|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
17-874 |
0e+00 |
|
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 1617.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 17 KRVQFGVISPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFHV 95
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 96 GFMTKIMKIMRCVCffcskllvdsnnpkikeilvkskgqprkrlthvyelckgkniceggeemdnkfgmepqeqeeditk 175
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 176 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIVTVLPVPP 255
Cdd:cd02733 93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 256 LAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 335
Cdd:cd02733 138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 336 SIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPGAK 415
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 416 YIIRDNGDRIDLRFHPKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 495
Cdd:cd02733 298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 496 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKMPQP 575
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 576 AILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPddedsGPYKHISPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISY 655
Cdd:cd02733 458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 656 LEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 735
Cdd:cd02733 533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 736 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 815
Cdd:cd02733 613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 1900307341 816 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd02733 693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
16-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 984.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 16 IKRVQFGVISPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFH 94
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 95 VGFMTKIMKIMRCVCFFCSKLLVDSNnpKIKEIL-----VKSKGQPRKRLT-HVYELCKGKNICeggeemdnkfgmePqe 168
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC-------------P-- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 169 qeeditkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIV 248
Cdd:PRK08566 150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 327
Cdd:PRK08566 212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 328 QKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRG 407
Cdd:PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 408 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 485
Cdd:PRK08566 371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 486 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 565
Cdd:PRK08566 450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 566 STWDGKMPQPAILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPDDEDSGPYKhiSPGDTKVIVENGELIMGILCKKSLGT 645
Cdd:PRK08566 530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:PRK08566 608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:PRK08566 688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 885
Cdd:PRK08566 768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847
|
....*...
gi 1900307341 886 QLRYGEDG 893
Cdd:PRK08566 848 QFKYGEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
16-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 939.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 16 IKRVQFGVISPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFH 94
Cdd:TIGR02390 4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 95 VGFMTKIMKIMRCVCFFCSKLlvdsnnpKIKEILVKskgQPRKRLthvyelckgkniceggEEMDNKFGMEPQEQEEDIT 174
Cdd:TIGR02390 82 VGFAKEIYKILRATCRKCGRI-------TLTEEEIE---QYLEKI----------------NKLKEEGGDLASTLIEKIV 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 175 KEKGHGG----CGRYQPRIRrsglelYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIVTV 250
Cdd:TIGR02390 136 KEAAKRMkcphCGEEQKKIK------FEKPTYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTV 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 251 LPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKS 330
Cdd:TIGR02390 210 LPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRS 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 331 GRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQ 410
Cdd:TIGR02390 290 GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDS 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 411 YPGAKYIIRDNGDRIDLRFHPKPSDL-HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTP 489
Cdd:TIGR02390 370 WPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPP 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 490 YNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLSTWD 569
Cdd:TIGR02390 450 YNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAGYF 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 570 GKMPQPAILKPRPLWTGKQIFSLIIPGHIN-VIRTHSTHPDDEDSgpyKHISPGDTKVIVENGELIMGILCKKSLGTSAG 648
Cdd:TIGR02390 529 GDPPEPAIEKPKEYWTGKQIFSAFLPEDLNfEGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAEKG 605
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 649 SLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPG 728
Cdd:TIGR02390 606 KILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPG 685
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 729 NTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHF 808
Cdd:TIGR02390 686 RTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHF 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 809 IKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLR 888
Cdd:TIGR02390 766 KKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFK 845
|
....*..
gi 1900307341 889 YGEDGLA 895
Cdd:TIGR02390 846 YGEDGVD 852
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1056-1474 |
0e+00 |
|
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain] Cd Length: 410 Bit Score: 821.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1056 FRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTP 1135
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1136 SLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDV--SRISPWLLRIE 1213
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVeqDRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEdeevvdkMDDDVFLRCIESNMLTD 1293
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1294 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVS 1453
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 1900307341 1454 ENIMLGQLAPAGTGCFDLLLD 1474
Cdd:cd02584 390 ENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
828-1425 |
6.24e-177 |
|
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: 546.95 E-value: 6.24e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 828 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGENVEFQNLATL 907
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 908 KPSNKAFEKKFRfdctneralrrvlqEDVVKDVLTNANVQSVLEREfekmredreilraifptgdskvvlpcnlarmiwn 987
Cdd:pfam04998 81 EFSDLKLEDKFK--------------NDLLDDLLLLSEFSLSYKKE---------------------------------- 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 988 aqkifrintrtptdlnplrvvegvqelSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMTEEFRLSTEAYDWLL 1067
Cdd:pfam04998 113 ---------------------------ILVRDSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1068 GEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAAR 1147
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1148 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDVSR--------ISPWLLRIELDRKHM 1219
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1220 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEDEEvvdKMDDDVFLRCIESNMLTDMTLQGI 1299
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDEL---FMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1300 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1378
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 1900307341 1379 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPL 1425
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
244-544 |
2.20e-172 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 525.55 E-value: 2.20e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 244 EWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNElpGL 323
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 324 PRAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQEL 403
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 404 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 482
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1900307341 483 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 544
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
13-352 |
4.79e-143 |
|
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: 446.35 E-value: 4.79e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 13 LRTIKRVQFGVISPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAK 90
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 91 PVFHVGFMTKIMKIMRCVCFFCSKLLVDSNNPKIKEILVKSKGQ--PRKRLTHVYELCKGKNICEGGEEMDnkfgmepqe 168
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 169 qeeditkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIV 248
Cdd:pfam04997 150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 328
Cdd:pfam04997 217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
|
330 340
....*....|....*....|....
gi 1900307341 329 KSGRPLKSIKQRLKGKEGRVRGNL 352
Cdd:pfam04997 297 KSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
894-1077 |
2.33e-93 |
|
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: 300.18 E-value: 2.33e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 894 LAGENVEFQNLATLKPSNKAFEKKFRFDCTNERA--LRRVLQEDVVKDVLTNANVQSVLEREFEKMREDREILRA-IFPT 970
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREiIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 971 GDSKVV-LPCNLARMIWNAQKIFRINTRTPTDLNPLRVVEGVQELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1049
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 1900307341 1050 RRMTEEFRLSTEAYDWLLGEIETKFNQS 1077
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1054-1477 |
2.09e-85 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 285.20 E-value: 2.09e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1054 EEFRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPK 1133
Cdd:PRK04309 31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1134 TPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaeDqewvnvYYEMpdfdvsrispwLLRIE 1213
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------TIIIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKFQEDEEVVDKmdddvflrciesnmLTD 1293
Cdd:PRK04309 161 LDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK--------------IRN 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1294 MTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:PRK04309 217 IKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAAR 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVS 1453
Cdd:PRK04309 279 NAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVT 358
|
410 420
....*....|....*....|....
gi 1900307341 1454 ENIMLGQLAPAGTGCFDLLLDAEK 1477
Cdd:PRK04309 359 ENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1058-1474 |
1.35e-84 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 282.33 E-value: 1.35e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1058 LSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSL 1137
Cdd:TIGR02389 20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1138 TVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaedqewvnvyyempdfDVSRISpwlLRIELDRK 1217
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VIIELDEE 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1218 HMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNaeklvlrIRIMNSDENKFQEDEEVVDKmdddvflrciesnmLTDMTLQ 1297
Cdd:TIGR02389 150 QLKERGITVDDVEKAIKKAKLGKVIEIDMDNN-------TITIKPGNPSLKELRKLKEK--------------IKNLHIK 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1298 GIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALE 1377
Cdd:TIGR02389 209 GIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAII 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1378 RELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVSENIM 1457
Cdd:TIGR02389 271 EEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENII 350
|
410
....*....|....*..
gi 1900307341 1458 LGQLAPAGTGCFDLLLD 1474
Cdd:TIGR02389 351 VGQPIPLGTGDVDLVMD 367
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
18-1112 |
6.15e-63 |
|
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: 236.60 E-value: 6.15e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 18 RVQFGVISPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIersgrCQTCAGN 75
Cdd:COG0086 9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 76 MTECP---GHFGHIELAKPVFHVGFMTKIMKIMRcvcffcskLLVDSNNPKIKEIL-------VKSKGQPRKRLTHVYEL 145
Cdd:COG0086 82 VTLSKvrrERMGHIELAMPVFHIWGLKSLPSRIG--------LLLDMSLRDLERVLyfesyvvIDPGDTPLEKGQLLTED 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 146 CKGKNICEGGEEMDNKFGMEP-QEQEEDITKEKGHGgcgryqprirrsglELYAEWKHVNedSQEKKIllspervhEIFK 224
Cdd:COG0086 154 EYREILEEYGDEFVAKMGAEAiKDLLGRIDLEKESE--------------ELREELKETT--SEQKRK--------KLIK 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 225 RIsdeeDIILGMDPKFARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAED 304
Cdd:COG0086 210 RL----KVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNE 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 305 VKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIA 383
Cdd:COG0086 286 KRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 384 AnmtfpEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqigykverhmcdgdiVIF 456
Cdd:COG0086 364 L-----ELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------------VLL 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 457 NRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQS 528
Cdd:COG0086 414 NRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPAN 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 529 NRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKMPQPAILKPRPLWTGKQ------------ 588
Cdd:COG0086 486 GKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgkivettvgry 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 589 IFSLIIP---GHINvirthsthpddedsgpykhispgdtKVIvengelimgilCKKSLGTsagsLVHISYLEMGHDITRL 665
Cdd:COG0086 561 LVNEILPqevPFYN-------------------------QVI-----------NKKHIEV----IIRQMYRRCGLKETVI 600
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 666 FYSNIQTVVNNWLLIEGHSIGIGDSIADAKTyldiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfENQVNRILND 745
Cdd:COG0086 601 FLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTK 669
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 746 ARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenS 824
Cdd:COG0086 670 ASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS---------------------N 728
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 825 YLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGEDglagenVEfqn 903
Cdd:COG0086 729 FREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEGGE------VI--- 798
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 904 lATLKpsnkafekkfrfdctnERALRRVLQEDVVKDVLTNANVQSVLEREFEkmredreilraifptgdskvvlpcnlar 983
Cdd:COG0086 799 -EPLK----------------ERILGRVAAEDVVDPGTGEVLVPAGTLIDEE---------------------------- 833
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 984 miwnaqkifrintrtptdlnplrVVEGVQELSKKLVIVngddplsrqaqenatllfnihlRSTLCsrrMTEEFRLSTEAY 1063
Cdd:COG0086 834 -----------------------VAEIIEEAGIDSVKV----------------------RSVLT---CETRGGVCAKCY 865
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....*....
gi 1900307341 1064 DWLLGEiETKFNQsiahpGEMVGALAAQSLGEPATQMTLNTFHYAGVSA 1112
Cdd:COG0086 866 GRDLAR-GHLVNI-----GEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS 908
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1854-1954 |
1.39e-15 |
|
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: 83.04 E-value: 1.39e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1854 TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1933
Cdd:pfam05109 521 TSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVGETSP 600
|
90 100
....*....|....*....|.
