18e-176 |
|
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: 545.03 E-value: 1.18e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 822 GLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRYGEDGLCGELVEFQNMPTV 901
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 902 KLSNKSFEKRFKFDWSNERLmkkvftddvikemtdsseaiqeLEAEWDRLVSDRDSLRQIFpngeskvvlpcnlqrmiwn 981
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLL----------------------LLSEFSLSYKKEILVRDSK------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 982 vqkifhinkrlptdlspirvikgvktllercvivTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLV 1061
Cdd:pfam04998 120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1062 GEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAAR 1141
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1142 DAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDF--------DPTRISPWLLRIELDRKRM 1213
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEvtneeeidPETGLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1214 TDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDEDEavdKMEDDMFLRCIEANMLSDMTLQGI 1293
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDEL---FMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1294 EAIgkvymhlpqtdskKRIVITETGEFKAIGEWLLETDGTSMMKVLSERD-VDPIRTSSNDICEIFQVLGIEAVRKSVEK 1372
Cdd:pfam04998 403 PGI-------------KRILVNEDDKGKVEPDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 17530899 1373 EMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGAL 1419
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
238-538 |
6.82e-167 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 509.75 E-value: 6.82e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 238 DWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDmpGM 317
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 318 PRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQEL 397
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 398 VRRGNsqyPGAKYIVRdnGERIDLRFHPKS-SDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRM 476
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17530899 477 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVR 538
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
11-346 |
5.42e-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: 440.19 E-value: 5.42e-141
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 11 LRQVKRVQFGILSPDEIRRMSVTEggVQFAETME--GGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAK 88
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 89 PVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIVMKSRGQ--PRKRLAYVYDLCKGKTICEGGEDMDltkenqqpd 166
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 167 pnkkpghGGCGHYQPSIRRTGLDLTAEWKHQNEDsqEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLP 246
Cdd:pfam04997 150 -------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLP 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 247 VPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGK 326
Cdd:pfam04997 221 VPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKR 300
|
330 340
....*....|....*....|
gi 17530899 327 PLKAIKARLKGKEGRIRGNL 346
Cdd:pfam04997 301 PLKSISQRLKGKEGRFRGNL 320
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1048-1471 |
8.56e-91 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 300.61 E-value: 8.56e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1048 EEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPK 1127
Cdd:PRK04309 31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1128 APSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANtaiyydpdpqrtvISEDqefvnvYYEMpdfdptrispwLLRIE 1207
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKD-------------ISVD------LANM-----------TIIIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1208 LDRKRMTDKKLTMEQIAEKINVGFGEDLncifnDDNADKLVLRIrimnnEENKFQDEDEAVDKmeddmflrcieanmLSD 1287
Cdd:PRK04309 161 LDEEMLEDRGLTVDDVKEAIEKKKGGEV-----EIEGNTLIISP-----KEPSYRELRKLAEK--------------IRN 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1288 MTLQGIEAIGKVymhlpqtdskkriVITETGEfkaigEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVR 1367
Cdd:PRK04309 217 IKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAAR 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1368 KSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVS 1447
Cdd:PRK04309 279 NAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVT 358
|
410 420
....*....|....*....|....
gi 17530899 1448 ENIIMGQLPKMGTGCFDLLLDAEK 1471
Cdd:PRK04309 359 ENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
890-1071 |
4.45e-90 |
|
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: 290.55 E-value: 4.45e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 890 GELVEFQNMPTVKLSNKSFEKRFKFDWSNER--LMKKVFTDDVIKEMTDSSEAIQELEAEWDRLVSDRDSLRQ-IFPNGE 966
Cdd:pfam04992 3 GAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKsgFLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREiIFPTGD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 967 SKVV-LPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTGNDRISKQANENATLLFQCLIRSTLCTKY 1045
Cdd:pfam04992 83 SKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLASKR 162
|
170 180
....*....|....*....|....*.
gi 17530899 1046 VSEEFRLSTEAFEWLVGEIETRFQQA 1071
Cdd:pfam04992 163 VLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1052-1468 |
1.40e-88 |
|
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: 293.88 E-value: 1.40e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1052 LSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSL 1131
Cdd:TIGR02389 20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1132 TVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYdpdPQRTVIsedqefvnvyyempdfdptrispwllrIELDRK 1211
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDL---ADMTVI---------------------------IELDEE 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1212 RMTDKKLTMEQIAEKInvgfgedlncifnddnadKLVLRIRIMNNEENKFQDEDEAVDKMEDDMFLRcieANMLSDMTLQ 1291
Cdd:TIGR02389 150 QLKERGITVDDVEKAI------------------KKAKLGKVIEIDMDNNTITIKPGNPSLKELRKL---KEKIKNLHIK 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1292 GIEAIgkvymhlpqtdskKRIVITETGEfkaigEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVE 1371
Cdd:TIGR02389 209 GIKGI-------------KRVVIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAII 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1372 KEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENII 1451
Cdd:TIGR02389 271 EEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENII 350
|
410
....*....|....*..
gi 17530899 1452 MGQLPKMGTGCFDLLLD 1468
Cdd:TIGR02389 351 VGQPIPLGTGDVDLVMD 367
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
16-1106 |
2.37e-59 |
|
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: 225.04 E-value: 2.37e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 16 RVQFGILSPDEIRRMSVTEggVQFAETM--EGGRPKLGGLMDPR--------------------QGVIdrtsrCQTCAGN 73
Cdd:COG0086 9 AIKIGLASPEKIRSWSYGE--VKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 74 MTECP---GHFGHIDLAKPVFHIGFiTKTIKilrcvcfycSKM-LVsphnpkikeIVMKSRGQPRKRL--AYV------Y 141
Cdd:COG0086 82 VTLSKvrrERMGHIELAMPVFHIWG-LKSLP---------SRIgLL---------LDMSLRDLERVLYfeSYVvidpgdT 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 142 DLCKGKTICEGgEDMDLTKENqqpdPNKKPGHGGCGHYQPSIRRTGLDLTAEwkhqnEDSQEKKIVVSAERVWEILKHIT 221
Cdd:COG0086 143 PLEKGQLLTED-EYREILEEY----GDEFVAKMGAEAIKDLLGRIDLEKESE-----ELREELKETTSEQKRKKLIKRLK 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 222 DEECFILgmdpKYARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKM 301
Cdd:COG0086 213 VVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRM 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 302 LQFHVATLVDNDMPGmpRAMQKSGK-PLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQnl 380
Cdd:COG0086 289 LQEAVDALFDNGRRG--RAVTGANKrPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL-- 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 381 tfpELVTPFnidRMQELVRRGNSQ-YPGAKYIV-RDNGERID-----LRFHPkssdlhlqcgykverhlrdddlVIFNRQ 453
Cdd:COG0086 365 ---ELFKPF---IYRKLEERGLATtIKSAKKMVeREEPEVWDileevIKEHP----------------------VLLNRA 416
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 454 PTLHKMSMM--------GHRVKVLPwstfrmnLSCTsPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKP 525
Cdd:COG0086 417 PTLHRLGIQafepvlieGKAIQLHP-------LVCT-AFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKP 488
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 526 VMGIVQDTLTAVRKMTKRD--------VFITREQVMNLLMF----LPTW-DAKMPQPCILKPRPLWT--GKQIFSLIIPG 590
Cdd:COG0086 489 IIVPSQDMVLGLYYLTRERegakgegmIFADPEEVLRAYENgavdLHARiKVRITEDGEQVGKIVETtvGRYLVNEILPQ 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 591 NVNMIRthsthpdeedegpykwispgdtKVMvehgelimgilCKKSLGTsagsLLHICFLELGHDIAGRFYGNIQTVINN 670
Cdd:COG0086 569 EVPFYN----------------------QVI-----------NKKHIEV----IIRQMYRRCGLKETVIFLDRLKKLGFK 611
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 671 WLLFEGHSIGIGDTIADPQTyneiQQAIKKAKDDVINvIQKAHNMELePTPGNTlrqtfENKVNRILNDARDKTGGSAKK 750
Cdd:COG0086 612 YATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTKASLETESFLMA 680
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 751 SLTEYNNLKAMVVSGSKGSNINISQVIACVG-QQNVEGKRI--PYG--FRkrtlphfikddygpesrgfvensylAGLTP 825
Cdd:COG0086 681 AFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIetPIGsnFR-------------------------EGLGV 735
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 826 SEFYFHAMGGREGLIDTAVKTAETGYIQRRLIK-AMESVMVNYDgtvrnsvgqliqlrygedglCGelvefqnmptvkls 904
Cdd:COG0086 736 LEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEED--------------------CG-------------- 781
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 905 nksfekrfkfdwsnerlmkkvfTDD--VIKEMTDSSEAIQELEaewDRLVSdRDSLRQIFPNGESKVVLPCNLQRMIWNV 982
Cdd:COG0086 782 ----------------------TDRgiTVTAIKEGGEVIEPLK---ERILG-RVAAEDVVDPGTGEVLVPAGTLIDEEVA 835
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 983 QKIfhinkrlptdlspirVIKGVKTLLERCVIVtgndriskqanenatllfqCLIRSTLCTKYVSEefRLSTEAFEwlvg 1062
Cdd:COG0086 836 EII---------------EEAGIDSVKVRSVLT-------------------CETRGGVCAKCYGR--DLARGHLV---- 875
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....
gi 17530899 1063 eietrfqqaqaNPGEMVGALAAQSLGEPATQMTLNTFHFAGVSS 1106
Cdd:COG0086 876 -----------NIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS 908
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
761-1109 |
1.03e-09 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 63.86 E-value: 1.03e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 761 MVVSGSKGsniNISQVIACVGQQ----NVEGKRIpygfrkrTLPhfIKDDygpesrgFVEnsylaGLTPSEFYFHAMGGR 836
Cdd:PRK02597 125 MAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----GLTVTEYVISSYGAR 180
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 837 EGLIDTAVKTAETGYIQRRLIKAMESVMVNYD--GTVRNsvgqlIQLRYgEDGLCGELVEFQNmptvklsnksfekrfkf 914
Cdd:PRK02597 181 KGLVDTALRTADSGYLTRRLVDVSQDVIVREEdcGTTRG-----IVVEA-MDDGDRVLIPLGD----------------- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 915 dwsneRLMKKVFTDDVIkemtdssEAIQELEAEWDRLVsDRDSLRQIFPNGESKVVLpcnlqrmiwnvqkifhinkRlpt 994
Cdd:PRK02597 238 -----RLLGRVLAEDVV-------DPEGEVIAERNTAI-DPDLAKKIEKAGVEEVMV-------------------R--- 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 995 dlSPIRvikgvktllerCvivtgndriskQANenatllfqcliRStLCTKyvseefrlsteAFEWLVgeietrfqqAQAN 1074
Cdd:PRK02597 283 --SPLT-----------C-----------EAA-----------RS-VCRK-----------CYGWSL---------AHNH 306
|
330 340 350
....*....|....*....|....*....|....*...
gi 17530899 1075 P---GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 1109
Cdd:PRK02597 307 LvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1707-1880 |
2.42e-08 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 59.32 E-value: 2.42e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1707 SPTSPSySPTSPNyTPVTPSY--SPTSPNYSASPQySPASP-----------AYSQTGVKYSPTSPTYSPPSPSYDGSPG 1773
Cdd:PTZ00449 629 SPKSPK-RPPPPQ-RPSSPERpeGPKIIKSPKPPK-SPKPPfdpkfkekfydDYLDAAAKSKETKTTVVLDESFESILKE 705
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1774 SPQYTPGSPQYSPAS-PKYSPTSPLYSpsspqhspsnqYSPTGStysATSPRYSPNMSIYSP--SSTKYSPTsPTYTP-- 1848
Cdd:PTZ00449 706 TLPETPGTPFTTPRPlPPKLPRDEEFP-----------FEPIGD---PDAEQPDDIEFFTPPeeERTFFHET-PADTPlp 770
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 17530899 1849 ------------TARNYSPTSPMYSPTAPSHYSPTSPAYSPSSP 1880
Cdd:PTZ00449 771 dilaeefkeediHAETGEPDEAMKRPDSPSEHEDKPPGDHPSLP 814
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1707-1881 |
1.40e-07 |
|
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.
Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 56.85 E-value: 1.40e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1707 SPTSPSYSPT-------SPNYTPVTPSYSPTSPNYSAspqysPAS--PAYSQTGVkysptsPTYSPPSPSYDGSPGSPQY 1777
Cdd:pfam05109 424 APESTTTSPTlnttgfaAPNTTTGLPSSTHVPTNLTA-----PAStgPTVSTADV------TSPTPAGTTSGASPVTPSP 492
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1778 TP------------GSPQYSPASPKYSPTSPlysPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPT 1845
Cdd:pfam05109 493 SPrdngteskapdmTSPTSAVTTPTPNATSP---TPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNA 569
|
170 180 190
....*....|....*....|....*....|....*.
gi 17530899 1846 YTPTARNYSPTSPMYSPTaPSHYSPTSPAYSPSSPT 1881
Cdd:pfam05109 570 TIPTLGKTSPTSAVTTPT-PNATSPTVGETSPQANT 604
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1498-1862 |
7.64e-07 |
|
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.
Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 54.54 E-value: 7.64e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1498 STPSMTPPMTPWANCNTPryfSPPGHVSAMTPGGPSFSP---SAASDASGM-SPSwspahpgsspsspgpsmspyfpasp 1573
Cdd:pfam05109 459 TAPASTGPTVSTADVTSP---TPAGTTSGASPVTPSPSPrdnGTESKAPDMtSPT------------------------- 510
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1574 svsPSYSPTSPNYTASSPGGASPNYSPSSPNYSPTSPLYA---------SPRYASTTPNFN---PQSTGYSPSSSGYSPT 1641
Cdd:pfam05109 511 ---SAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAvttptpnatSPTPAVTTPTPNatiPTLGKTSPTSAVTTPT 587
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1642 SPVYSPTVQfQSSPSFAGSGSNIYSPGNAYSPSSSNYSPNSPSYSPTSPSYSPSSPSYSPTSPCYSPT-SPSYSPTSPNY 1720
Cdd:pfam05109 588 PNATSPTVG-ETSPQANTTNHTLGGTSSTPVVTSPPKNATSAVTTGQHNITSSSTSSMSLRPSSISETlSPSTSDNSTSH 666
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1721 TPVTPSYSPT--------SPNYSASPQYSPASPAysqtgVKYSPTSPTYSPPSPSYDGSPGSPQYTPGSPQYSPASPKyS 1792
Cdd:pfam05109 667 MPLLTSAHPTggenitqvTPASTSTHHVSTSSPA-----PRPGTTSQASGPGNSSTSTKPGEVNVTKGTPPKNATSPQ-A 740
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1793 PTSPLYSPSSPQHSPSNQYSPTGSTYS------------------ATSPRYSPNMSIYSPSST------KYSPTSPTYTp 1848
Cdd:pfam05109 741 PSGQKTAVPTVTSTGGKANSTTGGKHTtghgartstepttdyggdSTTPRTRYNATTYLPPSTssklrpRWTFTSPPVT- 819
|
410
....*....|....
gi 17530899 1849 TARNYSPTSPMYSP 1862
Cdd:pfam05109 820 TAQATVPVPPTSQP 833
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1706-1880 |
5.21e-06 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 51.29 E-value: 5.21e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1706 YSPTSPSYSPTSPNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVkysptsptysppSPSYDGSPGSPQYTPGSPQYS 1785
Cdd:COG3469 48 SVVVAASGSAGSGTGTTAASSTAATSSTTSTTATATAAAAAATSTSA------------TLVATSTASGANTGTSTVTTT 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1786 PASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMS-IYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTA 1864
Cdd:COG3469 116 STGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETATgGTTTTSTTTTTTSASTTPSATTTATATTASGATT 195
|
170
....*....|....*.
gi 17530899 1865 PSHYSPTSPAYSPSSP 1880
Cdd:COG3469 196 PSATTTATTTGPPTPG 211
|
|
| |
|
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 ... |
15-868 |
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: 1612.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 15 KRVQFGILSPDEIRRMSVTEGGvqFAETME-GGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFHI 93
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIE--HPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 94 GFITKTIKILRCVCfycskmlvsphnpkikeivmksrgqprkrlayvydlckgkticeggedmdltkenqqpdpnkkpgh 173
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 174 ggcghyqpsirrtgldltaewkhqnedsqekKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLPVPPLAVR 253
Cdd:cd02733 93 -------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVR 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 254 PAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGKPLKAIKA 333
Cdd:cd02733 142 PSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQ 221
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 334 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIVR 413
Cdd:cd02733 222 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIR 301
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 414 DNGERIDLRFHPKSSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEM 493
Cdd:cd02733 302 DDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEM 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 494 NLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWDAKMPQPCILK 573
Cdd:cd02733 382 NLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQPAILK 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 574 PRPLWTGKQIFSLIIPGNVNMIRTHSTHPdeedeGPYKWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLHICFLELG 653
Cdd:cd02733 462 PKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYG 536
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 654 HDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLRQTFENKV 733
Cdd:cd02733 537 PEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKV 616
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 734 NRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDDYGPESRG 813
Cdd:cd02733 617 NRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRG 696
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*
gi 17530899 814 FVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYD 868
Cdd:cd02733 697 FVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
14-887 |
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: 983.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 14 VKRVQFGILSPDEIRRMSVTEggVQFAETM-EGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFH 92
Cdd:cd02582 4 IKGIKFGLLSPEEIRKMSVVE--IITPDTYdEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 93 IGFItKTI-KILRCVCFYCSKMLVSPHnpKIKEI------VMKSRGQPRKRLA-YVYDLCKGKTICeggedmdltkenqq 164
Cdd:cd02582 82 VGFA-KHIyDLLRATCRSCGRILLPEE--EIEKYlerirrLKEKWPELVKRVIeKVKKKAKKRKVC-------------- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 165 pdpnkkPgHggCGHYQPSIRrtgldLTAEWKHQNEDSQEKKIVVSAErVWEILKHITDEECFILGMDPKYARPDWMIVTV 244
Cdd:cd02582 145 ------P-H--CGAPQYKIK-----LEKPTTFYEEKEEGEVKLTPSE-IRERLEKIPDEDLELLGIDPKTARPEWMVLTV 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 245 LPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKS 324
Cdd:cd02582 210 LPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRS 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQ 404
Cdd:cd02582 290 GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDK 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 405 YPGAKYIVRDNGERIDLRFHPKSSDLH-LQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSP 483
Cdd:cd02582 370 WPGANYVIRPDGRRIRLRYVNREELAErLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPP 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 484 YNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLpTWD 563
Cdd:cd02582 450 YNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAA-GYD 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 564 AKMPQPCILKPRPLWTGKQIFSLIIPGNVNMI-RTHSTHPDEEDEGPYKwisPGDTKVMVEHGELIMGILCKKSLGT-SA 641
Cdd:cd02582 529 GLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEgKAKVCSGCSECKDEDC---PNDGYVVIKNGKLLEGVIDKKAIGAeQP 605
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 642 GSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTP 721
Cdd:cd02582 606 GSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLP 685
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 722 GNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPH 801
Cdd:cd02582 686 GRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPH 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 802 FIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQL 881
Cdd:cd02582 766 FKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQF 845
|
....*.
gi 17530899 882 RYGEDG 887
Cdd:cd02582 846 KYGEDG 851
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
14-887 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 975.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 14 VKRVQFGILSPDEIRRMSVTEggVQFAETM-EGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFH 92
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTYdDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 93 IGFiTKTI-KILRCVCFYCSKMLVSPHnpKIKEIV-----MKSRGQPRKRLA-YVYDLCKGKTICeggedmdltkenqqp 165
Cdd:PRK08566 87 VGF-AKLIyKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------- 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 166 dpnkkPgHggCGHYQPSIRrtgLDLTAEWKHQNEDSQEKkivVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVL 245
Cdd:PRK08566 149 -----P-H--CGEKQYKIK---FEKPTTFYEERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVL 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 246 PVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSG 325
Cdd:PRK08566 215 PVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSG 294
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 326 KPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQY 405
Cdd:PRK08566 295 RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKH 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 406 PGAKYIVRDNGERIDLRFHPKSsDL--HLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSP 483
Cdd:PRK08566 375 PGANYVIRPDGRRIKLTDKNKE-ELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPP 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 484 YNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTWD 563
Cdd:PRK08566 454 YNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDE 533
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 564 AKMPQPCILKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDEGPYKwiSPGDTKVMVEHGELIMGILCKKSLGTSAGS 643
Cdd:PRK08566 534 LPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGAEQGS 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 644 LLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGN 723
Cdd:PRK08566 612 ILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGR 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 724 TLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFI 803
Cdd:PRK08566 692 TLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFK 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 804 KDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRY 883
Cdd:PRK08566 772 PGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKY 851
|
....
gi 17530899 884 GEDG 887
Cdd:PRK08566 852 GEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
11-888 |
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: 927.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 11 LRQVKRVQFGILSPDEIRRMSVTEggVQFAETM-EGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKP 89
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVE--VVTADTYdDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 90 VFHIGFITKTIKILRCVCFYCSKMLVSP-----HNPKIKEIVMKSrGQPRKRLA-YVYDLCKGKTICeggedmdltkenq 163
Cdd:TIGR02390 79 VVHVGFAKEIYKILRATCRKCGRITLTEeeieqYLEKINKLKEEG-GDLASTLIeKIVKEAAKRMKC------------- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 164 qpdPNkkpghggCGHYQPSIRrtgLDLTAEWkHQNEDSQEKKIVVSAERvwEILKHITDEECFILGMDPKYARPDWMIVT 243
Cdd:TIGR02390 145 ---PH-------CGEEQKKIK---FEKPTYF-YEEGKEGDVKLTPSEIR--ERLEKIPDEDAELLGINPKVARPEWMVLT 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 244 VLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQK 323
Cdd:TIGR02390 209 VLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHR 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 324 SGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNS 403
Cdd:TIGR02390 289 SGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPD 368
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 404 QYPGAKYIVRDNGERIDLRFHPKSSDL-HLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTS 482
Cdd:TIGR02390 369 SWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCP 448
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 483 PYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLpTW 562
Cdd:TIGR02390 449 PYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVA-GY 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 563 DAKMPQPCILKPRPLWTGKQIFSLIIPGNVNMI------RTHSTHPDEEDegpykwisPGDTKVMVEHGELIMGILCKKS 636
Cdd:TIGR02390 528 FGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFEgrakicSGSDACKKEEC--------PHDAYVVIKNGKLLKGVIDKKA 599
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 637 LGTSAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNME 716
Cdd:TIGR02390 600 IGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGE 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 717 LEPTPGNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRK 796
Cdd:TIGR02390 680 LEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRN 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 797 RTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVG 876
Cdd:TIGR02390 760 RTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRG 839
|
890
....*....|..