gi 1900307341 1934 KGSTYSPTSPGYSPTSPTYSP 1954
Cdd:pfam05109 601 QANTTNHTLGGTSSTPVVTSP 621
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
762-1115 |
8.14e-13 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 74.26 E-value: 8.14e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 762 NNFKS---------MVVAGSKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 828
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 829 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGENVEFQNlatl 907
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 908 kpsnkafekkfrfdctneRALRRVLQEDVV---KDVLTNANvqsvlerefekmredreilRAIFPtgdskvvlpcNLARM 984
Cdd:PRK02597 238 ------------------RLLGRVLAEDVVdpeGEVIAERN-------------------TAIDP----------DLAKK 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 985 IWNAqkifrintrtptdlnplrvveGVQElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmteefrlsteAYD 1064
Cdd:PRK02597 271 IEKA---------------------GVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYG 299
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1900307341 1065 WllgeietkfnqSIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1115
Cdd:PRK02597 300 W-----------SLAHNhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
762-1115 |
3.31e-12 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 72.19 E-value: 3.31e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 762 NNFKSMVVAGSKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFH 837
Cdd:TIGR02388 119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 838 AMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqvvQLRYGEDGlaGENVEFQNlatlkpsnkafek 916
Cdd:TIGR02388 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTERSI----VVRAMTEG--DKKISLGD------------- 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 917 kfrfdctneRALRRVLQEDVVKdvltnanvqsvlerefekmredreilraifPTGDskVVLPCNlarmiwnaqkifrint 996
Cdd:TIGR02388 236 ---------RLLGRLVAEDVLH------------------------------PEGE--VIVPKN---------------- 258
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 997 rTPTDlnplrvvegvQELSKKLVivngddplsrqaqenATLLFNIHLRSTLCSRRMTEEFRLsteAYDWllgeietkfnq 1076
Cdd:TIGR02388 259 -TAID----------PDLAKTIE---------------TAGISEVVVRSPLTCEAARSVCRK---CYGW----------- 298
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 1900307341 1077 SIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1115
Cdd:TIGR02388 299 SLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1513-1612 |
5.21e-12 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 64.47 E-value: 5.21e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1513 PAMTP-WNTGA--TPAYGAWSPSVGSGMTPGAAGFSPSA------------ASDASGFSPGYSPAWSP--TPGSPGSPGP 1575
Cdd:smart01104 1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRtpawggagsrtpAWGGAGPTGSRTPAWGGasAWGNKSSEGS 80
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 1900307341 1576 VSPYIPSPG---GAMSPNYSPTSPAYEPRSPGGYTPQSPG 1612
Cdd:smart01104 81 ASSWAAGPGgayGAPTPGYGGTPSAYGPATPGGGAMAGSA 120
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1850-1950 |
3.05e-07 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 55.85 E-value: 3.05e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1850 EYTPTS-PKYS--PTSPK--YSPTSPKySPTSPTySPTTPKySPTSPTySPTSPTYT--PTSPKySPTSPTySPTSPKyS 1922
Cdd:PTZ00449 566 EHKPSKiPTLSkkPEFPKdpKHPKDPE-EPKKPK-RPRSAQ-RPTRPK-SPKLPELLdiPKSPK-RPESPK-SPKRPP-P 638
|
90 100
....*....|....*....|....*...
gi 1900307341 1923 PTSPTySPTSPKGsTYSPTSPGySPTSP 1950
Cdd:PTZ00449 639 PQRPS-SPERPEG-PKIIKSPK-PPKSP 663
|
|
| MISS |
pfam15822 |
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic ... |
1513-1611 |
5.18e-06 |
|
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic MAPK-interacting and spindle-stabilising protein-like proteins. MISS is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localization signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII spindle. MISS is the first example of a physiological MAPK-substrate that is stabilized in MII that specifically regulates MII spindle integrity during the CSF arrest.
Pssm-ID: 318115 [Multi-domain] Cd Length: 238 Bit Score: 49.98 E-value: 5.18e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1513 PAMTPWNTGATPaygawsPSVGSGMTPGAAGFSPSAASDASGFSPGYsPAWSPTPGSPGSPGPVSPYIPSPGGamsPNYS 1592
Cdd:pfam15822 31 PGSNPWNNPSAP------PAVPSGLPPSTAPSTVPFGPAPTGMYPSI-PLTGPSPGPPAPFPPSGPSCPPPGG---PYPA 100
|
90 100
....*....|....*....|
gi 1900307341 1593 PTSPAyePRSPGGY-TPQSP 1611
Cdd:pfam15822 101 PTVPG--PGPIGPYpTPNMP 118
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1851-1960 |
1.43e-05 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 50.14 E-value: 1.43e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1851 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1927
Cdd:COG3469 89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
|
90 100 110
....*....|....*....|....*....|...
gi 1900307341 1928 YSPTSPKGSTYSPTSPGYSPTSPTYSPAISPDD 1960
Cdd:COG3469 169 TTTTTSASTTPSATTTATATTASGATTPSATTT 201
|
|
| 2A1904 |
TIGR00927 |
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1850-1962 |
1.02e-04 |
|
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]
Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 47.68 E-value: 1.02e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1850 EYTPTSPKyspTSPKYSPTSPK--YSPTSPTY------SPTTPKYSPTSptYSPTSPtyTPTSPKYSPTS----PTYSPT 1917
Cdd:TIGR00927 109 ENTPSPPR---RTAKITPTTPKnnYSPTAAGTervkedTPATPSRALNH--YISTSG--RQRVKSYTPKPrgevKSSSPT 181
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1900307341 1918 SPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSPAISPDDSD 1962
Cdd:TIGR00927 182 QTREKVRKYTPSPLGRMVNSYAPSTFMTMPRSHGITPRTTVKDSE 226
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1861-1955 |
2.68e-04 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 42.51 E-value: 2.68e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1861 TSPKYSPTSPKysptSPTYSPTTPKYSPTSPTYSPT-SPTYTPT-------SPKYSPTSPTYSPTsPKYSPTS------- 1925
Cdd:smart01104 3 RTPAWGASGSK----TPAWGSRTPGTAAGGAPTARGgSGSRTPAwggagsrTPAWGGAGPTGSRT-PAWGGASawgnkss 77
|
90 100 110
....*....|....*....|....*....|..
gi 1900307341 1926 --PTYSPTSPKGSTYSPTSPGYSPTSPTYSPA 1955
Cdd:smart01104 78 egSASSWAAGPGGAYGAPTPGYGGTPSAYGPA 109
|
|
| PRK14959 |
PRK14959 |
DNA polymerase III subunits gamma and tau; Provisional |
1511-1612 |
5.67e-04 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 184923 [Multi-domain] Cd Length: 624 Bit Score: 45.06 E-value: 5.67e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1511 MSPAMTPWNTgATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPA--WSPTPGSPGSPGPV---SPYIPSPGG 1585
Cdd:PRK14959 361 MLPRLMPVES-LRPSGGGASAPSGSAAEGPASGGAATIPTPGTQGPQGTAPAagMTPSSAAPATPAPSaapSPRVPWDDA 439
|
90 100
....*....|....*....|....*..
gi 1900307341 1586 AMSPNYSPTSPAYEPRSPGgyTPQSPG 1612
Cdd:PRK14959 440 PPAPPRSGIPPRPAPRMPE--ASPVPG 464
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
17-874 |
0e+00 |
|
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 1617.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 17 KRVQFGVISPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFHV 95
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 96 GFMTKIMKIMRCVCffcskllvdsnnpkikeilvkskgqprkrlthvyelckgkniceggeemdnkfgmepqeqeeditk 175
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 176 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIVTVLPVPP 255
Cdd:cd02733 93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 256 LAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 335
Cdd:cd02733 138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 336 SIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPGAK 415
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 416 YIIRDNGDRIDLRFHPKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 495
Cdd:cd02733 298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 496 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKMPQP 575
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 576 AILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPddedsGPYKHISPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISY 655
Cdd:cd02733 458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 656 LEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 735
Cdd:cd02733 533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 736 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 815
Cdd:cd02733 613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 1900307341 816 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd02733 693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
13-893 |
0e+00 |
|
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 999.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 13 LRTIKRVQFGVISPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKP 91
Cdd:cd02582 1 PKRIKGIKFGLLSPEEIRKMSVVE--IITPDTyDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 92 VFHVGFMTKIMKIMRCVCFFCSKLLV-----DSNNPKIKEiLVKSKGQPRKRL-THVYELCKGKNICeggeemdnkfgme 165
Cdd:cd02582 79 VIHVGFAKHIYDLLRATCRSCGRILLpeeeiEKYLERIRR-LKEKWPELVKRViEKVKKKAKKRKVC------------- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 166 PqeqeeditkekgHggCGRYQPRIRrsgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEEDIILGMDPKFARPEW 245
Cdd:cd02582 145 P------------H--CGAPQYKIK---LEKPTTFYEEKEEGEVK---LTPSEIRERLEKIPDEDLELLGIDPKTARPEW 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 246 MIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPR 325
Cdd:cd02582 205 MVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPP 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 326 AMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVR 405
Cdd:cd02582 285 ARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVL 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 406 RGNSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLN 483
Cdd:cd02582 365 NGPDKWPGANYVIRPDGRRIRLRYVNR-EELaeRLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLN 443
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 484 LSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLM 563
Cdd:cd02582 444 LAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLS 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 564 FLStWDGKMPQPAILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPDDEDSGPYKHisPGDTKVIVENGELIMGILCKKSL 643
Cdd:cd02582 524 AAG-YDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEGKAKVCSGCSECKDEDC--PNDGYVVIKNGKLLEGVIDKKAI 600
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 644 GT-SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNE 722
Cdd:cd02582 601 GAeQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGE 680
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 723 LEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKH 802
Cdd:cd02582 681 LEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRN 760
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 803 RTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSIN 882
Cdd:cd02582 761 RTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRG 840
|
890
....*....|.
gi 1900307341 883 QVVQLRYGEDG 893
Cdd:cd02582 841 NIIQFKYGEDG 851
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
16-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 984.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 16 IKRVQFGVISPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFH 94
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 95 VGFMTKIMKIMRCVCFFCSKLLVDSNnpKIKEIL-----VKSKGQPRKRLT-HVYELCKGKNICeggeemdnkfgmePqe 168
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC-------------P-- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 169 qeeditkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIV 248
Cdd:PRK08566 150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 327
Cdd:PRK08566 212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 328 QKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRG 407
Cdd:PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 408 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 485
Cdd:PRK08566 371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 486 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 565
Cdd:PRK08566 450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 566 STWDGKMPQPAILKPRPLWTGKQIFSLIIPGHINVIRTHSTHPDDEDSGPYKhiSPGDTKVIVENGELIMGILCKKSLGT 645
Cdd:PRK08566 530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 646 SAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEP 725
Cdd:PRK08566 608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 726 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 805
Cdd:PRK08566 688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 806 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 885
Cdd:PRK08566 768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847
|
....*...
gi 1900307341 886 QLRYGEDG 893
Cdd:PRK08566 848 QFKYGEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
16-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 939.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 16 IKRVQFGVISPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFH 94
Cdd:TIGR02390 4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 95 VGFMTKIMKIMRCVCFFCSKLlvdsnnpKIKEILVKskgQPRKRLthvyelckgkniceggEEMDNKFGMEPQEQEEDIT 174
Cdd:TIGR02390 82 VGFAKEIYKILRATCRKCGRI-------TLTEEEIE---QYLEKI----------------NKLKEEGGDLASTLIEKIV 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 175 KEKGHGG----CGRYQPRIRrsglelYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIVTV 250
Cdd:TIGR02390 136 KEAAKRMkcphCGEEQKKIK------FEKPTYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTV 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 251 LPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKS 330
Cdd:TIGR02390 210 LPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRS 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 331 GRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQ 410
Cdd:TIGR02390 290 GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDS 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 411 YPGAKYIIRDNGDRIDLRFHPKPSDL-HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTP 489
Cdd:TIGR02390 370 WPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPP 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 490 YNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLSTWD 569
Cdd:TIGR02390 450 YNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAGYF 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 570 GKMPQPAILKPRPLWTGKQIFSLIIPGHIN-VIRTHSTHPDDEDSgpyKHISPGDTKVIVENGELIMGILCKKSLGTSAG 648
Cdd:TIGR02390 529 GDPPEPAIEKPKEYWTGKQIFSAFLPEDLNfEGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAEKG 605
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 649 SLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPG 728
Cdd:TIGR02390 606 KILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPG 685
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 729 NTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHF 808
Cdd:TIGR02390 686 RTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHF 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 809 IKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLR 888
Cdd:TIGR02390 766 KKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFK 845
|
....*..
gi 1900307341 889 YGEDGLA 895
Cdd:TIGR02390 846 YGEDGVD 852
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
12-1479 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 914.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 12 PLRTIKRVQFGVISPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAK 90
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAE--ITAPEAyDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 91 PVFHVGFMTKIMKIMRCVCFFCSKLLV---DSNNPK-IKEILVKSKGQPRKRLthvyelckgkniceggeemDNKFGMEP 166
Cdd:PRK14977 83 PVIHIAFIDNIKDLLNSTCHKCAKLKLpqeDLNVFKlIEEAHAAARDIPEKRI-------------------DDEIIEEV 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 167 QEQEEDITKE-KGHGGCGRYQPRirrsgLELYAEWKHVNEDSQEKKILLsPERVHEIFKRISDEEDIILGMDPKFARPEW 245
Cdd:PRK14977 144 RDQVKVYAKKaKECPHCGAPQHE-----LEFEEPTIFIEKTEIEEHRLL-PIEIRDIFEKIIDDDLELIGFDPKKARPEW 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 246 MIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPR 325
Cdd:PRK14977 218 AVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQ 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 326 AMQK-SGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELV 404
Cdd:PRK14977 298 AHHKgSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELV 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 405 RRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDL-------HLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPW 477
Cdd:PRK14977 378 INGPDEFPGANAIRKGDGTKIRLDFLEDKGKDalreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPG 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 478 STFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGE 557
Cdd:PRK14977 458 ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNE 537
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 558 VMNLLMfLSTWDGKMPQPAI-LKPRPLWTGKQIFSLIIPGHIN--VIRTHSTHPDDEDSGPYkhiSPGDTKVIVENGELI 634
Cdd:PRK14977 538 ASNIAM-LAGITDPLPEPAIkTKDGPAWTGKQLFSLFLPKDFNfeGIAKWSAGKAGEAKDPS---CLGDGYVLIKEGELI 613
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 635 MGILCKKSLGTSAG---SLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDV 711
Cdd:PRK14977 614 SGVIDDNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEV 693
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 712 IEVIEK--------AHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVI 783
Cdd:PRK14977 694 SDLIDQrkitrkitIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIA 773
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 784 AVVGQQNVE--------GKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAET 855
Cdd:PRK14977 774 GALGQQKRKtrigfvltGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDS 853
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 856 GYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLagenvefqnlatlkpsnkafekkfrfdctneralrrvlqed 935
Cdd:PRK14977 854 GYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGI----------------------------------------- 892
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 936 vvkdvltnaNVQSVLEREfekmredreilraifptgdskvvlPCNLARMIWNAQKIFRINTRTPtdlnplrvvEGVQELS 1015
Cdd:PRK14977 893 ---------DPQKLDHGE------------------------AFNLERIIEKQKIEDRGKGASK---------DEIEELA 930
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1016 KKlvivngddpLSRQAQENATLLFNIHLRSTlcsrrmteefRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGE 1095
Cdd:PRK14977 931 KE---------YTKTFNANLPKLLADAIHGA----------ELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAE 991
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1096 PATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIYY 1175
Cdd:PRK14977 992 PGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN 1071
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1176 dPNPQNTVVAEDQEWVNVYYEMPDFdvsrispwllrIELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeKLVl 1255
Cdd:PRK14977 1072 -ANEIKLIKPDKRALENGCIPMERF-----------AEIEAALAKGKKFEMELEDDLIIL----------------DLV- 1122
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1256 ririmnsdenkfqedeEVVDKMDDDVFLRCIeSNMLTDMTLQGIEQISKVYMHLPQTDNKKkiiitedgefkalqEWILE 1335
Cdd:PRK14977 1123 ----------------EAADRDKPLATLIAI-RNKILDKPVKGVPDIERAWVELVEKDGRD--------------EWIIQ 1171
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1336 TDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAI--- 1412
Cdd:PRK14977 1172 TSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglq 1251
|
1450 1460 1470 1480 1490 1500 1510
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1413 ---TRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK 1479
Cdd:PRK14977 1252 aagVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
25-878 |
0e+00 |
|
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 903.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 25 SPDELKRMSVTEggIKYPE--TTEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFHVGFMTKIM 102
Cdd:cd02583 2 SPEDIIRLSEVE--VTNRNlyDIETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAII 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 103 KIMRCVCFFCSKLLVDsnnPKIKEILVKSKGQPRKRLTH-------VYELCKGKNICeggeemdnkfgmePQeqeeditk 175
Cdd:cd02583 80 NILQCICKTCSRVLLP---EEEKRKFLKRLRRPNLDNLQkkalkkkILEKCKKVRKC-------------PH-------- 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 176 ekghggCGRYqprirrsglelyaewKHVNEDsqekkilLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIVTVLPVPP 255
Cdd:cd02583 136 ------CGLL---------------KKAQED-------LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPP 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 256 LAVRPAVVMQG-SARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSgRPL 334
Cdd:cd02583 188 LCIRPSVVMDEkSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPK-KPI 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 335 KSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPGA 414
Cdd:cd02583 267 RGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGA 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 415 KYII-RDNGDRIDLRF-HPKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNA 492
Cdd:cd02583 347 NFVIkRDGGKKKFLKYgNRRKIARELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNA 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 493 DFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwDGKM 572
Cdd:cd02583 427 DFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYML--DGEI 504
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 573 ----PQPAILKPRPLWTGKQIFSLII-PGHINVIRTHSTHPDDEDSGPYKHISPGDTKVIVENGELIMGILCKKSLGT-S 646
Cdd:cd02583 505 kidlPPPAILKPVELWTGKQIFSLLLrPNKKSPVLVNLEAKEKSYTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSgS 584
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 647 AGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPT 726
Cdd:cd02583 585 KNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQ 664
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 727 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 806
Cdd:cd02583 665 PGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLP 744
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1900307341 807 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR 878
Cdd:cd02583 745 HFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1056-1474 |
0e+00 |
|
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain] Cd Length: 410 Bit Score: 821.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1056 FRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTP 1135
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1136 SLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDV--SRISPWLLRIE 1213
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVeqDRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEdeevvdkMDDDVFLRCIESNMLTD 1293
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1294 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVS 1453
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 1900307341 1454 ENIMLGQLAPAGTGCFDLLLD 1474
Cdd:cd02584 390 ENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
20-874 |
0e+00 |
|
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain] Cd Length: 779 Bit Score: 636.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 20 QFGVISPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFHVGFM 98
Cdd:cd01435 1 SFSFYSAEEIRKLSVKE--ITNPVTfDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFF 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 99 TKIMKIMRCVCFFCSKLlvdsnnpKIKEILVKskgqprkRLTHVYELCkgkniceggeemdnkfgmepqeqeeditkekg 178
Cdd:cd01435 79 DLLYKLLRGSCFYCHRF-------RISKWEVK-------LFVAKLKLL-------------------------------- 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 179 hggcgryqprirRSGLElyaewkhvnedsQEKKILLSPervheifkrisdeediilgmdpkfarPEWMIVTVLPVPPLAV 258
Cdd:cd01435 113 ------------DKGLL------------VEAAELDFG--------------------------YDMFFLDVLLVPPNRF 142
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 259 RPAVVMQGSArnqddLTHK----LADIVKINNQLR------RNEQSGAAAHVIAEDVKL---------LQFHVATMVDNE 319
Cdd:cd01435 143 RPPSFLGDKV-----FENPqnvlLSKILKDNQQIRdllasmRQAESQSKLDLISGKTNSeklinawlqLQSAVNELFDST 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 320 LPGLPRAMQKSGrplksIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDR 399
Cdd:cd01435 218 KAPKSGKKSPPG-----IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEE 292
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 400 LQELVRRGNSQYPGAKYIIRDNGDRIDLRFH--------------PKPSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKM 465
Cdd:cd01435 293 LRQAVINGPDVYPGANAIEDEDGRLILLSALseerrkalakllllLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKP 372
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 466 SMMGHRVRILPWS-TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 544
Cdd:cd01435 373 SIMAHKVRVLPGEkTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGV 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 545 KFTKRDVFLERGEVMNLLMF-LSTWDG-------KMPQPAILKPRPLWTGKQIFSLIIpghINVIRTHStHPDDEDS--- 613
Cdd:cd01435 453 LLTSRDTFFTREEYQQLVYAaLRPLFTsdkdgriKLLPPAILKPKPLWTGKQVISTIL---KNLIPGNA-PLLNLSGkkk 528
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 614 ------GPYKHISPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGI 687
Cdd:cd01435 529 tkkkvgGGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGI 608
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 688 GDSI----ADAKTyldiQNTIKKAKQDVIEVIEKAhnneleptpgntlrqtFENQVNRILNDARDKTGSSAQKSLSEYNN 763
Cdd:cd01435 609 EDLLltpkADEKR----RKILRKAKKLGLEAAAEF----------------LGLKLNKVTSSIIKACLPKGLLKPFPENN 668
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 764 FKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGRE 843
Cdd:cd01435 669 LQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGRE 748
|
890 900 910
....*....|....*....|....*....|.
gi 1900307341 844 GLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd01435 749 GLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
25-874 |
7.33e-180 |
|
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: 555.51 E-value: 7.33e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 25 SPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAKPVFHVGFmtkim 102
Cdd:cd00399 2 SPEEIRKWSVAK--VIKPETIDnrTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGF----- 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 103 kimrcvcffcskllvdsnnpkIKEIlvkskgqprkrlthvyelckgkniceggeemdnkfgmepqeqeeditkekghggc 182
Cdd:cd00399 75 ---------------------IKKV------------------------------------------------------- 78
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 183 gryqprirrsglelyaewkhvnedsqekkillspervheifkrisdeediilgmdPKFARPEWMIVTVLPVPPLAVRPAV 262
Cdd:cd00399 79 -------------------------------------------------------PSFLGPEWMILTCLPVPPPCLRPSV 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 263 VmqgsarnqddlthkladivkinnqlrrneqsgaaahvIAEDVKLLQFHVATMVDNELPGLPRAMqKSGRPLKSIKQRLK 342
Cdd:cd00399 104 I-------------------------------------IEERWRLLQEHVDTYLDNGIAGQPQTQ-KSGRPLRSLAQRLK 145
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 343 GKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMtfpeivtpfnidrlqelvrrgnsqypgakyiirdng 422
Cdd:cd00399 146 GKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL------------------------------------ 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 423 dridlrfhpkpsdlhlqigykverhmcDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLH 502
Cdd:cd00399 190 ---------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLH 242
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 503 LPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKrdvflergevmnllmflstwdgkmpqpailkprp 582
Cdd:cd00399 243 VPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL---------------------------------- 288
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 583 lwtGKQIFSLIIPGhinvirthsthpddedsgpykhispgdtkvivengelimgilckkslgtsagSLVHISYLEMGHDI 662
Cdd:cd00399 289 ---GKQIVSAALPG----------------------------------------------------GLLHTVTRELGPEK 313
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 663 TRLFYSNIQTVVNNWLLIEGHSIGIGDSIADAKTYLDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRI 742
Cdd:cd00399 314 AAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDF 393
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 743 LNDARDKTGSSAQKSL---SEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRG 819
Cdd:cd00399 394 LNEARDKAGSAASVNLdlvSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAKG 473
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*
gi 1900307341 820 FVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 874
Cdd:cd00399 474 FIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
828-1425 |
6.24e-177 |
|
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: 546.95 E-value: 6.24e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 828 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGENVEFQNLATL 907
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 908 KPSNKAFEKKFRfdctneralrrvlqEDVVKDVLTNANVQSVLEREfekmredreilraifptgdskvvlpcnlarmiwn 987
Cdd:pfam04998 81 EFSDLKLEDKFK--------------NDLLDDLLLLSEFSLSYKKE---------------------------------- 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 988 aqkifrintrtptdlnplrvvegvqelSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMTEEFRLSTEAYDWLL 1067
Cdd:pfam04998 113 ---------------------------ILVRDSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1068 GEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAAR 1147
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1148 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDVSR--------ISPWLLRIELDRKHM 1219
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1220 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKFQEDEEvvdKMDDDVFLRCIESNMLTDMTLQGI 1299
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDEL---FMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1300 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1378
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 1900307341 1379 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPL 1425
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
244-544 |
2.20e-172 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 525.55 E-value: 2.20e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 244 EWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNElpGL 323
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 324 PRAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQEL 403
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 404 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 482
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1900307341 483 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 544
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
13-352 |
4.79e-143 |
|
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: 446.35 E-value: 4.79e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 13 LRTIKRVQFGVISPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERSGRCQTCAGNMTECPGHFGHIELAK 90
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 91 PVFHVGFMTKIMKIMRCVCFFCSKLLVDSNNPKIKEILVKSKGQ--PRKRLTHVYELCKGKNICEGGEEMDnkfgmepqe 168
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 169 qeeditkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEEDIILGMDPKFARPEWMIV 248
Cdd:pfam04997 150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 249 TVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 328
Cdd:pfam04997 217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
|
330 340
....*....|....*....|....