gi 17530899 877 QLIQLRYGEDGL 888
Cdd:TIGR02390 840 NLIQFKYGEDGV 851
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
10-1471 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 905.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 10 PLRQVKRVQFGILSPDEIRRMSVTEggVQFAETM-EGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAK 88
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAE--ITAPEAYdEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 89 PVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIVmksrgqPRKRLAYvydlckgKTICEGGEDMDLTKENQQPDPN 168
Cdd:PRK14977 83 PVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLI------EEAHAAA-------RDIPEKRIDDEIIEEVRDQVKV 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 169 KKPGHGGCGHYQPSIRRtgLDLTAEWKHQNEDSQEKKIVVSAErVWEILKHITDEECFILGMDPKYARPDWMIVTVLPVP 248
Cdd:PRK14977 150 YAKKAKECPHCGAPQHE--LEFEEPTIFIEKTEIEEHRLLPIE-IRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVP 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 249 PLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQK-SGKP 327
Cdd:PRK14977 227 PLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKgSGRP 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 328 LKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPG 407
Cdd:PRK14977 307 LKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPG 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 408 AKYIVRDNGERIDLRF-HPKSSDL------HLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSC 480
Cdd:PRK14977 387 ANAIRKGDGTKIRLDFlEDKGKDAlreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAV 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 481 TSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMfLP 560
Cdd:PRK14977 467 CPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAM-LA 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 561 TWDAKMPQPCI-LKPRPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDEGPyKWISPGDTKVMVEHGELIMGILCKKSLGT 639
Cdd:PRK14977 546 GITDPLPEPAIkTKDGPAWTGKQLFSLFLPKDFNFEGIAKWSAGKAGEAK-DPSCLGDGYVLIKEGELISGVIDDNIIGA 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 640 SAG---SLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQK----- 711
Cdd:PRK14977 625 LVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQrkitr 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 712 ---AHNMELEPTPGNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVE-- 786
Cdd:PRK14977 705 kitIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKtr 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 787 ------GKRIPYGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAM 860
Cdd:PRK14977 785 igfvltGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANAL 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 861 ESVMVNYDGTVRNSVGQLIQLRYGEDGLcgelvefqnmptvklsnksfekrfkfdwsnerlmkkvftdDVIKemtdssea 940
Cdd:PRK14977 865 EDIRLEYDETVRDPHGHIIQFKFGEDGI----------------------------------------DPQK-------- 896
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 941 iqeleaewdrlvSDRDSlrqifpngeskvvlPCNLQRMIwNVQKIFHINKRLPTDlspirvikGVKTLLErcvivtgndR 1020
Cdd:PRK14977 897 ------------LDHGE--------------AFNLERII-EKQKIEDRGKGASKD--------EIEELAK---------E 932
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1021 ISKQANENATLLFQCLIRSTlctkyvseefRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFH 1100
Cdd:PRK14977 933 YTKTFNANLPKLLADAIHGA----------ELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFH 1002
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1101 FAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYdPDPQRTVISE 1180
Cdd:PRK14977 1003 AAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN-ANEIKLIKPD 1081
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1181 DQEFVNVYYEMPDFdptrispwllrIELDRKRMTDKKLTMEQIAEKINVgfgedlncifnddnadKLVlririmnneenk 1260
Cdd:PRK14977 1082 KRALENGCIPMERF-----------AEIEAALAKGKKFEMELEDDLIIL----------------DLV------------ 1122
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1261 fqdedEAVDKMEDDMFLRCIEANMLsDMTLQGIEAIGKVYMHLPQTDSKKrivitetgefkaigEWLLETDGTSMMKVLS 1340
Cdd:PRK14977 1123 -----EAADRDKPLATLIAIRNKIL-DKPVKGVPDIERAWVELVEKDGRD--------------EWIIQTSGSNLAAVLE 1182
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1341 ERDVDPIRTSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAI------TRHGINRQ 1414
Cdd:PRK14977 1183 MKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglqaagVRHGFAGE 1262
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....*..
gi 17530899 1415 DTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGCFDLLLDAEK 1471
Cdd:PRK14977 1263 KDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSG 1319
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
22-872 |
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: 892.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 22 LSPDEIRRMSVTEGGVQFAETMEGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFHIGFITKTIK 101
Cdd:cd02583 1 LSPEDIIRLSEVEVTNRNLYDIETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIIN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 102 ILRCVCFYCSKMLVSPhnpKIKEIVMKSRGQP------RKRLAY-VYDLCKGKTICeggedmdltkenqqpdPNkkpghg 174
Cdd:cd02583 81 ILQCICKTCSRVLLPE---EEKRKFLKRLRRPnldnlqKKALKKkILEKCKKVRKC----------------PH------ 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 175 gCGHyqpsIRRTGLDLTAEwkhqnedsqekkivvsaeRVWEILKHITDEECFILGMDPKYARPDWMIVTVLPVPPLAVRP 254
Cdd:cd02583 136 -CGL----LKKAQEDLNPL------------------KVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRP 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 255 AVVM-FGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSgKPLKAIKA 333
Cdd:cd02583 193 SVVMdEKSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPK-KPIRGFCQ 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 334 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIV- 412
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFVIk 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 413 RDNGERIDLRF-HPKSSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGD 491
Cdd:cd02583 352 RDGGKKKFLKYgNRRKIARELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGD 431
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 492 EMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLL--MFLPTWDAKMPQP 569
Cdd:cd02583 432 EMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCsyMLDGEIKIDLPPP 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 570 CILKPRPLWTGKQIFSLII------PGNVNMirthsthpdEEDEGPY----KWISPGDTKVMVEHGELIMGILCKKSLGT 639
Cdd:cd02583 512 AILKPVELWTGKQIFSLLLrpnkksPVLVNL---------EAKEKSYtkksPDMCPNDGYVVIRNSELLCGRLDKSTLGS 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 640 -SAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELE 718
Cdd:cd02583 583 gSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLE 662
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 719 PTPGNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRT 798
Cdd:cd02583 663 LQPGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRT 742
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17530899 799 LPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVR 872
Cdd:cd02583 743 LPHFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1050-1468 |
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: 798.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1050 FRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 1129
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1130 SLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPT--RISPWLLRIE 1207
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1208 LDRKRMTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDedeavdkMEDDMFLRCIEANMLSD 1287
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1288 MTLQGIEAIgkvYMHLPQTDSKKRiVITETGEFKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVR 1367
Cdd:cd02584 234 MTLKGIEGI---RKVFIREENKKK-VDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1368 KSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVS 1447
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 17530899 1448 ENIIMGQLPKMGTGCFDLLLD 1468
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 ... |
18-868 |
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: 657.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 18 QFGILSPDEIRRMSVTEggVQFAETM-EGGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFHIGFI 96
Cdd:cd01435 1 SFSFYSAEEIRKLSVKE--ITNPVTFdSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFF 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 97 TKTIKILRCVCFYCskmlvspHNPKIKeivmksrgqPRKRLAYVydlCKGKTICEG--GEDMDLtkenqqpdpnkkpghg 174
Cdd:cd01435 79 DLLYKLLRGSCFYC-------HRFRIS---------KWEVKLFV---AKLKLLDKGllVEAAEL---------------- 123
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 175 gcghyqpsirrtgldltaewkhqnedsqekkivvsaervweilkhitdeecfilgmdpkYARPDWMIVTVLPVPPLAVRP 254
Cdd:cd01435 124 -----------------------------------------------------------DFGYDMFFLDVLLVPPNRFRP 144
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 255 aVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKM---------------LQFHVATLVDNDMPGMPR 319
Cdd:cd01435 145 -PSFLGDKVFENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDSTKAPKSG 223
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 320 AMQKSGkplkaIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVR 399
Cdd:cd01435 224 KKSPPG-----IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVI 298
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 400 RGNSQYPGAKYIVRDNGERIDLRFHPK-------------SSDLHLQCG-YKVERHLRDDDLVIFNRQPTLHKMSMMGHR 465
Cdd:cd01435 299 NGPDVYPGANAIEDEDGRLILLSALSEerrkalaklllllSSAKLLLNGpKKVYRHLLDGDVVLLNRQPTLHKPSIMAHK 378
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 466 VKVLPWS-TFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKRD 544
Cdd:cd01435 379 VRVLPGEkTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRD 458
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 545 VFITREQVMNLLM--FLPTWDA------KMPQPCILKPRPLWTGKQIFSLI----IPGNVNMIRTHSTHPDEED-EGPYK 611
Cdd:cd01435 459 TFFTREEYQQLVYaaLRPLFTSdkdgriKLLPPAILKPKPLWTGKQVISTIlknlIPGNAPLLNLSGKKKTKKKvGGGKW 538
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 612 WISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLHiCFLEL-GHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQT 690
Cdd:cd01435 539 GGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVH-AVYELyGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKA 617
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 691 YNEIQQAIKKAKDDVINVIQKAhnmeleptpgntlrqtFENKVNRILNDARDKT--GGSAKKSLteYNNLKAMVVSGSKG 768
Cdd:cd01435 618 DEKRRKILRKAKKLGLEAAAEF----------------LGLKLNKVTSSIIKAClpKGLLKPFP--ENNLQLMVQSGAKG 679
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 769 SNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAE 848
Cdd:cd01435 680 SMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSR 759
|
890 900
....*....|....*....|
gi 17530899 849 TGYIQRRLIKAMESVMVNYD 868
Cdd:cd01435 760 SGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
22-868 |
0e+00 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 557.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 22 LSPDEIRRMSVTEggVQFAETME--GGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAKPVFHIGFITKT 99
Cdd:cd00399 1 MSPEEIRKWSVAK--VIKPETIDnrTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKV 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 100 IKILRcvcfycskmlvsphnpkikeivmksrgqprkrlayvydlckgkticeggedmdltkenqqpdpnkkpghggcghy 179
Cdd:cd00399 79 PSFLG--------------------------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 180 qpsirrtgldltaewkhqnedsqekkivvsaervweilkhitdeecfilgmdpkyarPDWMIVTVLPVPPLAVRPAVVmf 259
Cdd:cd00399 84 ---------------------------------------------------------PEWMILTCLPVPPPCLRPSVI-- 104
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 260 gaaknqddlthklsdiikannelrkneasgaaahvIQENIKMLQFHVATLVDNDMPGMPRAMqKSGKPLKAIKARLKGKE 339
Cdd:cd00399 105 -----------------------------------IEERWRLLQEHVDTYLDNGIAGQPQTQ-KSGRPLRSLAQRLKGKE 148
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 340 GRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLtfpelvtpfnidrmqelvrrgnsqypgakyivrdngeri 419
Cdd:cd00399 149 GRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL--------------------------------------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 420 dlrfhpkssdlhlqcgykverhlrDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQ 499
Cdd:cd00399 190 ------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQ 245
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 500 SMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMTKrdvfitreqvmnllmflptwdakmpqpcilkprplwt 579
Cdd:cd00399 246 SEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL------------------------------------- 288
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 580 GKQIFSLIIPGnvnmirthsthpdeedegpykwispgdtkvmvehgelimgilckkslgtsagSLLHICFLELGHDIAGR 659
Cdd:cd00399 289 GKQIVSAALPG----------------------------------------------------GLLHTVTRELGPEKAAK 316
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 660 FYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKAKDDVINVIQKAHNMELEPTPGNTLRQTFENKVNRILND 739
Cdd:cd00399 317 LLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDFLNE 396
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 740 ARDKTGGSAKKSLTE---YNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFRKRTLPHFIKDDYGPESRGFVE 816
Cdd:cd00399 397 ARDKAGSAASVNLDLvskFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAKGFIR 476
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|..
gi 17530899 817 NSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYD 868
Cdd:cd00399 477 NSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
822-1419 |
1.18e-176 |
|
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: 545.03 E-value: 1.18e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 822 GLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYDGTVRNSVGQLIQLRYGEDGLCGELVEFQNMPTV 901
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 902 KLSNKSFEKRFKFDWSNERLmkkvftddvikemtdsseaiqeLEAEWDRLVSDRDSLRQIFpngeskvvlpcnlqrmiwn 981
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLL----------------------LLSEFSLSYKKEILVRDSK------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 982 vqkifhinkrlptdlspirvikgvktllercvivTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLV 1061
Cdd:pfam04998 120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1062 GEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAAR 1141
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1142 DAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDF--------DPTRISPWLLRIELDRKRM 1213
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEvtneeeidPETGLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1214 TDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNNEENKFQDEDEavdKMEDDMFLRCIEANMLSDMTLQGI 1293
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDEL---FMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1294 EAIgkvymhlpqtdskKRIVITETGEFKAIGEWLLETDGTSMMKVLSERD-VDPIRTSSNDICEIFQVLGIEAVRKSVEK 1372
Cdd:pfam04998 403 PGI-------------KRILVNEDDKGKVEPDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 17530899 1373 EMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGAL 1419
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
238-538 |
6.82e-167 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 509.75 E-value: 6.82e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 238 DWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDmpGM 317
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 318 PRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQEL 397
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 398 VRRGNsqyPGAKYIVRdnGERIDLRFHPKS-SDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRM 476
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17530899 477 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVR 538
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
11-346 |
5.42e-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: 440.19 E-value: 5.42e-141
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 11 LRQVKRVQFGILSPDEIRRMSVTEggVQFAETME--GGRPKLGGLMDPRQGVIDRTSRCQTCAGNMTECPGHFGHIDLAK 88
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 89 PVFHIGFITKTIKILRCVCFYCSKMLVSPHNPKIKEIVMKSRGQ--PRKRLAYVYDLCKGKTICEGGEDMDltkenqqpd 166
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 167 pnkkpghGGCGHYQPSIRRTGLDLTAEWKHQNEDsqEKKIVVSAERVWEILKHITDEECFILGMDPKYARPDWMIVTVLP 246
Cdd:pfam04997 150 -------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLP 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 247 VPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMPRAMQKSGK 326
Cdd:pfam04997 221 VPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKR 300
|
330 340
....*....|....*....|
gi 17530899 327 PLKAIKARLKGKEGRIRGNL 346
Cdd:pfam04997 301 PLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
348-510 |
2.89e-96 |
|
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: 307.31 E-value: 2.89e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 348 GKRVDFSARTVITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIVRDNGERIDLRFHPKS 427
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 428 SDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEV 507
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
...