gi 1900307341 329 KSGRPLKSIKQRLKGKEGRVRGNL 352
Cdd:pfam04997 297 KSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
354-519 |
2.07e-98 |
|
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: 313.47 E-value: 2.07e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 354 GKRVDFSARTVITPDPNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKP 433
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 434 SDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEI 513
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 1900307341 514 QELAMV 519
Cdd:pfam00623 161 EELMLV 166
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
55-878 |
9.21e-97 |
|
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: 330.91 E-value: 9.21e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 55 LMDPRQGVIERSGRCQTC-AGNMTECPGHFGHIELAKPVFHVGFMTKIMKIMRCVCffcskllvdsnnPKIKEILVKSKG 133
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKIC------------PGCKSIKQKKKK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 134 QPRKRLTHVYElckgkNICEGgeemdnkfgmEPQEQEEDITKekghggcgryqprirrsglelyaewkhvnedsqekkil 213
Cdd:cd10506 88 PPRETLPPDYW-----DFIPK----------DGQQEESCVTK-------------------------------------- 114
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 214 LSPERVHEIFKRISDEediilgMDPKFA-----RPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQL 288
Cdd:cd10506 115 NLPILSLAQVKKILKE------IDPKLIakglpRQEGLFLKCLPVPPNCHRVTEFTHGFSTGSRLIFDERTRAYKKLVDF 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 289 RRNEQSGAAAHviaedvkllqfhvatmvdnelpglpramqKSGrpLKSIKQrlkgkegrvrgNLMGKRVDFSARTVITPD 368
Cdd:cd10506 189 IGTANESAASK-----------------------------KSG--LKWMKD-----------LLLGKRSGHSFRSVVVGD 226
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 369 PNLQIDQVGVPRSIAANMTFPEIVTPFNIDRLQELVRRGnsqyPGAKYII--RDNGDRIDLRFHPKpsdlhLQIGYKVER 446
Cdd:cd10506 227 PYLELNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLT----LLLKGVIgvRRNGRLVGVRSHNT-----LQIGDVIHR 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 447 HMCDGDIVIFNRQPTLHKMSMMGHRVRILPW-STFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVT 525
Cdd:cd10506 298 PLVDGDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLIS 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 526 PQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTwdgKMPQPAILK--PR--PLWTGKQIFSLIIPghinvi 601
Cdd:cd10506 378 SQSGQNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKspPSngPLWTGKQLFQMLLP------ 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 602 rthsthPDDEDSGPykhispgDTKVIVENGELIMGiLCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIE 681
Cdd:cd10506 449 ------TDLDYSFP-------SNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMR 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 682 GHSIGIGD------SIADAKTYLDIQNTIKKAKQ----DVIEV----IEKAHNNELEPTPGNTLRQTFENQVN-RILNDA 746
Cdd:cd10506 515 GFSVSLSDlylssdSYSRQKMIEEISLGLREAEIacniKQLLVdsrkDFLSGSGEENDVSSDVERVIYERQKSaALSQAS 594
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 747 RDK-------TGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEGKrIPFGFKH---------RTLPHFIK 810
Cdd:cd10506 595 VSAfkqvfrdIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVK-LSYRIPRqlscaawnsQKSPRVIE 673
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1900307341 811 DDY-----GPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDtavKTAET-GYIQRRLIKSMESVMVKYDATVR 878
Cdd:cd10506 674 KDGsecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
894-1077 |
2.33e-93 |
|
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: 300.18 E-value: 2.33e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 894 LAGENVEFQNLATLKPSNKAFEKKFRFDCTNERA--LRRVLQEDVVKDVLTNANVQSVLEREFEKMREDREILRA-IFPT 970
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREiIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 971 GDSKVV-LPCNLARMIWNAQKIFRINTRTPTDLNPLRVVEGVQELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1049
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 1900307341 1050 RRMTEEFRLSTEAYDWLLGEIETKFNQS 1077
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1052-1475 |
1.10e-87 |
|
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: 291.08 E-value: 1.10e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1052 MTEEFRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKR 1131
Cdd:cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1132 PKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpNPQNTVVaedqewvnvyyempdfdvsrispwllR 1211
Cdd:cd06528 90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI----DLFNMRI--------------------------T 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1212 IELDRKHMTDRKLTMEQIAEKINAGFGDDlncIFNDDNAEKLVLRIrimnsDENKFQEDEEVVDKmdddvflrciesnmL 1291
Cdd:cd06528 140 IELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKA-----EEPSIKELRKLAEK--------------I 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1292 TDMTLQGIEQISKVymhlpqtdnkkkIIITEDGefkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEA 1371
Cdd:cd06528 198 LNTKIKGIKGIKRV------------IVRKEED------EYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEA 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1372 VRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKG 1451
Cdd:cd06528 260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRG 339
|
410 420
....*....|....*....|....
gi 1900307341 1452 VSENIMLGQLAPAGTGCFDLLLDA 1475
Cdd:cd06528 340 VIENIIVGQPIPLGTGDVELTMDP 363
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1054-1477 |
2.09e-85 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 285.20 E-value: 2.09e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1054 EEFRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPK 1133
Cdd:PRK04309 31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1134 TPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaeDqewvnvYYEMpdfdvsrispwLLRIE 1213
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------TIIIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1214 LDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKFQEDEEVVDKmdddvflrciesnmLTD 1293
Cdd:PRK04309 161 LDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK--------------IRN 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1294 MTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1373
Cdd:PRK04309 217 IKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAAR 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1374 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVS 1453
Cdd:PRK04309 279 NAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVT 358
|
410 420
....*....|....*....|....
gi 1900307341 1454 ENIMLGQLAPAGTGCFDLLLDAEK 1477
Cdd:PRK04309 359 ENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1058-1474 |
1.35e-84 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 282.33 E-value: 1.35e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1058 LSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSL 1137
Cdd:TIGR02389 20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1138 TVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqntvvaedqewvnvyyempdfDVSRISpwlLRIELDRK 1217
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VIIELDEE 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1218 HMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNaeklvlrIRIMNSDENKFQEDEEVVDKmdddvflrciesnmLTDMTLQ 1297
Cdd:TIGR02389 150 QLKERGITVDDVEKAIKKAKLGKVIEIDMDNN-------TITIKPGNPSLKELRKLKEK--------------IKNLHIK 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1298 GIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALE 1377
Cdd:TIGR02389 209 GIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAII 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1378 RELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVSENIM 1457
Cdd:TIGR02389 271 EEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENII 350
|
410
....*....|....*..
gi 1900307341 1458 LGQLAPAGTGCFDLLLD 1474
Cdd:TIGR02389 351 VGQPIPLGTGDVDLVMD 367
|
|
| RNA_pol_Rpb1_7 |
pfam04990 |
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1162-1297 |
1.53e-76 |
|
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).
Pssm-ID: 461510 [Multi-domain] Cd Length: 136 Bit Score: 249.76 E-value: 1.53e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1162 TTLRKVTANTAIYYDPNPQNTVVAEDQEWVNVYYEMPDFDV---SRISPWLLRIELDRKHMTDRKLTMEQIAEKINAGFG 1238
Cdd:pfam04990 1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDVedlDRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1900307341 1239 DDLNCIFNDDNAEKLVLRIRIMNSDENKfqeDEEVVDKMDDDVFLRCIESNMLTDMTLQ 1297
Cdd:pfam04990 81 NDLFVIFSDDNAEKLVIRIRIINDEKEK---DEEQEDKAEDDVFLKRLEANMLDSLTLR 136
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
18-1133 |
3.41e-74 |
|
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: 271.54 E-value: 3.41e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 18 RVQFGVISPDELKRMSvtEGGIKYPETT--EGGRPKLGGLMDPR---------------QGVIERSGRCQTCAGNMTECP 80
Cdd:TIGR02386 1 AIKISIASPDTIRNWS--YGEVKKPETInyRTLKPEKDGLFCEKifgptkdwecycgkyKKIRYKGVVCERCGVEVTESK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 81 ---GHFGHIELAKPVFHVGF-------MTKIMKI----MRCVCFFCSKLLVDSNNPKIKEILVKSKGQPRKRLThvyelc 146
Cdd:TIGR02386 79 vrrERMGHIELAAPVAHIWYfkglpsrIGLLLDItakeLESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLK------ 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 147 kgknicEGGEEMDNKFGMEPQE---QEEDITKEkghggcgryqprIRRSGLELyaewKHVNEDSQEKKILlspervheif 223
Cdd:TIGR02386 153 ------RYGDGFRAGMGAEAIKellEKIDLDKE------------IEELKIQL----RESKSDQKRKKLL---------- 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 224 KRISDEEDIIlgmDPKfARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAE 303
Cdd:TIGR02386 201 KRLEIVEAFK---DSG-NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRN 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 304 DVKLLQFHVATMVDNELPGLPrAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIA 383
Cdd:TIGR02386 277 EKRMLQEAVDALFDNGRRGKP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMA 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 384 AnmtfpEIVTPFNIDRLQELvrrgnsqypGAKYIIRDNGDRIdLRFHPKPSDLhlqIGYKVERHMcdgdiVIFNRQPTLH 463
Cdd:TIGR02386 356 L-----ELFKPFIIKRLIDR---------ELAANIKSAKKMI-EQEDPEVWDV---LEDVIKEHP-----VLLNRAPTLH 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 464 KMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDT---- 539
Cdd:TIGR02386 413 RLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMvlgl 492
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 540 --LTAVRKFTKRD--VFLERGEVM----NLLMFLSTWDGKMPQPAILKPRPlwtGKQIFSLIIPghinvirthsthpdde 611
Cdd:TIGR02386 493 yyLTTEKPGAKGEgkIFSNVDEAIraydNGKVHLHALIGVRTSGEILETTV---GRVIFNEILP---------------- 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 612 DSGPYKHIS-PGDTKVIvengelimgilckkslgtsaGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGDS 690
Cdd:TIGR02386 554 EGFPYINDNePLSKKEI--------------------SSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDI 613
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 691 IadakTYLDIQNTIKKAKQDVIEVIEKAHNNELepTPGNTLRQTFEnqvnrILNDARDKTGSSAQKSLS----EYNNFKS 766
Cdd:TIGR02386 614 V----VPDEKYEILKEADKEVAKIQKFYNKGLI--TDEERYRKVVS-----IWSETKDKVTDAMMKLLKkdtyKFNPIFM 682
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 767 MVVAGSKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenSYLAGLTPTEFFFHAMGGREGL 845
Cdd:TIGR02386 683 MADSGARGNISQFRQLAGMRGlMAKPSGDIIELPIKS---------------------SFREGLTVLEYFISTHGARKGL 741
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 846 IDTAVKTAETGYIQRRLIKSMESVMVKY-DATVRNSInQVVQLRYGEDGLagenvefqnLATLKpsnkafekkfrfdctn 924
Cdd:TIGR02386 742 ADTALKTADSGYLTRRLVDVAQDVVVREeDCGTEEGI-EVEAIVEGKDEI---------IESLK---------------- 795
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 925 ERALRRVLQEDVVKDVltnaNVQSVLEREFEKmreDREILRAIFPTGDSKV----VLPCNLARMIwnAQKIFRINtrtpt 1000
Cdd:TIGR02386 796 DRIVGRYSAEDVYDPD----TGKLIAEANTLI---TEEIAEKIENSGIEKVkvrsVLTCESEHGV--CQKCYGRD----- 861
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1001 dlnplrvvegvqelskklvivngddplsrqaqenatllfnihlrstlcsrrmteefrLSTEAydwllgEIETkfnqsiah 1080
Cdd:TIGR02386 862 ---------------------------------------------------------LATGK------LVEI-------- 870
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*
gi 1900307341 1081 pGEMVGALAAQSLGEPATQMTLNTFHYAGVSA--KNVTLGVPRLKELINiSKRPK 1133
Cdd:TIGR02386 871 -GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPK 923
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1073-1469 |
2.43e-69 |
|
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: 235.96 E-value: 2.43e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1073 KFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQaaRDAERA 1152
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLEND--RDEKSA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1153 KDILCRLEHTTLRKVTANTAIYYDPNpqntvvaedqewvNVYyempdfdvsrispwlLRIELDRKHMTDRKLTMEQIAEK 1232
Cdd:cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPD-------------DCY---------------ILIKLDKKIIEKLQLSKSNLYFL 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1233 INagfgddlncifnddnaeklvlririmnsdenkfqedeevvdkmdddvFLRciesNMLTDMTLQGIEQISKVYMHLPQT 1312
Cdd:cd02736 131 LQ-----------------------------------------------SLK----RKLPDVVVSGIPEVKRAVINKDKK 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1313 DNKKKIIItEDGEFKAlqewILETDGVslmrvlsekdvDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVN 1392
Cdd:cd02736 160 KGKYKLLV-EGYGLRA----VMNTPGV-----------IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSID 223
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1900307341 1393 YRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVSENIMLGQLAPAGTGCF 1469
Cdd:cd02736 224 PRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1051-1472 |
5.09e-69 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 242.41 E-value: 5.09e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1051 RMTEEFRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISK 1130
Cdd:PRK14897 151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1131 RPKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVtANTAIyydpnpqntvvaedqewvnvyyempdfDVSRISpwlL 1210
Cdd:PRK14897 231 KPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDV-ADIIT---------------------------DIAEMS---V 279
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1211 RIELDRKHMTDRKLTMEQIAEKInagfgddlncifnddnaEKLVLRIRIMNSDENKFQEDEEVVDKmdddvfLRCIESNm 1290
Cdd:PRK14897 280 VVELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDDGIIRLKPQQPSFKK------LYLLAEK- 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1291 LTDMTLQGIEQISKVymhlpqtdnkkkIIITEDGEfkalQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIE 1370
Cdd:PRK14897 336 VKSLTIKGIKGIKRA------------IARKENDE----RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIE 399
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1371 AVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLMEASSHGECDPMK 1450
Cdd:PRK14897 400 AARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLA 479
|
410 420
....*....|....*....|..
gi 1900307341 1451 GVSENIMLGQLAPAGTGCFDLL 1472
Cdd:PRK14897 480 GVAENIIVGQPITLGTGAVSLV 501
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
18-1112 |
6.15e-63 |
|
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: 236.60 E-value: 6.15e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 18 RVQFGVISPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIersgrCQTCAGN 75
Cdd:COG0086 9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 76 MTECP---GHFGHIELAKPVFHVGFMTKIMKIMRcvcffcskLLVDSNNPKIKEIL-------VKSKGQPRKRLTHVYEL 145
Cdd:COG0086 82 VTLSKvrrERMGHIELAMPVFHIWGLKSLPSRIG--------LLLDMSLRDLERVLyfesyvvIDPGDTPLEKGQLLTED 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 146 CKGKNICEGGEEMDNKFGMEP-QEQEEDITKEKGHGgcgryqprirrsglELYAEWKHVNedSQEKKIllspervhEIFK 224
Cdd:COG0086 154 EYREILEEYGDEFVAKMGAEAiKDLLGRIDLEKESE--------------ELREELKETT--SEQKRK--------KLIK 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 225 RIsdeeDIILGMDPKFARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAED 304
Cdd:COG0086 210 RL----KVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNE 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 305 VKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIA 383
Cdd:COG0086 286 KRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 384 AnmtfpEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqigykverhmcdgdiVIF 456
Cdd:COG0086 364 L-----ELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------------VLL 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 457 NRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQS 528
Cdd:COG0086 414 NRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPAN 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 529 NRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKMPQPAILKPRPLWTGKQ------------ 588
Cdd:COG0086 486 GKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgkivettvgry 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 589 IFSLIIP---GHINvirthsthpddedsgpykhispgdtKVIvengelimgilCKKSLGTsagsLVHISYLEMGHDITRL 665
Cdd:COG0086 561 LVNEILPqevPFYN-------------------------QVI-----------NKKHIEV----IIRQMYRRCGLKETVI 600
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 666 FYSNIQTVVNNWLLIEGHSIGIGDSIADAKTyldiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfENQVNRILND 745
Cdd:COG0086 601 FLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTK 669
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 746 ARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenS 824
Cdd:COG0086 670 ASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS---------------------N 728
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 825 YLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGEDglagenVEfqn 903
Cdd:COG0086 729 FREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEGGE------VI--- 798
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 904 lATLKpsnkafekkfrfdctnERALRRVLQEDVVKDVLTNANVQSVLEREFEkmredreilraifptgdskvvlpcnlar 983
Cdd:COG0086 799 -EPLK----------------ERILGRVAAEDVVDPGTGEVLVPAGTLIDEE---------------------------- 833
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 984 miwnaqkifrintrtptdlnplrVVEGVQELSKKLVIVngddplsrqaqenatllfnihlRSTLCsrrMTEEFRLSTEAY 1063
Cdd:COG0086 834 -----------------------VAEIIEEAGIDSVKV----------------------RSVLT---CETRGGVCAKCY 865
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....*....
gi 1900307341 1064 DWLLGEiETKFNQsiahpGEMVGALAAQSLGEPATQMTLNTFHYAGVSA 1112
Cdd:COG0086 866 GRDLAR-GHLVNI-----GEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS 908
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
523-689 |
4.59e-62 |
|
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 209.02 E-value: 4.59e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 523 IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwdgKMPQPAILKP-RPLWTGKQIFSLIIPGHINVI 601
Cdd:pfam04983 2 ILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 602 RTHSTHPDDEdsgpykhiSPGDTKVIVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIE 681
Cdd:pfam04983 78 GKPKTNEEDL--------CENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKS 149
|
....*...
gi 1900307341 682 GHSIGIGD 689
Cdd:pfam04983 150 GFSIGIDD 157
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
20-1114 |
1.11e-61 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 235.20 E-value: 1.11e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 20 QFGVISPDELkrMSVTEGGIKYPETT--EGGRPKLGGLM-------------------DPR-QGViersGRCQTCAGNMT 77
Cdd:PRK09603 1400 QLTLASPEKI--HSWSYGEVKKPETInyRTLKPERDGLFcmkifgptkdyeclcgkykKPRfKDI----GTCEKCGVAIT 1473
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 78 ECP---GHFGHIELAKPVFHVGFmtkimkimrcvcffcskllVDSNNPKIKEILvkskGQPRKRLTHV--YELCKGKNIC 152
Cdd:PRK09603 1474 HSKvrrFRMGHIELATPVAHIWY-------------------VNSLPSRIGTLL----GVKMKDLERVlyYEAYIVKEPG 1530
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 153 EG-----GEEMDNKFGMEPQEQEEDITKEKGHGG-CGRYQPRIRRSGLE----------LYAEWKHVNEDSQEKKILlsp 216
Cdd:PRK09603 1531 EAaydneGTKLVMKYDILNEEQYQNISRRYEDRGfVAQMGGEAIKDLLEeidlitllqsLKEEVKDTNSDAKKKKLI--- 1607
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 217 ervheifKRISDEEDIILGMDpkfaRPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGA 296
Cdd:PRK09603 1608 -------KRLKVVESFLNSGN----RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGA 1676
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 297 AAHVIAEDVKLLQFHVATMVDNelpGLPRAMQKSG--RPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQID 374
Cdd:PRK09603 1677 PEIIVRNEKRMLQEAVDVLFDN---GRSTNAVKGAnkRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMD 1753
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 375 QVGVPRSIAANMTFPEIvtpfnidrLQELVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqigYKVERHMCDGDI 453
Cdd:PRK09603 1754 ECGLPKNMALELFKPHL--------LSKLEERGYaTTLKQAKRMIEQKSNEV----------------WECLQEITEGYP 1809
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 454 VIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVM 533
Cdd:PRK09603 1810 VLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVA 1889
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 534 GIVQDTLTAVRKFT--KRDVFLER---GEVMNLLMFLST--WDGKMPQPAILKPRPLWT--GKQIFSLIIPGHINVirth 604
Cdd:PRK09603 1890 IPSQDMVLGLYYLSleKSGVKGEHklfSSVNEIITAIDTkeLDIHAKIRVLDQGNIIATsaGRMIIKSILPDFIPT---- 1965
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 605 sthpddedsgpykhispgdtkvivengELIMGILCKKSLGTsagsLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHS 684
Cdd:PRK09603 1966 ---------------------------DLWNRPMKKKDIGV----LVDYVHKVGGIGITATFLDNLKTLGFRYATKAGIS 2014
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 685 IgigdSIADAKTYLDIQNTIKKAKQDVIEViekahnnELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSE---- 760
Cdd:PRK09603 2015 I----SMEDIITPKDKQKMVEKAKVEVKKI-------QQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKdkeg 2083
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 761 YNNFKSMVVAGSKGSKINISQVIAVVGqqnVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFFFHAMG 840
Cdd:PRK09603 2084 FNSIYMMADSGARGSAAQIRQLSAMRG---LMTK--PDGSIIET----------PIISNFKE-----GLNVLEYFNSTHG 2143
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 841 GREGLIDTAVKTAETGYIQRRLIKSMESVMVKYdatvrnsinqvvqlrygEDGLAGENVEFQNLATLKPSNKAFEkkfrf 920
Cdd:PRK09603 2144 ARKGLADTALKTANAGYLTRKLIDVSQNVKVVS-----------------DDCGTHEGIEITDIAVGSELIEPLE----- 2201
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 921 dctnERALRRVLQEDVVkDVLTNanvqsvlerefekmredrEILRAifptgdSKVVLPCNLARMIwnaqkifrintrtpt 1000
Cdd:PRK09603 2202 ----ERIFGRVLLEDVI-DPITN------------------EILLY------ADTLIDEEGAKKV--------------- 2237
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1001 dlnplrvvegvQELSKKLVIVNgdDPLSRQAQENatllfnihlrstLCSRrmteefrlsteAYDWLLGEietkfnQSIAH 1080
Cdd:PRK09603 2238 -----------VEAGIKSITIR--TPVTCKAPKG------------VCAK-----------CYGLNLGE------GKMSY 2275
|
1130 1140 1150
....*....|....*....|....*....|....