gi 17530899 508 ENI 510
Cdd:pfam00623 161 EEL 163
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
53-872 |
1.93e-92 |
|
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: 318.19 E-value: 1.93e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 53 LMDPRQGVIDRTSRCQTC-AGNMTECPGHFGHIDLAKPVFHIGFITKTIKILRCVCfycskmlvsphnPKIKEIVMKSRG 131
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKIC------------PGCKSIKQKKKK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 132 QPRKRLAYVY-DLckgkticeggedmdLTKENQQPDpnkkpghggcGHYQPSIRRTGLdltaewkhqnedsqekkivvsa 210
Cdd:cd10506 88 PPRETLPPDYwDF--------------IPKDGQQEE----------SCVTKNLPILSL---------------------- 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 211 ervwEILKHITDEecfilgMDPK-----YARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKN 285
Cdd:cd10506 122 ----AQVKKILKE------IDPKliakgLPRQEGLFLKCLPVPPNCHRVTEFTHGFSTGSRLIFDERTRAYKKLVDFIGT 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 286 EASGAAAHviqenikmlqfhvatlvdndmpgmpramqKSGKPlkaikarlkgkegRIRGNLMGKRVDFSARTVITPDPNL 365
Cdd:cd10506 192 ANESAASK-----------------------------KSGLK-------------WMKDLLLGKRSGHSFRSVVVGDPYL 229
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 366 RIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGnsqyPGAKYI--VRDNGERIDLRFHPKssdlhLQCGYKVERHLR 443
Cdd:cd10506 230 ELNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLT----LLLKGVigVRRNGRLVGVRSHNT-----LQIGDVIHRPLV 300
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 444 DDDLVIFNRQPTLHKMSMMGHRVKVLPW-STFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQA 522
Cdd:cd10506 301 DGDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQS 380
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 523 NKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPTwdaKMPQPCILK--PR--PLWTGKQIFSLIIPgnvnmirth 598
Cdd:cd10506 381 GQNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKspPSngPLWTGKQLFQMLLP--------- 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 599 sthPDEEDEGPykwispgDTKVMVEHGELIMGiLCKKSLGTSAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHS 678
Cdd:cd10506 449 ---TDLDYSFP-------SNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFS 517
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 679 IGIGDTIADPQTYN------EIQQAIKKAKD----DVINV----IQKAHNMELEPTPGNTLRQTFENKVN-RILN---DA 740
Cdd:cd10506 518 VSLSDLYLSSDSYSrqkmieEISLGLREAEIacniKQLLVdsrkDFLSGSGEENDVSSDVERVIYERQKSaALSQasvSA 597
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 741 RDKTGGSAKKSLTEY----NNLKAMVVSGSKGSNINISQVIACVGQQNVEGK---RIP-----YGFRKRTLPHFIKDDY- 807
Cdd:cd10506 598 FKQVFRDIQNLVYKYaskdNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVKlsyRIPrqlscAAWNSQKSPRVIEKDGs 677
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 808 ----GPESRGFVENSYLAGLTPSEFYFHAMGGREGLIDtavKTAET-GYIQRRLIKAMESVMVNYDGTVR 872
Cdd:cd10506 678 ecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1046-1469 |
2.33e-91 |
|
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: 301.48 E-value: 2.33e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1046 VSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKK 1125
Cdd:cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1126 PKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIyyDPDPQRtvisedqefvnvyyempdfdptrispwlLR 1205
Cdd:cd06528 90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--DLFNMR----------------------------IT 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1206 IELDRKRMTDKKLTMEQIAEKINVGFGEDlncIFNDDNADKLVLRIRIMNNEEnkfqdedeavdkmeddmfLRCIeANML 1285
Cdd:cd06528 140 IELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKAEEPSIKE------------------LRKL-AEKI 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1286 SDMTLQGIEAIGKVymhlpqtdskkrIVITETGEfkaigeWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEA 1365
Cdd:cd06528 198 LNTKIKGIKGIKRV------------IVRKEEDE------YVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEA 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1366 VRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRG 1445
Cdd:cd06528 260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRG 339
|
410 420
....*....|....*....|....
gi 17530899 1446 VSENIIMGQLPKMGTGCFDLLLDA 1469
Cdd:cd06528 340 VIENIIVGQPIPLGTGDVELTMDP 363
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1048-1471 |
8.56e-91 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 300.61 E-value: 8.56e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1048 EEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPK 1127
Cdd:PRK04309 31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1128 APSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANtaiyydpdpqrtvISEDqefvnvYYEMpdfdptrispwLLRIE 1207
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKD-------------ISVD------LANM-----------TIIIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1208 LDRKRMTDKKLTMEQIAEKINVGFGEDLncifnDDNADKLVLRIrimnnEENKFQDEDEAVDKmeddmflrcieanmLSD 1287
Cdd:PRK04309 161 LDEEMLEDRGLTVDDVKEAIEKKKGGEV-----EIEGNTLIISP-----KEPSYRELRKLAEK--------------IRN 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1288 MTLQGIEAIGKVymhlpqtdskkriVITETGEfkaigEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVR 1367
Cdd:PRK04309 217 IKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAAR 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1368 KSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVS 1447
Cdd:PRK04309 279 NAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVT 358
|
410 420
....*....|....*....|....
gi 17530899 1448 ENIIMGQLPKMGTGCFDLLLDAEK 1471
Cdd:PRK04309 359 ENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
890-1071 |
4.45e-90 |
|
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: 290.55 E-value: 4.45e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 890 GELVEFQNMPTVKLSNKSFEKRFKFDWSNER--LMKKVFTDDVIKEMTDSSEAIQELEAEWDRLVSDRDSLRQ-IFPNGE 966
Cdd:pfam04992 3 GAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKsgFLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREiIFPTGD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 967 SKVV-LPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTGNDRISKQANENATLLFQCLIRSTLCTKY 1045
Cdd:pfam04992 83 SKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLASKR 162
|
170 180
....*....|....*....|....*.
gi 17530899 1046 VSEEFRLSTEAFEWLVGEIETRFQQA 1071
Cdd:pfam04992 163 VLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1052-1468 |
1.40e-88 |
|
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: 293.88 E-value: 1.40e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1052 LSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSL 1131
Cdd:TIGR02389 20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1132 TVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYdpdPQRTVIsedqefvnvyyempdfdptrispwllrIELDRK 1211
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDL---ADMTVI---------------------------IELDEE 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1212 RMTDKKLTMEQIAEKInvgfgedlncifnddnadKLVLRIRIMNNEENKFQDEDEAVDKMEDDMFLRcieANMLSDMTLQ 1291
Cdd:TIGR02389 150 QLKERGITVDDVEKAI------------------KKAKLGKVIEIDMDNNTITIKPGNPSLKELRKL---KEKIKNLHIK 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1292 GIEAIgkvymhlpqtdskKRIVITETGEfkaigEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVE 1371
Cdd:TIGR02389 209 GIKGI-------------KRVVIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAII 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1372 KEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENII 1451
Cdd:TIGR02389 271 EEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENII 350
|
410
....*....|....*..
gi 17530899 1452 MGQLPKMGTGCFDLLLD 1468
Cdd:TIGR02389 351 VGQPIPLGTGDVDLVMD 367
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1067-1463 |
5.08e-80 |
|
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: 266.39 E-value: 5.08e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1067 RFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGaaRDAEKA 1146
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLEND--RDEKSA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1147 KNVLCRLEHTTLRKVTANTAIYYDPDpqrtvisedqefvNVYyempdfdptrispwlLRIELDRKRMTDKKLTmeqiaeK 1226
Cdd:cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPD-------------DCY---------------ILIKLDKKIIEKLQLS------K 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1227 INVGFgedlncifnddnadklvlrirIMNneenkfqdedeavdkmeddmFLRcieaNMLSDMTLQGIEAIgkvymhlpqt 1306
Cdd:cd02736 125 SNLYF---------------------LLQ--------------------SLK----RKLPDVVVSGIPEV---------- 149
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1307 dskKRIVITETgefKAIGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVN 1386
Cdd:cd02736 150 ---KRAVINKD---KKKGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSID 223
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17530899 1387 YRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGCF 1463
Cdd:cd02736 224 PRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| RNA_pol_Rpb1_7 |
pfam04990 |
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1156-1291 |
1.17e-77 |
|
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: 252.84 E-value: 1.17e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1156 TTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFD---PTRISPWLLRIELDRKRMTDKKLTMEQIAEKINVGFG 1232
Cdd:pfam04990 1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDvedLDRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 17530899 1233 EDLNCIFNDDNADKLVLRIRIMNNEENKfqdEDEAVDKMEDDMFLRCIEANMLSDMTLQ 1291
Cdd:pfam04990 81 NDLFVIFSDDNAEKLVIRIRIINDEKEK---DEEQEDKAEDDVFLKRLEANMLDSLTLR 136
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
16-1128 |
1.14e-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: 276.16 E-value: 1.14e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 16 RVQFGILSPDEIRRMSvtEGGVQFAETM--EGGRPKLGGLMDPR--------------------QGVIdrtsrCQTCAGN 73
Cdd:TIGR02386 1 AIKISIASPDTIRNWS--YGEVKKPETInyRTLKPEKDGLFCEKifgptkdwecycgkykkiryKGVV-----CERCGVE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 74 MTECP---GHFGHIDLAKPVFHIGF-----------ITKTIKILRCVCFYCSKMLVSPHNPKIKE---IVMKSRGQPRKR 136
Cdd:TIGR02386 74 VTESKvrrERMGHIELAAPVAHIWYfkglpsrigllLDITAKELESVLYFENYVVLDPGDTKLDKkevLDETEYREVLKR 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 137 LAYVYDLCKG-KTICEGGEDMDLTKENQQpdpnkkpghggcghyqpsirrtgldLTAEWKHQNEDSQEKKIVvsaeRVWE 215
Cdd:TIGR02386 154 YGDGFRAGMGaEAIKELLEKIDLDKEIEE-------------------------LKIQLRESKSDQKRKKLL----KRLE 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 216 ILKHITDEEcfilgmdpkyARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVI 295
Cdd:TIGR02386 205 IVEAFKDSG----------NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIV 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 296 QENIKMLQFHVATLVDNDMPGMPrAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRS 375
Cdd:TIGR02386 275 RNEKRMLQEAVDALFDNGRRGKP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKK 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 376 IAQnltfpELVTPFnidRMQELVRRgnsqypGAKYIVRdNGERIDLRFHPKSSDLhlqcgykVERHLRDDDlVIFNRQPT 455
Cdd:TIGR02386 354 MAL-----ELFKPF---IIKRLIDR------ELAANIK-SAKKMIEQEDPEVWDV-------LEDVIKEHP-VLLNRAPT 410
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 456 LHKMSMMGHRVKVLPWSTFRMN-LSCTSpYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDT- 533
Cdd:TIGR02386 411 LHRLGIQAFEPVLVEGKAIRLHpLVCTA-FNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMv 489
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 534 -----LTAVRKMTKRD--VFITREQVmnlLMFLPTWDAKMPQPC-------ILKPRPlwtGKQIFSLIIPGNVNMIrtHS 599
Cdd:TIGR02386 490 lglyyLTTEKPGAKGEgkIFSNVDEA---IRAYDNGKVHLHALIgvrtsgeILETTV---GRVIFNEILPEGFPYI--ND 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 600 THPdeedegpykwispgdtkvmvehgelimgiLCKKSLgtsaGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSI 679
Cdd:TIGR02386 562 NEP-----------------------------LSKKEI----SSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTI 608
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 680 GIGDTIADPQTYNEIQQAikkakDDVINVIQKAHNMeleptpGNTLRQTFENKVNRILNDARDKTGGSAKKSL----TEY 755
Cdd:TIGR02386 609 SASDIVVPDEKYEILKEA-----DKEVAKIQKFYNK------GLITDEERYRKVVSIWSETKDKVTDAMMKLLkkdtYKF 677
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 756 NNLKAMVVSGSKGsniNISQVIACVGQQNVEGKriPYGfrkRTLPHFIKddygpesrgfveNSYLAGLTPSEFYFHAMGG 835
Cdd:TIGR02386 678 NPIFMMADSGARG---NISQFRQLAGMRGLMAK--PSG---DIIELPIK------------SSFREGLTVLEYFISTHGA 737
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 836 REGLIDTAVKTAETGYIQRRLIKAMESVMVNYD--GTVRN-SVGQLIQlryGEDglcgELVEfqnmptvKLsnksfekrf 912
Cdd:TIGR02386 738 RKGLADTALKTADSGYLTRRLVDVAQDVVVREEdcGTEEGiEVEAIVE---GKD----EIIE-------SL--------- 794
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 913 kfdwsNERLMKKVFTDDVIKEMTdsseaiqeleaewDRLVSDRDSLrqifpngeskvvlpcnlqrmiwnvqkifhINKRL 992
Cdd:TIGR02386 795 -----KDRIVGRYSAEDVYDPDT-------------GKLIAEANTL-----------------------------ITEEI 827
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 993 PTDLSPIrvikGVKTLLERCVIVtgndriskqanenatllfqCLIRSTLCTKYVSEEfrLSTeafewlvgeietrfqQAQ 1072
Cdd:TIGR02386 828 AEKIENS----GIEKVKVRSVLT-------------------CESEHGVCQKCYGRD--LAT---------------GKL 867
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 17530899 1073 ANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSS--KNVTLGVPRLKEIINiSKKPKA 1128
Cdd:TIGR02386 868 VEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPKD 924
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1046-1466 |
1.17e-72 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 252.81 E-value: 1.17e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1046 VSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKK 1125
Cdd:PRK14897 152 AMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKK 231
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1126 PKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVtantaiyydpdpqrtvisedQEFVNVYYEMPdfdptrispwlLR 1205
Cdd:PRK14897 232 PSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDV--------------------ADIITDIAEMS-----------VV 280
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1206 IELDRKRMTDKKLTMEQIAEKInvgfgedlncifnddnaDKLVLRIRIMNNEENKFQDEDEAVDKMeddmFLRcieANML 1285
Cdd:PRK14897 281 VELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDDGIIRLKPQQPSFKKL----YLL---AEKV 336
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1286 SDMTLQGIEAIGKVymhlpqtdskkrIVITETGEfkaiGEWLLETDGTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEA 1365
Cdd:PRK14897 337 KSLTIKGIKGIKRA------------IARKENDE----RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEA 400
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1366 VRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAETDPMRG 1445
Cdd:PRK14897 401 ARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAG 480
|
410 420
....*....|....*....|.