gi 1900307341 1081 PGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKN 1114
Cdd:PRK09603 2276 PGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
242-872 |
1.16e-58 |
|
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 215.85 E-value: 1.16e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 242 RPEWMIVTVLPVPPLAVRPAVVMQG-----SARNqdDLTHKladIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMV 316
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGgrfatSDLN--DLYRR---VINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALI 212
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 317 DNELPGLPrAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVTPFN 396
Cdd:cd01609 213 DNGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMAL-----ELFKPFV 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 397 IdrlQELVRRGNSQYP-GAKYIIRDNGDRIdlrfhpkpsdlhlqigYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRIL 475
Cdd:cd01609 287 I---RELIERGLAPNIkSAKKMIERKDPEV----------------WDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLI 347
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 476 PWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDtltavrkftkrdvfler 555
Cdd:cd01609 348 EGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQD----------------- 410
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 556 gevMNLLMFLSTWDGKMPQPA-ILKPRPlwtGKQIFSLIIPghinvirthsthpddedsgpykhispgdtkvivENGELI 634
Cdd:cd01609 411 ---MVLGLYYLTKERKGDKGEgIIETTV---GRVIFNEILP---------------------------------EGLPFI 451
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 635 MGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIGD-SIADAKtyldiQNTIKKAKQDVIE 713
Cdd:cd01609 452 NKTLKKKVL----KKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDiVVPPEK-----KEIIKEAEEKVKE 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 714 vIEKAHNNeleptpGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEY--NNFKSMVVAGSKGSKINISQVIAVVG-QQN 790
Cdd:cd01609 523 -IEKQYEK------GLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDpfNPIYMMADSGARGSKSQIRQLAGMRGlMAK 595
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 791 VEGKRIPfgfkhrtLPhfIKDdygpesrgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVM 870
Cdd:cd01609 596 PSGKIIE-------LP--IKS------------NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVI 654
|
..
gi 1900307341 871 VK 872
Cdd:cd01609 655 VT 656
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1098-1476 |
3.68e-56 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 212.06 E-value: 3.68e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1098 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKRPKTPSLTVFLLGQAARDAERAKDILCRLEHTTLRKVTANTAIyydp 1177
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI---- 616
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1178 npqntvvaedqewvnvyyempDFDVSRIspwllRIELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRI 1257
Cdd:PRK14898 617 ---------------------DLWTQSI-----KVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYL 663
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1258 RImnsDENKFQEDEEVVDKmdddvflrciesnmLTDMTLQGIEQISKVYMHLPQTDNKkkiiitedgefkalQEWILETD 1337
Cdd:PRK14898 664 KP---KTPSYKALRKRIPK--------------IKNIVLKGIPGIERVLVKKEEHEND--------------EEYVLYTQ 712
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1338 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGI 1417
Cdd:PRK14898 713 GSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGV 792
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 1900307341 1418 NRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVSENIMLGQLAPAGTGCFDLLLDAE 1476
Cdd:PRK14898 793 AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDRE 851
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1073-1472 |
9.18e-54 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 191.25 E-value: 9.18e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1073 KFNQSIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKE-LINISKRPKTPSLTV-FLLGQAARDAE 1150
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREiLMTASKNIKTPSMTLpLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1151 RAK---------DILCRLEHTTLRKVTANTAIyydpnPQNtvvaedQEWVNVYYEMPdfdvsrispwllrieLDRKhmtd 1221
Cdd:cd02735 81 TLKkrlsrvtlsDVVEKVEVTEILKTIERVFK-----KLL------GKWCEVTIKLP---------------LSSP---- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1222 rKLTMEQIAEKInagfgddlncifnddnAEKLVLRirimnsdenkfqedeEVvdkmdddvflrciesnmltdmtlQGIEQ 1301
Cdd:cd02735 131 -KLLLLSIVEKL----------------ARKAVIR---------------EI-----------------------PGITR 155
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1302 ISKVYmhlpqTDNKKKiiitedgefkalQEWILETDGVSL--MRVLSEKdVDPVRTTSNDIVEIFTVLGIEAVRKALERE 1379
Cdd:cd02735 156 CFVVE-----EDKGGK------------TKYLVITEGVNLaaLWKFSDI-LDVNRIYTNDIHAMLNTYGIEAARRAIVKE 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1380 LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGInRQDTGPLMKCSFEETVDVLMEASSHGECDPMKGVSENIMLG 1459
Cdd:cd02735 218 ISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVG 296
|
410
....*....|...
gi 1900307341 1460 QLAPAGTGCFDLL 1472
Cdd:cd02735 297 KPVNGGTGLFDLL 309
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
14-1467 |
1.04e-53 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 209.09 E-value: 1.04e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 14 RTIKRVQFGVISPDELKRMS------VTEGGIKYPETTEGGR--PKLGGLMDPRQGVIER------SGR-CQTCAGNMTE 78
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSygeiedVSTANYRTFKVEKGGLfcPKIFGPVNDDECLCGKykkrrhRGRiCEKCGVEVTS 1525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 79 CP---GHFGHIELAKPVFHVGFMTKIMKIMRCvcffcsklLVDSNNPKIKEILVKSKGQPRKRLTHVYElcKGKNICEGG 155
Cdd:PRK14844 1526 SKvrrERMGHIELASPVAHIWFLKSLPSRIGA--------LLDMSLRDIENILYSDNYIVIDPLVSPFE--KGEIISEKA 1595
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 156 -EEMDNKFGMEP-------QEQEEDITKEKGHggcgryqpRIRRsglELYAEWKHVNEDSQEKKILlspervheifKRIS 227
Cdd:PRK14844 1596 yNEAKDSYGIDSfvamqgvEAIRELLTRLDLH--------EIRK---DLRLELESVASEIRRKKII----------KRLR 1654
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 228 DEEDIILGMDpkfaRPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKL 307
Cdd:PRK14844 1655 IVENFIKSGN----RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRM 1730
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 308 LQFHVATMVDNELPGlpRAMQKSGRP--LKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAn 385
Cdd:PRK14844 1731 LQEAVDSLFDNSRRN--ALVNKAGAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMAL- 1807
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 386 mtfpEIVTPFNIDRLQELVRRGNSQYpgAKYIIRDNgdridlrfHPKPSDLHLQIgykVERHMcdgdiVIFNRQPTLHKM 465
Cdd:PRK14844 1808 ----ELFKPFVYSKLKMYGMAPTIKF--ASKLIRAE--------KPEVWDMLEEV---IKEHP-----VLLNRAPTLHRL 1865
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 466 SMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRK 545
Cdd:PRK14844 1866 GIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYY 1945
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 546 FT----KRD---VFLERGEVMNllmflSTWDGKMpqpailkprplwtgkqifsliipgHINV-IRTHSTHPDDEDSGPYK 617
Cdd:PRK14844 1946 LTlqepKEDdlpSFGAFCEVEH-----SLSDGTL------------------------HIHSsIKYRMEYINSSGETHYK 1996
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 618 HISPGDTKVIV-------EN--GELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVVNNWLLIEGHSIGIG 688
Cdd:PRK14844 1997 TICTTPGRLILwqifpkhENlgFDLINQVLTVKEI----TSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRC 2072
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 689 D-SIADAK-TYLD-IQNTIKKAK---QDVIEVIEKAHNNELEptpgntlrqTFENQVNRILNDARDKTgsSAQKSLSEYN 762
Cdd:PRK14844 2073 DmVIPETKaTHVDhARGEIKKFSmqyQDGLITRSERYNKVID---------EWSKCTDMIANDMLKAI--SIYDGNSKYN 2141
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 763 NFKSMVVAGSKGSKiniSQVIAVVGQQNVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFFFHAMGGR 842
Cdd:PRK14844 2142 SVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIISNFRE-----GLNVFEYFNSTHGAR 2201
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 843 EGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSInqVVQlrygedglagenvefqnlATLKPSnkafekkfrfd 921
Cdd:PRK14844 2202 KGLADTALKTANSGYLTRRLVDvSQNCIVTKHDCKTKNGL--VVR------------------ATVEGS----------- 2250
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 922 cTNERALRRVLQEDVVKDVLTNANVQSVLEREFEKMREDReilraifptgdskvVLPCNLARMiwnaqKIFRINTRTPTD 1001
Cdd:PRK14844 2251 -TIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDK--------------VKQINIAGL-----DVVKIRSPLTCE 2310
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1002 LNPlrvveGVqelskklvivngddplsrqaqenatllfnihlrSTLCSRRmteefrlsteayDWLLGEIetkfnQSIahp 1081
Cdd:PRK14844 2311 ISP-----GV---------------------------------CSLCYGR------------DLATGKI-----VSI--- 2332
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1082 GEMVGALAAQSLGEPATQMTLNTFHYAGVsaknVTLGVPRLKELINISKRPKTPSLTVFLLGQAARDA-ERAKDILC--- 1157
Cdd:PRK14844 2333 GEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIViSRSCEVVLids 2408
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1158 ----RLEHTtlrkVTANTAIYYDPNPQNTVVAEDQEW-------------VNVYYEMPD-------FDVSR------ISP 1207
Cdd:PRK14844 2409 lgseKLKHS----VPYGAKLYVDEGGSVKIGDKVAEWdpytlpiitektgTVSYQDLKDgisitevMDESTgisskvVKD 2484
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1208 WLL---------RIELdrkhMTDRKLTMeQIAEKINAGFGDDLNCIFNDDNAEK-----LVLRI---------------R 1258
Cdd:PRK14844 2485 WKLysgganlrpRIVL----LDDNGKVM-TLASGVEACYFIPIGAVLNVQDGQKvhagdVITRTpresvktrditgglpR 2559
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1259 IMNSDENKFQEDEEVVDKMDDDVFLRCIESNMLTDMTLQGI-EQISKVYMHLpqtdNKKKIIITEDGEFkaLQEWILETD 1337
Cdd:PRK14844 2560 VIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVdEQISPVEYLV----SRSKHVIVNEGDF--VRKGDLLMD 2633
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1338 GvslmrvlsekdvDPvrttsnDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTM------TCRGHLMA 1411
Cdd:PRK14844 2634 G------------DP------DLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMlqkveiTDPGDTMY 2695
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1412 ITRHGINR----------QDTG-------PLMK---------------CSFEETVDVLMEASSHGECDPMKGVSENIMLG 1459
Cdd:PRK14844 2696 LVGESIDKlevdrendamSNSGkrpahylPILQgitrasletssfisaASFQETTKVLTEAAFCGKSDPLSGLKENVIVG 2775
|
....*...
gi 1900307341 1460 QLAPAGTG 1467
Cdd:PRK14844 2776 RLIPAGTG 2783
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
242-1130 |
1.24e-53 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 207.80 E-value: 1.24e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 242 RPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNELP 321
Cdd:PRK14906 311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 322 GLPrAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVTPFNIDRLQ 401
Cdd:PRK14906 391 GRP-VTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMAL-----ELFKPFVMKRLV 464
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 402 ELVRRGNSQypGAKYIIrdngdridlrfhpkpsDLHLQIGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFR 481
Cdd:PRK14906 465 ELEYAANIK--AAKRAV----------------DRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIK 526
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 482 LNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT-KRDVFLERGEVmn 560
Cdd:PRK14906 527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDGFEGEGRT-- 604
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 561 llmFLSTWDGKMpqpAILKPRPLWTGKQIFsliipghINVIRTHSTHPDDEDSGPYKHISPGDTKVivenGELIMGILCK 640
Cdd:PRK14906 605 ---FADFDDALN---AYDARADLDLQAKIV-------VRLSRDMTVRGSYGDLEETKAGERIETTV----GRIIFNQVLP 667
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 641 KSLGtsagslvHISYLEMGHDITRLfysnIQTVVNNWLLIEGHSI---------------GIGDSIADAKTYLDIQNTIK 705
Cdd:PRK14906 668 EDYP-------YLNYKMVKKDIGRL----VNDCCNRYSTAEVEPIldgikktgfhyatraGLTVSVYDATIPDDKPEILA 736
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 706 KAKQDVIEVIEKAHNNELEPtpgntlrQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAV 785
Cdd:PRK14906 737 EADEKVAAIDEDYEDGFLSE-------RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGM 809
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 786 VG-QQNVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLik 864
Cdd:PRK14906 810 RGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRL-- 866
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 865 smesVMVKYDATVRNsinqvvqlrygEDGLAGENVEFqnlATLKPSNKafekkfrfdcTNERALRRVLQEDVVKdvltna 944
Cdd:PRK14906 867 ----VDVAQDVIVRE-----------EDCGTDEGVTY---PLVKPKGD----------VDTNLIGRCLLEDVCD------ 912
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 945 nvqsvlerefekmrEDREILraiFPTGDskvvlpcnlarmiwnaqkifrintrtptdlnplrvvegvqelskklvIVNGD 1024
Cdd:PRK14906 913 --------------PNGEVL---LSAGD-----------------------------------------------YIESM 928
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1025 DPLSRQAQENATllfNIHLRSTLCSRrmtEEFRLSTEAYDWLLgeietkfnqSIAHP---GEMVGALAAQSLGEPATQMT 1101
Cdd:PRK14906 929 DDLKRLVEAGVT---KVQIRTLMTCH---AEYGVCQKCYGWDL---------ATRRPvniGTAVGIIAAQSIGEPGTQLT 993
|
890 900
....*....|....*....|....*....
gi 1900307341 1102 LNTFHYAGVSAKNVTLGVPRLKELINISK 1130
Cdd:PRK14906 994 MRTFHSGGVAGDDITQGLPRVAELFEARK 1022
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
242-1135 |
5.52e-50 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 195.29 E-value: 5.52e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 242 RPEWMIVTVLPVPPLAVRPAVVMQG-----SARNqdDLTHKLadivkI--NNQLRRNEQSGAAAHVIAEDVKLLQFHVAT 314
Cdd:PRK00566 223 KPEWMILDVLPVIPPDLRPLVQLDGgrfatSDLN--DLYRRV-----InrNNRLKRLLELGAPEIIVRNEKRMLQEAVDA 295
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 315 MVDNELPGlpRAMQ-KSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVT 393
Cdd:PRK00566 296 LFDNGRRG--RPVTgPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL-----ELFK 368
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 394 PFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqigykverhmcdgdiVIFNRQP 460
Cdd:PRK00566 369 PFIMKKLVErglattiksakkMVEREDPEvWDVLEEVIKE---------HP----------------------VLLNRAP 417
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 461 TLHKMSMM--------GHRVRILPwstfrLnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPV 532
Cdd:PRK00566 418 TLHRLGIQafepvlieGKAIQLHP-----L---VCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPI 489
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 533 mgIV--QD------TLTAVRKFTKrdvflerGEVMnllMFLSTWD-----------------GKMPQPAILKPRPlwtGK 587
Cdd:PRK00566 490 --IVpsQDmvlglyYLTREREGAK-------GEGM---VFSSPEEalrayengevdlharikVRITSKKLVETTV---GR 554
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 588 QIFSLIIPGHInvirthsthpddedsgPYkhispgdtkvivENGELIMGilcKKSLgtsaGSLVHISYLEMGHDITRLFY 667
Cdd:PRK00566 555 VIFNEILPEGL----------------PF------------INVNKPLK---KKEI----SKIINEVYRRYGLKETVIFL 599
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 668 SNIQTVVNNWLLIEGHSIGIGD-SIADAKtyldiQNTIKKAKQDVIEvIEKAHNNELeptpgntlrQTFE---NQVNRIL 743
Cdd:PRK00566 600 DKIKDLGFKYATRSGISIGIDDiVIPPEK-----KEIIEEAEKEVAE-IEKQYRRGL---------ITDGeryNKVIDIW 664
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 744 NDARDKTGSSAQKSLSEYNN-FKS---MVVAGSKGSKINISQVIAVVG-QQNVEGKRIPfgfkhrtLPhfIKddygpesr 818
Cdd:PRK00566 665 SKATDEVAKAMMKNLSKDQEsFNPiymMADSGARGSASQIRQLAGMRGlMAKPSGEIIE-------TP--IK-------- 727
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 819 gfveNSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLiksmesVMVKYDATVRN----SINQVVQLRYGEDGL 894
Cdd:PRK00566 728 ----SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVREddcgTDRGIEVTAIIEGGE 797
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 895 AGENVEfqnlatlkpsnkafekkfrfdctnERALRRVLQEDVV----KDVLTNANvqsvlerefEKMREDReilraifpt 970
Cdd:PRK00566 798 VIEPLE------------------------ERILGRVLAEDVVdpetGEVIVPAG---------TLIDEEI--------- 835
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 971 gdskvvlpcnlarmiwnAQKIfrintrtptdlnplrVVEGVQElskklvivngddplsrqaqenatllfnIHLRSTL-Cs 1049
Cdd:PRK00566 836 -----------------ADKI---------------EEAGIEE---------------------------VKIRSVLtC- 855
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1050 rrmteefrlsteaydwllgeiETKF---------NQSIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVsakNVTL 1117
Cdd:PRK00566 856 ---------------------ETRHgvcakcygrDLATGKLvniGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITG 911
|
970
....*....|....*...
gi 1900307341 1118 GVPRLKELINiSKRPKTP 1135
Cdd:PRK00566 912 GLPRVAELFE-ARKPKGP 928
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
715-821 |
1.50e-44 |
|
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: 157.14 E-value: 1.50e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 715 IEKA-HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVAGSKGSKINISQVIAVVGQQNVEG 793
Cdd:pfam05000 1 ITDAeRYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 1900307341 794 KRIPFGFKHRTLPHFIKDDYGPESRGFV 821
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
241-538 |
1.02e-41 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 164.54 E-value: 1.02e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 241 ARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQSGAAAHVIAEDVKLLQFHVATMVDNEL 320
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 321 PGlPRAMQKSGRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVPRSIAAnmtfpEIVTPFNIDRl 400
Cdd:PRK02625 320 RG-RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAI-----ELFQPFVIHR- 392
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 401 qeLVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqigYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST 479
Cdd:PRK02625 393 --LIRQGIvNNIKAAKKLIQRADPEV----------------WQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 1900307341 480 FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD 538
Cdd:PRK02625 455 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
84-512 |
1.60e-41 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 164.31 E-value: 1.60e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 84 GHIELAKPVFHVGFMtkimKIMRCvcfFCSKLLvdsnNPKIKEI--LVKSKGQPRKRLTHVYELCKGKNICEGG----EE 157
Cdd:CHL00018 105 GYIKLACPVTHVWYL----KRLPS---YIANLL----DKPLKELegLVYCDFSFARPIAKKPTFLRLRGLFEYEiqswKY 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 158 MDNKFgMEPQEQEEDITKEKGHGGcgryqPRIRR--SGLEL-------YAEWKHVNEDSQ------EKKIllsPERVHEI 222
Cdd:CHL00018 174 SIPLF-FSTQGFDTFRNREISTGA-----GAIREqlADLDLriiidnsLVEWKELGEEGStgneweDRKI---GRRKDFL 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 223 FKRISDEEDIILgmdpKFARPEWMIVTVLPVPPLAVRPAVVMQGSARNQDDLTHKLADIVKINNQLRR-NEQSGAAAH-V 300
Cdd:CHL00018 245 VRRIKLAKHFIR----TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDlLTTSRSTPGeL 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 301 IAEDVKLLQFHVATMVDNELPGLPraMQKS-GRPLKSIKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLQIDQVGVP 379
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQP--MRDGhNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLP 398
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 380 RSIAAnmtfpEIVTPFNIdrlQELVRRGNSQYPG-AKYIIRDNGdridlrfhpkpsdlhlQIGYKVERHMCDGDIVIFNR 458
Cdd:CHL00018 399 REIAI-----ELFQPFVI---RGLIRQHLASNIRaAKSKIREKE----------------PIVWEILQEVMQGHPVLLNR 454
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1900307341 459 QPTLHKMSMM--------GHRVRILPwstfrlnlSVTTPYNADFDGDEMNLHLPQSLETRAE 512
Cdd:CHL00018 455 APTLHRLGIQafqpilveGRAICLHP--------LVCKGFNADFDGDQMAVHVPLSLEAQAE 508
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1359-1468 |
9.08e-37 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 136.78 E-value: 9.08e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1359 DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDTGPLMKCSFEETVDVLM 1438
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 1900307341 1439 EASSHGECDPMKGVSENIMLGQLAPAGTGC 1468
Cdd:cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1082-1129 |
4.66e-21 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 91.71 E-value: 4.66e-21
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1900307341 1082 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1129
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1854-1954 |
1.39e-15 |
|
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: 83.04 E-value: 1.39e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1854 TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1933
Cdd:pfam05109 521 TSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVGETSP 600
|
90 100
....*....|....*....|.
gi 1900307341 1934 KGSTYSPTSPGYSPTSPTYSP 1954
Cdd:pfam05109 601 QANTTNHTLGGTSSTPVVTSP 621
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
762-1115 |
8.14e-13 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 74.26 E-value: 8.14e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 762 NNFKS---------MVVAGSKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 828
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 829 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGENVEFQNlatl 907
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 908 kpsnkafekkfrfdctneRALRRVLQEDVV---KDVLTNANvqsvlerefekmredreilRAIFPtgdskvvlpcNLARM 984
Cdd:PRK02597 238 ------------------RLLGRVLAEDVVdpeGEVIAERN-------------------TAIDP----------DLAKK 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 985 IWNAqkifrintrtptdlnplrvveGVQElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmteefrlsteAYD 1064
Cdd:PRK02597 271 IEKA---------------------GVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYG 299
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1900307341 1065 WllgeietkfnqSIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1115
Cdd:PRK02597 300 W-----------SLAHNhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
762-1115 |
3.31e-12 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 72.19 E-value: 3.31e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 762 NNFKSMVVAGSKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFH 837
Cdd:TIGR02388 119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 838 AMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqvvQLRYGEDGlaGENVEFQNlatlkpsnkafek 916
Cdd:TIGR02388 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTERSI----VVRAMTEG--DKKISLGD------------- 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 917 kfrfdctneRALRRVLQEDVVKdvltnanvqsvlerefekmredreilraifPTGDskVVLPCNlarmiwnaqkifrint 996
Cdd:TIGR02388 236 ---------RLLGRLVAEDVLH------------------------------PEGE--VIVPKN---------------- 258
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 997 rTPTDlnplrvvegvQELSKKLVivngddplsrqaqenATLLFNIHLRSTLCSRRMTEEFRLsteAYDWllgeietkfnq 1076
Cdd:TIGR02388 259 -TAID----------PDLAKTIE---------------TAGISEVVVRSPLTCEAARSVCRK---CYGW----------- 298
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 1900307341 1077 SIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1115
Cdd:TIGR02388 299 SLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1513-1612 |
5.21e-12 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 64.47 E-value: 5.21e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1513 PAMTP-WNTGA--TPAYGAWSPSVGSGMTPGAAGFSPSA------------ASDASGFSPGYSPAWSP--TPGSPGSPGP 1575
Cdd:smart01104 1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRtpawggagsrtpAWGGAGPTGSRTPAWGGasAWGNKSSEGS 80
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 1900307341 1576 VSPYIPSPG---GAMSPNYSPTSPAYEPRSPGGYTPQSPG 1612
Cdd:smart01104 81 ASSWAAGPGgayGAPTPGYGGTPSAYGPATPGGGAMAGSA 120
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1077-1125 |
6.27e-11 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 63.70 E-value: 6.27e-11
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1900307341 1077 SIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVsAKNVTLGVPRLKEL 1125
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEEL 48
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1852-1966 |
1.83e-10 |
|
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: 66.48 E-value: 1.83e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1852 TPTSPKYSPTSPKYSPT----SPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPT 1927
Cdd:pfam05109 536 SPTLGKTSPTSAVTTPTpnatSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVGETSPQANTTNHTLGGTSST 615
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1928 YSPTS-PKGSTYSPTSPGYSPTSPTYSP----------AISPDDSDEENN 1966
Cdd:pfam05109 616 PVVTSpPKNATSAVTTGQHNITSSSTSSmslrpssiseTLSPSTSDNSTS 665
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1495-1595 |
6.65e-10 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 58.69 E-value: 6.65e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1495 GPTGMFFGSVPSPmsGMSPAMTP-WN--TGATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSPAW-SPT 1566
Cdd:smart01104 21 TPGTAAGGAPTAR--GGSGSRTPaWGgaGSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGGAYgAPT 96
|
90 100
....*....|....*....|....*....