gi 17530899 1446 VSENIIMGQLPKMGTGCFDLL 1466
Cdd:PRK14897 481 VAENIIVGQPITLGTGAVSLV 501
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
516-684 |
1.77e-61 |
|
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: 207.48 E-value: 1.77e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 516 QIITPQANKPVMGIVQDTLTAVRKMTKRDVFITREQVMNLLMFLPtwdaKMPQPCILKP-RPLWTGKQIFSLIIPGNVNM 594
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 595 IRTHSTHPDeedegpykWISPGDTKVMVEHGELIMGILCKKSLGTSAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLF 674
Cdd:pfam04983 77 KGKPKTNEE--------DLCENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTK 148
|
170
....*....|
gi 17530899 675 EGHSIGIGDT 684
Cdd:pfam04983 149 SGFSIGIDDI 158
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
236-866 |
1.01e-59 |
|
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: 218.93 E-value: 1.01e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 236 RPDWMIVTVLPVPPLAVRPAVVMFG---AAKNQDDLTHKlsdIIKANNELRKNEASGAAaHVIQENIK-MLQFHVATLVD 311
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGgrfATSDLNDLYRR---VINRNNRLKKLLELGAP-EIIVRNEKrMLQEAVDALID 213
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 312 NDMPGMPrAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQnltfpELVTPFNI 391
Cdd:cd01609 214 NGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMAL-----ELFKPFVI 287
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 392 drmQELVRRGNSQYP-GAKYIVRDNGERIdlrfhpkssdlhlqcgYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLP 470
Cdd:cd01609 288 ---RELIERGLAPNIkSAKKMIERKDPEV----------------WDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIE 348
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 471 WSTFRMN-LSCTsPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDT------LTAVRKMTKR 543
Cdd:cd01609 349 GKAIQLHpLVCT-AFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMvlglyyLTKERKGDKG 427
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 544 DVFITreqvmnllmflptwdakmpqpcilkprplwT--GKQIFSLIIPGNVNMIRThsthpdeedegpykwispgdtkvm 621
Cdd:cd01609 428 EGIIE------------------------------TtvGRVIFNEILPEGLPFINK------------------------ 453
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 622 vehgelimgILCKKSLgtsaGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQTYNEIQQAIKKA 701
Cdd:cd01609 454 ---------TLKKKVL----KKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKV 520
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 702 KDdvinvIQKAHNMeleptpGNTLRQTFENKVNRILNDARDKTGGSAKKSL--TEYNNLKAMVVSGSKGSNINISQVIAC 779
Cdd:cd01609 521 KE-----IEKQYEK------GLLTEEERYNKVIEIWTEVTEKVADAMMKNLdkDPFNPIYMMADSGARGSKSQIRQLAGM 589
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 780 VG-QQNVEGKRIPygfrkrtLPhfIKDdygpesrgfvenSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIK 858
Cdd:cd01609 590 RGlMAKPSGKIIE-------LP--IKS------------NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVD 648
|
....*...
gi 17530899 859 AMESVMVN 866
Cdd:cd01609 649 VAQDVIVT 656
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1092-1470 |
2.30e-59 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 222.08 E-value: 2.30e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1092 TQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIyydp 1171
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI---- 616
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1172 dpqrtvisedqefvnvyyempDFDPTRIspwllRIELDRKRMTDKKLTMEQIAEKINVGFGEDLNcifnddnADKLVLRI 1251
Cdd:PRK14898 617 ---------------------DLWTQSI-----KVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYL 663
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1252 RImnnEENKFQDEDEAVDKmeddmflrcieanmLSDMTLQGIEAIGKVYMHLPQTDSKkrivitetgefkaiGEWLLETD 1331
Cdd:PRK14898 664 KP---KTPSYKALRKRIPK--------------IKNIVLKGIPGIERVLVKKEEHEND--------------EEYVLYTQ 712
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1332 GTSMMKVLSERDVDPIRTSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGI 1411
Cdd:PRK14898 713 GSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGV 792
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 17530899 1412 NRQDTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGCFDLLLDAE 1470
Cdd:PRK14898 793 AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDRE 851
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
16-1106 |
2.37e-59 |
|
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: 225.04 E-value: 2.37e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 16 RVQFGILSPDEIRRMSVTEggVQFAETM--EGGRPKLGGLMDPR--------------------QGVIdrtsrCQTCAGN 73
Cdd:COG0086 9 AIKIGLASPEKIRSWSYGE--VKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 74 MTECP---GHFGHIDLAKPVFHIGFiTKTIKilrcvcfycSKM-LVsphnpkikeIVMKSRGQPRKRL--AYV------Y 141
Cdd:COG0086 82 VTLSKvrrERMGHIELAMPVFHIWG-LKSLP---------SRIgLL---------LDMSLRDLERVLYfeSYVvidpgdT 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 142 DLCKGKTICEGgEDMDLTKENqqpdPNKKPGHGGCGHYQPSIRRTGLDLTAEwkhqnEDSQEKKIVVSAERVWEILKHIT 221
Cdd:COG0086 143 PLEKGQLLTED-EYREILEEY----GDEFVAKMGAEAIKDLLGRIDLEKESE-----ELREELKETTSEQKRKKLIKRLK 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 222 DEECFILgmdpKYARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKM 301
Cdd:COG0086 213 VVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRM 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 302 LQFHVATLVDNDMPGmpRAMQKSGK-PLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQnl 380
Cdd:COG0086 289 LQEAVDALFDNGRRG--RAVTGANKrPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL-- 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 381 tfpELVTPFnidRMQELVRRGNSQ-YPGAKYIV-RDNGERID-----LRFHPkssdlhlqcgykverhlrdddlVIFNRQ 453
Cdd:COG0086 365 ---ELFKPF---IYRKLEERGLATtIKSAKKMVeREEPEVWDileevIKEHP----------------------VLLNRA 416
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 454 PTLHKMSMM--------GHRVKVLPwstfrmnLSCTsPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKP 525
Cdd:COG0086 417 PTLHRLGIQafepvlieGKAIQLHP-------LVCT-AFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKP 488
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 526 VMGIVQDTLTAVRKMTKRD--------VFITREQVMNLLMF----LPTW-DAKMPQPCILKPRPLWT--GKQIFSLIIPG 590
Cdd:COG0086 489 IIVPSQDMVLGLYYLTRERegakgegmIFADPEEVLRAYENgavdLHARiKVRITEDGEQVGKIVETtvGRYLVNEILPQ 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 591 NVNMIRthsthpdeedegpykwispgdtKVMvehgelimgilCKKSLGTsagsLLHICFLELGHDIAGRFYGNIQTVINN 670
Cdd:COG0086 569 EVPFYN----------------------QVI-----------NKKHIEV----IIRQMYRRCGLKETVIFLDRLKKLGFK 611
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 671 WLLFEGHSIGIGDTIADPQTyneiQQAIKKAKDDVINvIQKAHNMELePTPGNTlrqtfENKVNRILNDARDKTGGSAKK 750
Cdd:COG0086 612 YATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTKASLETESFLMA 680
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 751 SLTEYNNLKAMVVSGSKGSNINISQVIACVG-QQNVEGKRI--PYG--FRkrtlphfikddygpesrgfvensylAGLTP 825
Cdd:COG0086 681 AFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIetPIGsnFR-------------------------EGLGV 735
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 826 SEFYFHAMGGREGLIDTAVKTAETGYIQRRLIK-AMESVMVNYDgtvrnsvgqliqlrygedglCGelvefqnmptvkls 904
Cdd:COG0086 736 LEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEED--------------------CG-------------- 781
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 905 nksfekrfkfdwsnerlmkkvfTDD--VIKEMTDSSEAIQELEaewDRLVSdRDSLRQIFPNGESKVVLPCNLQRMIWNV 982
Cdd:COG0086 782 ----------------------TDRgiTVTAIKEGGEVIEPLK---ERILG-RVAAEDVVDPGTGEVLVPAGTLIDEEVA 835
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 983 QKIfhinkrlptdlspirVIKGVKTLLERCVIVtgndriskqanenatllfqCLIRSTLCTKYVSEefRLSTEAFEwlvg 1062
Cdd:COG0086 836 EII---------------EEAGIDSVKVRSVLT-------------------CETRGGVCAKCYGR--DLARGHLV---- 875
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....
gi 17530899 1063 eietrfqqaqaNPGEMVGALAAQSLGEPATQMTLNTFHFAGVSS 1106
Cdd:COG0086 876 -----------NIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS 908
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1067-1466 |
3.23e-57 |
|
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: 201.27 E-value: 3.23e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1067 RFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEII-NISKKPKAPSLTVFLtggaaRDAEK 1145
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILmTASKNIKTPSMTLPL-----KNGKS 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1146 AKnvlcrlehttlrkvtantaiyydpdpqrtvisedqefvnvyyempdfdptrispwllRIELDRKRMTdkKLTMEQIAE 1225
Cdd:cd02735 76 AE---------------------------------------------------------RAETLKKRLS--RVTLSDVVE 96
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1226 KINVgfGEDLNCIFNddnadklvlriRIMNNEENKFQDEDEaVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQ 1305
Cdd:cd02735 97 KVEV--TEILKTIER-----------VFKKLLGKWCEVTIK-LPLSSPKLLLLSIVEKLARKAVIREIPGITRCFVVEED 162
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1306 TDSK-KRIVITETGEFKAigewlletdgtsMMKVLSERDVDPIrtSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLY 1384
Cdd:cd02735 163 KGGKtKYLVITEGVNLAA------------LWKFSDILDVNRI--YTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIA 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1385 VNYRHLALLCDVMTAKGHLMAITRHGINRQDTGaLMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGCFD 1464
Cdd:cd02735 229 VDPRHLSLIADYMTFEGGYRPFNRIGMESSTSP-LQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFD 307
|
..
gi 17530899 1465 LL 1466
Cdd:cd02735 308 LL 309
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
67-1108 |
5.22e-55 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 213.25 E-value: 5.22e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 67 CQTCAGNMTECP---GHFGHIDLAKPVFHIGFITK-----------TIKILRCVCFYcskmlvsphnpkiKEIVMKSRGQ 132
Cdd:PRK09603 1465 CEKCGVAITHSKvrrFRMGHIELATPVAHIWYVNSlpsrigtllgvKMKDLERVLYY-------------EAYIVKEPGE 1531
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 133 PrkrlayVYDLCKGKTICEggedMDLTKENQQPDPNKKPGHGG-CGHYQPSIRRTGLD----------LTAEWKHQNEDS 201
Cdd:PRK09603 1532 A------AYDNEGTKLVMK----YDILNEEQYQNISRRYEDRGfVAQMGGEAIKDLLEeidlitllqsLKEEVKDTNSDA 1601
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 202 QEKKIVvsaervweilKHITDEECFILGMDpkyaRPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNE 281
Cdd:PRK09603 1602 KKKKLI----------KRLKVVESFLNSGN----RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQR 1667
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 282 LRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGmpRAMQKSGK-PLKAIKARLKGKEGRIRGNLMGKRVDFSARTVIT 360
Cdd:PRK09603 1668 LKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRST--NAVKGANKrPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIV 1745
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 361 PDPNLRIDQVGVPRSIAQNLTFPELvtpfnidrMQELVRRGN-SQYPGAKYIVRDngeridlrfhpKSSDLhlqcgYKVE 439
Cdd:PRK09603 1746 VGPNLKMDECGLPKNMALELFKPHL--------LSKLEERGYaTTLKQAKRMIEQ-----------KSNEV-----WECL 1801
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 440 RHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIIT 519
Cdd:PRK09603 1802 QEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILL 1881
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 520 PQANKPVMGIVQDTLTAVRKMT--------KRDVFITREQVMnLLMFLPTWDAKMPQPCILKPRPLWT--GKQIFSLIIP 589
Cdd:PRK09603 1882 PASGKAVAIPSQDMVLGLYYLSleksgvkgEHKLFSSVNEII-TAIDTKELDIHAKIRVLDQGNIIATsaGRMIIKSILP 1960
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 590 GNVNMirthsthpdeedegpykwispgdtkvmvehgELIMGILCKKSLGTsagsLLHICFLELGHDIAGRFYGNIQTVIN 669
Cdd:PRK09603 1961 DFIPT-------------------------------DLWNRPMKKKDIGV----LVDYVHKVGGIGITATFLDNLKTLGF 2005
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 670 NWLLFEGHSIGIGDTIadpqTYNEIQQAIKKAKDDVinviqkaHNMELEPTPGNTLRQTFENKVNRILNDARDKTGGSAK 749
Cdd:PRK09603 2006 RYATKAGISISMEDII----TPKDKQKMVEKAKVEV-------KKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMM 2074
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 750 KSLTE----YNNLKAMVVSGSKGSNINISQVIACVGqqnVEGKriPYGFRKRTlphfikddygPESRGFVEnsylaGLTP 825
Cdd:PRK09603 2075 TAIAKdkegFNSIYMMADSGARGSAAQIRQLSAMRG---LMTK--PDGSIIET----------PIISNFKE-----GLNV 2134
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 826 SEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVnydgtVRNSVGQLIQLRYGEDGLCGELVEfqnmptvklsn 905
Cdd:PRK09603 2135 LEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKV-----VSDDCGTHEGIEITDIAVGSELIE----------- 2198
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 906 kSFEkrfkfdwsnERLMKKVFTDDVIKEMTDsseaiqELEAEWDRLVsDRDSLRQIfpngeskvvlpcnlqrmiwnvqki 985
Cdd:PRK09603 2199 -PLE---------ERIFGRVLLEDVIDPITN------EILLYADTLI-DEEGAKKV------------------------ 2237
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 986 fhinkrlptdlspirVIKGVKTLLERCVIVtgndriskqanenatllfqCLIRSTLCTKyvseefrlsteAFEWLVGEie 1065
Cdd:PRK09603 2238 ---------------VEAGIKSITIRTPVT-------------------CKAPKGVCAK-----------CYGLNLGE-- 2270
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|...
gi 17530899 1066 trfqQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKN 1108
Cdd:PRK09603 2271 ----GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
202-1461 |
2.13e-50 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 197.92 E-value: 2.13e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 202 QEKKIVVSAERVWEILKHITDEECFILGMDpkyaRPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNE 281
Cdd:PRK14844 1635 LELESVASEIRRKKIIKRLRIVENFIKSGN----RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNR 1710
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 282 LRKNEASGAAAHVIQENIKMLQFHVATLVDNDMPGMprAMQKSGKP--LKAIKARLKGKEGRIRGNLMGKRVDFSARTVI 359
Cdd:PRK14844 1711 LRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNA--LVNKAGAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVI 1788
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 360 TPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIVRDNGERIdLRFHPkssdlhlqcgykve 439
Cdd:PRK14844 1789 VVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEEV-IKEHP-------------- 1853
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 440 rhlrdddlVIFNRQPTLHKMSMMGHRVKVLPWSTFRMN-LSCTSpYNADFDGDEMNLHVPQSMETRAEVENIHITPRQII 518
Cdd:PRK14844 1854 --------VLLNRAPTLHRLGIQAFEPILIEGKAIQLHpLVCTA-FNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVL 1924
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 519 TPQANKPVMGIVQDTLTAVRKMTkrdvfiTREQVMNLLMFLPTWdakmpqpcilkprplwtGKQIFSLiipgNVNMIRTH 598
Cdd:PRK14844 1925 SPSNGRPIIVPSKDIVLGIYYLT------LQEPKEDDLPSFGAF-----------------CEVEHSL----SDGTLHIH 1977
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 599 ST------HPDEEDEGPYKWI--SPGDT---KVMVEHGELIMGILCKKSLGTSAGSLLHICFLELGHDIAGRFYGNIQTV 667
Cdd:PRK14844 1978 SSikyrmeYINSSGETHYKTIctTPGRLilwQIFPKHENLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVL 2057
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 668 INNWLLFEGHSIGIGDTIAdPQTYNEiqqAIKKAKDDVinviqKAHNMELEptPGNTLRQTFENKVNRILNDARDKTGGS 747
Cdd:PRK14844 2058 GFEYATFSGVSFSRCDMVI-PETKAT---HVDHARGEI-----KKFSMQYQ--DGLITRSERYNKVIDEWSKCTDMIAND 2126
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 748 AKKSL------TEYNNLKAMVVSGSKGSNiniSQVIACVGQQNVEGKriPYGFRKRTlphfikddygPESRGFVEnsyla 821
Cdd:PRK14844 2127 MLKAIsiydgnSKYNSVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIISNFRE----- 2186
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 822 GLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMV-NYDGTVRNSvgqlIQLRYGEDGlcgelvefqnmPT 900
Cdd:PRK14844 2187 GLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVtKHDCKTKNG----LVVRATVEG-----------ST 2251
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 901 VKLSNKSFekrfkfdwsnerLMKKVFTDDVIKEMTdsseaiQELEAEWDRLVsDRDSLRQIFPNGESKVvlpcnlqrmiw 980
Cdd:PRK14844 2252 IVASLESV------------VLGRTAANDIYNPVT------KELLVKAGELI-DEDKVKQINIAGLDVV----------- 2301
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 981 nvqkifHINKRLPTDLSPirvikGVktllerCVIVTGNDriskqanenatllfqclirstlctkyvseefrLSTeafewl 1060
Cdd:PRK14844 2302 ------KIRSPLTCEISP-----GV------CSLCYGRD--------------------------------LAT------ 2326
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1061 vGEIetrfqqaqANPGEMVGALAAQSLGEPATQMTLNTFHFAGVssknVTLGVPRLKEIINISKKPKAPSLTVFL--TGG 1138
Cdd:PRK14844 2327 -GKI--------VSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVESSNIIASINAKIKLNNSNIIIdkNGN 2393
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1139 AARDAEKAKNVLC------RLEHTtlrkVTANTAIYYDP-------------DPQRTVISEDQEFVNVYYEMPDF----- 1194
Cdd:PRK14844 2394 KIVISRSCEVVLIdslgseKLKHS----VPYGAKLYVDEggsvkigdkvaewDPYTLPIITEKTGTVSYQDLKDGisite 2469
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1195 ---DPTRISP-----WLLRIELDRKR----MTDKKLTMEQIAEKINVGFGEDLNCIFNDDNADKLVLRIRIMNN--EENK 1260
Cdd:PRK14844 2470 vmdESTGISSkvvkdWKLYSGGANLRprivLLDDNGKVMTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTprESVK 2549
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1261 FQDEDEAVDKMeddmfLRCIEANMLSDMTLQGiEAIGKVYMHLPQTDSKKRIVITETGEFKAIGEWLLEtdgTSMMKVLS 1340
Cdd:PRK14844 2550 TRDITGGLPRV-----IELFEARRPKEHAIVS-EIDGYVAFSEKDRRGKRSILIKPVDEQISPVEYLVS---RSKHVIVN 2620
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1341 ERDV----DPIRTSSNDICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVNYRHLALLC---------------------- 1394
Cdd:PRK14844 2621 EGDFvrkgDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILkqmlqkveitdpgdtmylvges 2700
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1395 ----------DVMTAKG----HLMAITRhGINR---QDTGALMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPK 1457
Cdd:PRK14844 2701 idklevdrenDAMSNSGkrpaHYLPILQ-GITRaslETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIP 2779
|
....
gi 17530899 1458 MGTG 1461
Cdd:PRK14844 2780 AGTG 2783
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
236-1129 |
2.26e-49 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 193.36 E-value: 2.26e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 236 RPDWMIVTVLPVPPLAVRPAVvmfgaaknQDD----LTHKLSD----IIKANNELRKNEASGAAAhVIQENIK-MLQFHV 306
Cdd:PRK00566 223 KPEWMILDVLPVIPPDLRPLV--------QLDggrfATSDLNDlyrrVINRNNRLKRLLELGAPE-IIVRNEKrMLQEAV 293
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 307 ATLVDNDMPGmpRAMQKSGK-PLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAqnLtfpEL 385
Cdd:PRK00566 294 DALFDNGRRG--RPVTGPNNrPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA--L---EL 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 386 VTPFnIdrMQELVRRGNSQ-YPGAKYIVrdngERID----------LRFHPkssdlhlqcgykverhlrdddlVIFNRQP 454
Cdd:PRK00566 367 FKPF-I--MKKLVERGLATtIKSAKKMV----EREDpevwdvleevIKEHP----------------------VLLNRAP 417
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 455 TLHKMSMM--------GHRVKVLPwstfrmnLSCTsPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPV 526
Cdd:PRK00566 418 TLHRLGIQafepvlieGKAIQLHP-------LVCT-AFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPI 489
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 527 mgIV--QD------TLTAVRKMTKRD--VFITREQVMNLLmflptwDAK-----------MPQPCILKPRPlwtGKQIFS 585
Cdd:PRK00566 490 --IVpsQDmvlglyYLTREREGAKGEgmVFSSPEEALRAY------ENGevdlharikvrITSKKLVETTV---GRVIFN 558
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 586 LIIPGNVnmirthsthpdeedegPYkwispgdtkvmvehgELIMGILCKKSLgtsaGSLLHICFlelghdiagRFYGNIQ 665
Cdd:PRK00566 559 EILPEGL----------------PF---------------INVNKPLKKKEI----SKIINEVY---------RRYGLKE 594
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 666 TVInnwLL-------FE-----GHSIGIGDTIADPQTYNEIQQAIKKAKDdvinvIQKAHNMELeptpgntlrQTFE--- 730
Cdd:PRK00566 595 TVI---FLdkikdlgFKyatrsGISIGIDDIVIPPEKKEIIEEAEKEVAE-----IEKQYRRGL---------ITDGery 657
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 731 NKVNRILNDARDKTGGSAKKSLTEY----NNLKAMVVSGSKGSNINISQVIACVG-QQNVEGKRIPygfrkrtLPhfIKd 805
Cdd:PRK00566 658 NKVIDIWSKATDEVAKAMMKNLSKDqesfNPIYMMADSGARGSASQIRQLAGMRGlMAKPSGEIIE-------TP--IK- 727
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 806 dygpesrgfveNSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYD--GTVRnsvGqlIQLRY 883
Cdd:PRK00566 728 -----------SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDdcGTDR---G--IEVTA 791
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 884 GEDGlcGELVEfqnmptvKLSnksfekrfkfdwsnERLMKKVFTDDVIKEMTDsseaiqELEAEWDRLVsDRDSLRQIFP 963
Cdd:PRK00566 792 IIEG--GEVIE-------PLE--------------ERILGRVLAEDVVDPETG------EVIVPAGTLI-DEEIADKIEE 841
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 964 NGESKV----VLPCNLQRmiwnvqkifhinkrlptdlspirvikGVktllerCVIVTGNDriskqanenatllfqclirs 1039
Cdd:PRK00566 842 AGIEEVkirsVLTCETRH--------------------------GV------CAKCYGRD-------------------- 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1040 tlctkyvseefrLSTeafewlvGEIetrfqqaqANPGEMVGALAAQSLGEPATQMTLNTFHFAGVsskNVTLGVPRLKEI 1119
Cdd:PRK00566 870 ------------LAT-------GKL--------VNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAEL 919
|
970
....*....|
gi 17530899 1120 INiSKKPKAP 1129
Cdd:PRK00566 920 FE-ARKPKGP 928
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
236-1127 |
1.59e-48 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 191.24 E-value: 1.59e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 236 RPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDMP 315
Cdd:PRK14906 311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 316 GMPrAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQnltfpELVTPFNIDRMQ 395
Cdd:PRK14906 391 GRP-VTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMAL-----ELFKPFVMKRLV 464
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 396 ELVRRGNSQypGAKYIVrDNGERIdlrfhpkssdlhlqcGYKVERHLRDDDLVIFNRQPTLHKMSMM--------GHRVK 467
Cdd:PRK14906 465 ELEYAANIK--AAKRAV-DRGASY---------------VWDVLEEVIQDHPVLLNRAPTLHRLGIQafepvlveGKAIK 526
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 468 VLPwstfrmnLSCTsPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVRKMT-KRD-- 544
Cdd:PRK14906 527 LHP-------LVCT-AFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDgf 598
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 545 -----VFITREQVMNllmflpTWDAKmpqpcilkpRPLWTGKQIfsliipgNVNMIRTHSTHPDEEDEGPYKWISPGDTK 619
Cdd:PRK14906 599 egegrTFADFDDALN------AYDAR---------ADLDLQAKI-------VVRLSRDMTVRGSYGDLEETKAGERIETT 656
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 620 VmvehGELIMG--------ILCKKSLGTSAGSLLHICFLELGHDIAGRFYGNIQTVINNWLLFEGHSIGIGDTIADPQty 691
Cdd:PRK14906 657 V----GRIIFNqvlpedypYLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDD-- 730
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 692 neiQQAIKKAKDDVINVIQKAHNMELEptpgnTLRQTFENKVNrILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNI 771
Cdd:PRK14906 731 ---KPEILAEADEKVAAIDEDYEDGFL-----SERERHKQVVD-IWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIK 801
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 772 NISQVIACVG-QQNVEGKRIpygfrkrTLPhfikddygpesrgfVENSYLAGLTPSEFYFHAMGGREGLIDTAVKTAETG 850
Cdd:PRK14906 802 QIRQLAGMRGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRTADSG 860
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 851 YIQRRLIKAMESVMVNYdgtvrnsvgqliqlrygEDglCGElVEFQNMPTVKLSNKsfekrfkfdwSNERLMKKVFTDDV 930
Cdd:PRK14906 861 YLTRRLVDVAQDVIVRE-----------------ED--CGT-DEGVTYPLVKPKGD----------VDTNLIGRCLLEDV 910
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 931 ikemtdsSEAIQELEAEWDRLVSDRDSLRQIFPNGESKVVLpcnlqrmiwnvqkifhinkrlptdlspirvikgvKTLLe 1010
Cdd:PRK14906 911 -------CDPNGEVLLSAGDYIESMDDLKRLVEAGVTKVQI----------------------------------RTLM- 948
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1011 rcvivtgndriskqanenatllfQCLIRSTLCTKyvseefrlsteAFEWlvgEIETRfqqAQANPGEMVGALAAQSLGEP 1090
Cdd:PRK14906 949 -----------------------TCHAEYGVCQK-----------CYGW---DLATR---RPVNIGTAVGIIAAQSIGEP 988
|
890 900 910
....*....|....*....|....*....|....*..
gi 17530899 1091 ATQMTLNTFHFAGVSSKNVTLGVPRLKEIINIsKKPK 1127
Cdd:PRK14906 989 GTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPK 1024
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
716-815 |
7.44e-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: 157.91 E-value: 7.44e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 716 ELEPTPGNTLRQTFENKVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIACVGQQNVEGKRIPYGFR 795
Cdd:pfam05000 9 KLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGKRIPFGFS 88
|
90 100
....*....|....*....|
gi 17530899 796 KRTLPHFIKDDYGPESRGFV 815
Cdd:pfam05000 89 GRTLPHFKKDDEGPESRGFV 108
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
82-534 |
1.85e-39 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 158.14 E-value: 1.85e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 82 GHIDLAKPVFHIGFI-----------TKTIKILRCVCfYCSKMLVSPHNPKIKEIvmksrgqpRKRLAYVYDLCKGKTIc 150
Cdd:CHL00018 105 GYIKLACPVTHVWYLkrlpsyianllDKPLKELEGLV-YCDFSFARPIAKKPTFL--------RLRGLFEYEIQSWKYS- 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 151 eggEDMDLTKENQQPDPNKKPGHGGcghyqPSIRR--TGLDLTA-------EWKHQNEDSQ----------EKKIVVSAE 211
Cdd:CHL00018 175 ---IPLFFSTQGFDTFRNREISTGA-----GAIREqlADLDLRIiidnslvEWKELGEEGStgnewedrkiGRRKDFLVR 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 212 RVwEILKHitdeecFILgmdpKYARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRK-NEASGA 290
Cdd:CHL00018 247 RI-KLAKH------FIR----TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDlLTTSRS 315
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 291 AAH---VIQEniKMLQFHVATLVDNDMPGMPraMQKS-GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLR 366
Cdd:CHL00018 316 TPGelvMCQK--KLLQEAVDALLDNGIRGQP--MRDGhNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLS 391
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 367 IDQVGVPRSIAQnltfpELVTPFNIdrmQELVRRGNSQYPG-AKYIVRDNGERID--LRF----HPkssdlhlqcgykve 439
Cdd:CHL00018 392 LHQCGLPREIAI-----ELFQPFVI---RGLIRQHLASNIRaAKSKIREKEPIVWeiLQEvmqgHP-------------- 449
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 440 rhlrdddlVIFNRQPTLHKMSMM--------GHRVKVLPwstfrmnLSCTSpYNADFDGDEMNLHVPQSMETRAEVENIH 511
Cdd:CHL00018 450 --------VLLNRAPTLHRLGIQafqpilveGRAICLHP-------LVCKG-FNADFDGDQMAVHVPLSLEAQAEARLLM 513
|
490 500
....*....|....*....|...
gi 17530899 512 ITPRQIITPQANKPVMGIVQDTL 534
Cdd:CHL00018 514 FSHMNLLSPAIGDPISVPSQDML 536
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
235-532 |
2.50e-38 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 154.14 E-value: 2.50e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 235 ARPDWMIVTVLPVPPLAVRPAVVMFGAAKNQDDLTHKLSDIIKANNELRKNEASGAAAHVIQENIKMLQFHVATLVDNDM 314
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 315 PGMPrAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAqnltfPELVTPFNIDRm 394
Cdd:PRK02625 320 RGRT-VVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMA-----IELFQPFVIHR- 392
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 395 qeLVRRGN-SQYPGAKYIVRDNGERIdlrfhpkssdlhlqcgYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWST 473
Cdd:PRK02625 393 --LIRQGIvNNIKAAKKLIQRADPEV----------------WQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 474 FRMN-LSCTSpYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQD 532
Cdd:PRK02625 455 IQLHpLVCPA-FNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1353-1462 |
1.65e-36 |
|
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: 136.01 E-value: 1.65e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1353 DICEIFQVLGIEAVRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLM 1432
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 17530899 1433 DAAAHAETDPMRGVSENIIMGQLPKMGTGC 1462
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 ... |
1076-1123 |
9.53e-23 |
|
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: 96.72 E-value: 9.53e-23
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 17530899 1076 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINIS 1123
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
756-1109 |
1.53e-11 |
|
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: 69.88 E-value: 1.53e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 756 NNLKAMVVSGSKGsniNISQVIACVGQQ----NVEGKRIpygfrkrTLPhfikddygpesrgfVENSYLAGLTPSEFYFH 831
Cdd:TIGR02388 119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 832 AMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVNYD--GTVRNsvgqlIQLRYGEDGlcGELVEFQNmptvklsnksfe 909
Cdd:TIGR02388 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEdcGTERS-----IVVRAMTEG--DKKISLGD------------ 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 910 krfkfdwsneRLMKKVFTDDVIKemtdsseaiqeleaewdrlvsdrdslrqifPNGEskvvlpcnlqrmiwnvqkifhin 989
Cdd:TIGR02388 236 ----------RLLGRLVAEDVLH------------------------------PEGE----------------------- 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 990 krlptdlspirvikgvktllercVIVTGNDRISKQ-ANENATLLF-QCLIRSTLCTKYVSEEFRLsteAFEWLVGeietr 1067
Cdd:TIGR02388 253 -----------------------VIVPKNTAIDPDlAKTIETAGIsEVVVRSPLTCEAARSVCRK---CYGWSLA----- 301
|
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 17530899 1068 fQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 1109
Cdd:TIGR02388 302 -HAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1074-1119 |
1.18e-10 |
|
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: 62.93 E-value: 1.18e-10
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 17530899 1074 NPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSkNVTLGVPRLKEI 1119
Cdd:cd02655 4 ELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEEL 48
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1076-1467 |
1.03e-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: 62.82 E-value: 1.03e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1076 GEMVGALAAQSLGEPATQMTLNTfhfagvSSKNVTLGVPRLKEII--NISKKPKAPSLTVFLTGGAARDA---EKAKNVL 1150
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDP------PQSLESSPLELLKEVLecRSKSKSKENDRRVILSLHLCKCDhgfEYERAAL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1151 C---RLEHTTLRKVTANTAIYYDPDPQRTVISE--DQEFVNVYYEMPD-----FDPTRISPWllrieldrkrmtdkkltm 1220
Cdd:cd02737 75 EvknHLERVTLEDLATTSMIKYSPQATEAIVGEigDQLNTKKKGKKKAifstsLKITKFSPW------------------ 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1221 eqiaekinvgfgedlNCIFNDDNADKLVLRIRIMNNEENKFQDED--EAVDKMEDDMFlrcieaNMLSDMTLQGIEAIGK 1298
Cdd:cd02737 137 ---------------VCHFHLDKECQKLSDGPCLTFSVSKEVSKSseELLDVLRDRII------PFLLETVIKGDERIKS 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1299 VymHLPQTDSKKRIVITETGEFKAiGEWLLETD-------------GTSMMKVLSERD-VDPIRTSSNDICEIFQVLGIE 1364
Cdd:cd02737 196 V--NILWEDSPSTSWVKSVGKSSR-GELVLEVTveesckktrgnawNVVMDACIPVMDlIDWERSMPYSIQQIKSVLGID 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1365 AVRKSVEKEMNAVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGA-----LMRCSFEETVDVLMDAAAHAE 1439
Cdd:cd02737 273 AAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRSLkisapFTEACFSSPIKCFLKAAKKGA 352
|
410 420
....*....|....*....|....*....
gi 17530899 1440 TDPMRGVSENIIMGQLPKMGTGC-FDLLL 1467
Cdd:cd02737 353 SDSLSGVLDACAWGKEAPVGTGSkFEILW 381
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
761-1109 |
1.03e-09 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 63.86 E-value: 1.03e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 761 MVVSGSKGsniNISQVIACVGQQ----NVEGKRIpygfrkrTLPhfIKDDygpesrgFVEnsylaGLTPSEFYFHAMGGR 836
Cdd:PRK02597 125 MAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----GLTVTEYVISSYGAR 180
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 837 EGLIDTAVKTAETGYIQRRLIKAMESVMVNYD--GTVRNsvgqlIQLRYgEDGLCGELVEFQNmptvklsnksfekrfkf 914
Cdd:PRK02597 181 KGLVDTALRTADSGYLTRRLVDVSQDVIVREEdcGTTRG-----IVVEA-MDDGDRVLIPLGD----------------- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 915 dwsneRLMKKVFTDDVIkemtdssEAIQELEAEWDRLVsDRDSLRQIFPNGESKVVLpcnlqrmiwnvqkifhinkRlpt 994
Cdd:PRK02597 238 -----RLLGRVLAEDVV-------DPEGEVIAERNTAI-DPDLAKKIEKAGVEEVMV-------------------R--- 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 995 dlSPIRvikgvktllerCvivtgndriskQANenatllfqcliRStLCTKyvseefrlsteAFEWLVgeietrfqqAQAN 1074
Cdd:PRK02597 283 --SPLT-----------C-----------EAA-----------RS-VCRK-----------CYGWSL---------AHNH 306
|
330 340 350
....*....|....*....|....*....|....*...
gi 17530899 1075 P---GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 1109
Cdd:PRK02597 307 LvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1707-1880 |
2.42e-08 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 59.32 E-value: 2.42e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1707 SPTSPSySPTSPNyTPVTPSY--SPTSPNYSASPQySPASP-----------AYSQTGVKYSPTSPTYSPPSPSYDGSPG 1773
Cdd:PTZ00449 629 SPKSPK-RPPPPQ-RPSSPERpeGPKIIKSPKPPK-SPKPPfdpkfkekfydDYLDAAAKSKETKTTVVLDESFESILKE 705
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1774 SPQYTPGSPQYSPAS-PKYSPTSPLYSpsspqhspsnqYSPTGStysATSPRYSPNMSIYSP--SSTKYSPTsPTYTP-- 1848
Cdd:PTZ00449 706 TLPETPGTPFTTPRPlPPKLPRDEEFP-----------FEPIGD---PDAEQPDDIEFFTPPeeERTFFHET-PADTPlp 770
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 17530899 1849 ------------TARNYSPTSPMYSPTAPSHYSPTSPAYSPSSP 1880
Cdd:PTZ00449 771 dilaeefkeediHAETGEPDEAMKRPDSPSEHEDKPPGDHPSLP 814
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1707-1881 |
1.40e-07 |
|
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.
Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 56.85 E-value: 1.40e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1707 SPTSPSYSPT-------SPNYTPVTPSYSPTSPNYSAspqysPAS--PAYSQTGVkysptsPTYSPPSPSYDGSPGSPQY 1777
Cdd:pfam05109 424 APESTTTSPTlnttgfaAPNTTTGLPSSTHVPTNLTA-----PAStgPTVSTADV------TSPTPAGTTSGASPVTPSP 492
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1778 TP------------GSPQYSPASPKYSPTSPlysPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPT 1845
Cdd:pfam05109 493 SPrdngteskapdmTSPTSAVTTPTPNATSP---TPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNA 569
|
170 180 190
....*....|....*....|....*....|....*.
gi 17530899 1846 YTPTARNYSPTSPMYSPTaPSHYSPTSPAYSPSSPT 1881
Cdd:pfam05109 570 TIPTLGKTSPTSAVTTPT-PNATSPTVGETSPQANT 604
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1498-1862 |
7.64e-07 |
|
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.
Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 54.54 E-value: 7.64e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1498 STPSMTPPMTPWANCNTPryfSPPGHVSAMTPGGPSFSP---SAASDASGM-SPSwspahpgsspsspgpsmspyfpasp 1573
Cdd:pfam05109 459 TAPASTGPTVSTADVTSP---TPAGTTSGASPVTPSPSPrdnGTESKAPDMtSPT------------------------- 510
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1574 svsPSYSPTSPNYTASSPGGASPNYSPSSPNYSPTSPLYA---------SPRYASTTPNFN---PQSTGYSPSSSGYSPT 1641
Cdd:pfam05109 511 ---SAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAvttptpnatSPTPAVTTPTPNatiPTLGKTSPTSAVTTPT 587
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1642 SPVYSPTVQfQSSPSFAGSGSNIYSPGNAYSPSSSNYSPNSPSYSPTSPSYSPSSPSYSPTSPCYSPT-SPSYSPTSPNY 1720
Cdd:pfam05109 588 PNATSPTVG-ETSPQANTTNHTLGGTSSTPVVTSPPKNATSAVTTGQHNITSSSTSSMSLRPSSISETlSPSTSDNSTSH 666
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1721 TPVTPSYSPT--------SPNYSASPQYSPASPAysqtgVKYSPTSPTYSPPSPSYDGSPGSPQYTPGSPQYSPASPKyS 1792
Cdd:pfam05109 667 MPLLTSAHPTggenitqvTPASTSTHHVSTSSPA-----PRPGTTSQASGPGNSSTSTKPGEVNVTKGTPPKNATSPQ-A 740
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1793 PTSPLYSPSSPQHSPSNQYSPTGSTYS------------------ATSPRYSPNMSIYSPSST------KYSPTSPTYTp 1848
Cdd:pfam05109 741 PSGQKTAVPTVTSTGGKANSTTGGKHTtghgartstepttdyggdSTTPRTRYNATTYLPPSTssklrpRWTFTSPPVT- 819
|
410
....*....|....
gi 17530899 1849 TARNYSPTSPMYSP 1862
Cdd:pfam05109 820 TAQATVPVPPTSQP 833
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1076-1104 |
1.02e-06 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 54.17 E-value: 1.02e-06
10 20
....*....|....*....|....*....
gi 17530899 1076 GEMVGALAAQSLGEPATQMTLNTFHFAGV 1104
Cdd:CHL00117 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1385-1462 |
1.48e-06 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 50.99 E-value: 1.48e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17530899 1385 VNYRHLALLCDVMTAKGHLMAITRHGINRQdtGALMRCSFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTGC 1462
Cdd:cd02655 129 ENKRLLLLGKKPAKYEPVLLGITKASLNTE--SFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1706-1880 |
5.21e-06 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 51.29 E-value: 5.21e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1706 YSPTSPSYSPTSPNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVkysptsptysppSPSYDGSPGSPQYTPGSPQYS 1785
Cdd:COG3469 48 SVVVAASGSAGSGTGTTAASSTAATSSTTSTTATATAAAAAATSTSA------------TLVATSTASGANTGTSTVTTT 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1786 PASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMS-IYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTA 1864
Cdd:COG3469 116 STGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETATgGTTTTSTTTTTTSASTTPSATTTATATTASGATT 195
|
170
....*....|....*.
gi 17530899 1865 PSHYSPTSPAYSPSSP 1880
Cdd:COG3469 196 PSATTTATTTGPPTPG 211
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1046-1096 |
1.74e-05 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 49.89 E-value: 1.74e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 17530899 1046 VSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTL 1096
Cdd:PRK14898 27 LSKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| Pneumo_att_G |
pfam05539 |
Pneumovirinae attachment membrane glycoprotein G; |
1708-1879 |
1.38e-04 |
|
Pneumovirinae attachment membrane glycoprotein G;
Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 46.58 E-value: 1.38e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1708 PTSPSYSPTSPNYTPVTpsySPTSPNYSAsPQYSPASPAYSQTGVKYSPTSPTYSPPSPSYDGSPGSPQYTPGSPQYSPA 1787
Cdd:pfam05539 169 KTAVTTSKTTSWPTEVS---HPTYPSQVT-PQSQPATQGHQTATANQRLSSTEPVGTQGTTTSSNPEPQTEPPPSQRGPS 244
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1788 -SPKYSPTSPlySPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTkysPTSPTYTPTARnysPTSPMYSPTAPS 1866
Cdd:pfam05539 245 gSPQHPPSTT--SQDQSTTGDGQEHTQRRKTPPATSNRRSPHSTATPPPTT---KRQETGRPTPR---PTATTQSGSSPP 316
|
170
....*....|...
gi 17530899 1867 HYSPTSPAYSPSS 1879
Cdd:pfam05539 317 HSSPPGVQANPTT 329
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1709-1881 |
5.81e-04 |
|
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.
Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 44.91 E-value: 5.81e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1709 TSPSYSPTSPNYTPVTPSYSPTSpNYSASPQYSPASPAYSQTGVKYSPTSPTYSPPSPSYDGSpgSPQYTPGSPQYSPAS 1788
Cdd:pfam05109 474 TSPTPAGTTSGASPVTPSPSPRD-NGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNAT--SPTLGKTSPTSAVTT 550
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1789 PKYSPTSPlysPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARNYSPTSPMYSPTAPSHY 1868
Cdd:pfam05109 551 PTPNATSP---TPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVGETSPQANTTNHTLGGTSSTPVVTSPPKNATS 627
|
170
....*....|...
gi 17530899 1869 SPTSPAYSPSSPT 1881
Cdd:pfam05109 628 AVTTGQHNITSSS 640
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1708-1874 |
7.53e-04 |
|
translocon at the inner envelope of chloroplast subunit 62; Provisional
Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 44.53 E-value: 7.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1708 PTSPSYSPTS---PNYTPVTPSYSPTSPNYSASPQYSPASPAYSQTGVKYSPTSptysppspsydgsPGSP--QYTPGSP 1782
Cdd:PLN03209 383 PTSPIPTPPSsspASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQVEAKKTR-------------PLSPyaRYEDLKP 449
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1783 QYSPASPKYSPTSPLYSPSSPQHSPSNQYSPTGSTYSATSPrySPNMSIYSPSSTKYS---PTSPTYTPTARNYSPTSPM 1859
Cdd:PLN03209 450 PTSPSPTAPTGVSPSVSSTSSVPAVPDTAPATAATDAAAPP--PANMRPLSPYAVYDDlkpPTSPSPAAPVGKVAPSSTN 527
|
170
....*....|....*
gi 17530899 1860 YSPTAPSHYSPTSPA 1874
Cdd:PLN03209 528 EVVKVGNSAPPTALA 542
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1423-1461 |
1.08e-03 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 44.22 E-value: 1.08e-03
10 20 30
....*....|....*....|....*....|....*....
gi 17530899 1423 SFEETVDVLMDAAAHAETDPMRGVSENIIMGQLPKMGTG 1461
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1518-1881 |
4.78e-03 |
|
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.
Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 41.83 E-value: 4.78e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1518 FSPPGHVSAMTPGGPSFSPSAASDASGMSPSWSPAHPGSSPSSPgpsmspyfpaspsvspSYSPTSPNYTASSPGGASPN 1597
Cdd:pfam05109 421 FSKAPESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTNLTAPAST----------------GPTVSTADVTSPTPAGTTSG 484
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1598 YSPSSPNYSP-------TSPLYASPRYASTTPnfNPQSTgyspsssgysptspvySPTvqfqssPSFAGSGSNIYSPGNA 1670
Cdd:pfam05109 485 ASPVTPSPSPrdngtesKAPDMTSPTSAVTTP--TPNAT----------------SPT------PAVTTPTPNATSPTLG 540
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1671 YSpsssnyspnspsysptspsyspsspsysptspcySPTSPSYSPTsPNYTPVTPSYSPTSPNYS------ASPQYSPAS 1744
Cdd:pfam05109 541 KT----------------------------------SPTSAVTTPT-PNATSPTPAVTTPTPNATiptlgkTSPTSAVTT 585
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1745 PAYSQTGVKYSPTSPTYSPPSPSYDGSPGSPQYTpgspqyspaSPKYSPTSPLyspsspqhsPSNQYSPTGSTYSATSPR 1824
Cdd:pfam05109 586 PTPNATSPTVGETSPQANTTNHTLGGTSSTPVVT---------SPPKNATSAV---------TTGQHNITSSSTSSMSLR 647
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17530899 1825 YSPNMSIYSPS----STKYSPTSPTYTPT-ARNYSPTSPmySPTAPSHYSPTSPAYSPSSPT 1881
Cdd:pfam05109 648 PSSISETLSPStsdnSTSHMPLLTSAHPTgGENITQVTP--ASTSTHHVSTSSPAPRPGTTS 707
|
|
| PRK10263 |
PRK10263 |
DNA translocase FtsK; Provisional |
1709-1887 |
7.81e-03 |
|
DNA translocase FtsK; Provisional
Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 41.22 E-value: 7.81e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1709 TSPSYSPTSPNYTPVTPSYSPtspnysaSPQYSPASPAYSQtgvkysptsptysppspsydgsPGSPQYTPGSPQYSPAS 1788
Cdd:PRK10263 362 PVPGPQTGEPVIAPAPEGYPQ-------QSQYAQPAVQYNE----------------------PLQQPVQPQQPYYAPAA 412
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17530899 1789 PKySPTSPLYSPSSPQHSPSNQYSPTGSTYSATSP-RYSPNMSIYSPSSTkYSPTSPTYTPTARNYSPTSPMYSPTAPS- 1866
Cdd:PRK10263 413 EQ-PAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAwQAEEQQSTFAPQST-YQTEQTYQQPAAQEPLYQQPQPVEQQPVv 490
|
170 180
....*....|....*....|....
gi 17530899 1867 HYSPTSPAYSPSSPT---FEESED 1887
Cdd:PRK10263 491 EPEPVVEETKPARPPlyyFEEVEE 514
|
|
| |