gi 1900307341 1567 PGSPGSPGPVSPyiPSPGGAMspNYSPTS 1595
Cdd:smart01104 97 PGYGGTPSAYGP--ATPGGGA--MAGSAS 121
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1082-1473 |
1.64e-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: 62.05 E-value: 1.64e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1082 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAknvtlgVPRLKELI--NISKRPKTPSLTVFLLGQAARDA------ERAK 1153
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESSP------LELLKEVLecRSKSKSKENDRRVILSLHLCKCDhgfeyeRAAL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1154 DILCRLEHTTLRKVTANTAIYYDPNPQntvvaedqewvnvyyEMPDFDVSRISPWLLRIELDRKHMTDRKLTmeqiaeKI 1233
Cdd:cd02737 75 EVKNHLERVTLEDLATTSMIKYSPQAT---------------EAIVGEIGDQLNTKKKGKKKAIFSTSLKIT------KF 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1234 NAGfgddlNCIFNDDNAEKLVLR---IRIMNSDENKfQEDEEVVDKMDDDVFlrciesNMLTDMTLQGIEQISKVYMhLP 1310
Cdd:cd02737 134 SPW-----VCHFHLDKECQKLSDgpcLTFSVSKEVS-KSSEELLDVLRDRII------PFLLETVIKGDERIKSVNI-LW 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1311 QTDNKKKIIITEDGEFKAlqEWILETdGVSLMRVLSEKD---------------VDPVRTTSNDIVEIFTVLGIEAVRKA 1375
Cdd:cd02737 201 EDSPSTSWVKSVGKSSRG--ELVLEV-TVEESCKKTRGNawnvvmdacipvmdlIDWERSMPYSIQQIKSVLGIDAAFEQ 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1376 LERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGINRQDT-----GPLMKCSFEETVDVLMEASSHGECDPMK 1450
Cdd:cd02737 278 FVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRslkisAPFTEACFSSPIKCFLKAAKKGASDSLS 357
|
410 420
....*....|....*....|....
gi 1900307341 1451 GVSENIMLGQLAPAGTGC-FDLLL 1473
Cdd:cd02737 358 GVLDACAWGKEAPVGTGSkFEILW 381
|
|
| PARM |
pfam17061 |
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present ... |
1852-1966 |
1.44e-08 |
|
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present in most tissues, with high levels in the heart, kidney and placenta. It has been shown to be induced and expressed in prostate after castration and may have a role in cell proliferation and immortalization in prostate cancer.
Pssm-ID: 465341 [Multi-domain] Cd Length: 296 Bit Score: 58.33 E-value: 1.44e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1852 TPTSPKY--SPTSPKYSPTSPKySPTSPTYSPTTPKYSPTSPT----------YSPTSPT-------YTPTSPKYSPTS- 1911
Cdd:pfam17061 22 TPPTATWtsSPQNTAAVTASPT-SGTHNNSVLPVTASAPTSPLpknvsvepreEESTSPAsnwegtsTDPSPPGLSPTSs 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1912 -----PT---YSPTSPKYS-PT----SPTYSP--TSPKGSTYSPTSPGYSPtSPTYSPAISPDDSDEENN 1966
Cdd:pfam17061 101 gvhltPTpeeHSSGTPETSvPAtgsqSPAESPtlTSPQAPASSPSSPSTSP-PEVSSASVTTNHSSTETS 169
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
828-1110 |
5.44e-08 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 58.41 E-value: 5.44e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 828 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMV-KYDATVRNSInqvvqlrygedglagenvefqnlaT 906
Cdd:CHL00117 172 GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVrETDCGTTRGI------------------------S 227
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 907 LKPSNKAFEKKFrfdcTNERALRRVLQEDVvkdvltnanvqsvlerefekmredreilraifptgdskvvlpcnlarmIW 986
Cdd:CHL00117 228 VSPRNGMMIERI----LIQTLIGRVLADDI------------------------------------------------YI 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 987 NAQKIFRINTrtptDLNPlrvvegvqELSKKLVivngddplSRQAQenatllfNIHLRSTL-CSrrmteefrlSTEA--- 1062
Cdd:CHL00117 256 GSRCIATRNQ----DIGI--------GLANRFI--------TFRAQ-------PISIRSPLtCR---------STSWicq 299
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*
gi 1900307341 1063 --YDWllgeietkfnqSIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGV 1110
Cdd:CHL00117 300 lcYGW-----------SLAHGdlvelGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1852-1963 |
1.90e-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: 56.46 E-value: 1.90e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1852 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1929
Cdd:pfam05109 517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1930 PTSPKGSTYSPTSPGYSPT----------------------------------------SP------------------- 1950
Cdd:pfam05109 597 ETSPQANTTNHTLGGTSSTpvvtsppknatsavttgqhnitssstssmslrpssisetlSPstsdnstshmplltsahpt 676
|
170 180 190
....*....|....*....|....*....|..
gi 1900307341 1951 -------------------TYSPAISPDDSDE 1963
Cdd:pfam05109 677 ggenitqvtpaststhhvsTSSPAPRPGTTSQ 708
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1850-1950 |
3.05e-07 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 55.85 E-value: 3.05e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1850 EYTPTS-PKYS--PTSPK--YSPTSPKySPTSPTySPTTPKySPTSPTySPTSPTYT--PTSPKySPTSPTySPTSPKyS 1922
Cdd:PTZ00449 566 EHKPSKiPTLSkkPEFPKdpKHPKDPE-EPKKPK-RPRSAQ-RPTRPK-SPKLPELLdiPKSPK-RPESPK-SPKRPP-P 638
|
90 100
....*....|....*....|....*...
gi 1900307341 1923 PTSPTySPTSPKGsTYSPTSPGySPTSP 1950
Cdd:PTZ00449 639 PQRPS-SPERPEG-PKIIKSPK-PPKSP 663
|
|
| MISS |
pfam15822 |
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic ... |
1513-1611 |
5.18e-06 |
|
MAPK-interacting and spindle-stabilising protein-like; MISS is a family of eukaryotic MAPK-interacting and spindle-stabilising protein-like proteins. MISS is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localization signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII spindle. MISS is the first example of a physiological MAPK-substrate that is stabilized in MII that specifically regulates MII spindle integrity during the CSF arrest.
Pssm-ID: 318115 [Multi-domain] Cd Length: 238 Bit Score: 49.98 E-value: 5.18e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1513 PAMTPWNTGATPaygawsPSVGSGMTPGAAGFSPSAASDASGFSPGYsPAWSPTPGSPGSPGPVSPYIPSPGGamsPNYS 1592
Cdd:pfam15822 31 PGSNPWNNPSAP------PAVPSGLPPSTAPSTVPFGPAPTGMYPSI-PLTGPSPGPPAPFPPSGPSCPPPGG---PYPA 100
|
90 100
....*....|....*....|
gi 1900307341 1593 PTSPAyePRSPGGY-TPQSP 1611
Cdd:pfam15822 101 PTVPG--PGPIGPYpTPNMP 118
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1856-1964 |
8.73e-06 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 50.34 E-value: 8.73e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1856 PKYSPTSPKYSPTSPKYSPTSpTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKg 1935
Cdd:PHA03291 181 SADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTPTPSTTTSPPSTTIPAPSTTIAAPQAGTTPEAEGTPA- 258
|
90 100
....*....|....*....|....*....
gi 1900307341 1936 stysPTSPGYSPTSPTySPAISPDDSDEE 1964
Cdd:PHA03291 259 ----PPTPGGGEAPPA-NATPAPEASRYE 282
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1851-1960 |
1.43e-05 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 50.14 E-value: 1.43e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1851 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1927
Cdd:COG3469 89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
|
90 100 110
....*....|....*....|....*....|...
gi 1900307341 1928 YSPTSPKGSTYSPTSPGYSPTSPTYSPAISPDD 1960
Cdd:COG3469 169 TTTTTSASTTPSATTTATATTASGATTPSATTT 201
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1429-1467 |
3.49e-05 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 49.22 E-value: 3.49e-05
10 20 30
....*....|....*....|....*....|....*....
gi 1900307341 1429 SFEETVDVLMEASSHGECDPMKGVSENIMLGQLAPAGTG 1467
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1873-1951 |
4.62e-05 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 48.27 E-value: 4.62e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1873 SPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPT--YSPTSPKGSTYSPTSPGYSPTSP 1950
Cdd:PRK14950 370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTpeSAPKLTRAAIPVDEKPKYTPPAP 449
|
.
gi 1900307341 1951 T 1951
Cdd:PRK14950 450 P 450
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1869-1958 |
8.26e-05 |
|
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: 47.60 E-value: 8.26e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1869 SPKYSPTSPTYSpTTPKYSPTSPTYSPTSpTYTPTS--------PKYSP---TSPTYSPTSPKYSPTSPTYSP------- 1930
Cdd:pfam05109 424 APESTTTSPTLN-TTGFAAPNTTTGLPSS-THVPTNltapastgPTVSTadvTSPTPAGTTSGASPVTPSPSPrdngtes 501
|
90 100 110
....*....|....*....|....*....|....*.
gi 1900307341 1931 -----TSPKGSTYSPTSPGYSPTSPTYSP---AISP 1958
Cdd:pfam05109 502 kapdmTSPTSAVTTPTPNATSPTPAVTTPtpnATSP 537
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1850-1950 |
8.56e-05 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 47.44 E-value: 8.56e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1850 EYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS------PTSPTYTPTSPKYSPTSPTYSPTSPKYSP 1923
Cdd:COG3469 109 TSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVsgtetaTGGTTTTSTTTTTTSASTTPSATTTATAT 188
|
90 100
....*....|....*....|....*..
gi 1900307341 1924 TSPTYSPTSPKGSTysPTSPGYSPTSP 1950
Cdd:COG3469 189 TASGATTPSATTTA--TTTGPPTPGLP 213
|
|
| Aft1_HRA |
pfam11786 |
Aft1 HRA domain; This domain is found in the transcription factor Aft1 which is required for a ... |
1495-1572 |
9.38e-05 |
|
Aft1 HRA domain; This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The HRA domain is involved in meiotic recombination. It has been shown to be necessary and sufficient to activate recombination.
Pssm-ID: 371723 Cd Length: 76 Bit Score: 42.52 E-value: 9.38e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1900307341 1495 GPTGMFFGSVPSPMSG-MSPAMTPWNTGATPAYGAWSPSVGSGMTPGAAGFSpsaasdaSGFSPGYSPAWSPTPgSPGS 1572
Cdd:pfam11786 1 DPTGFPWGATNSLRSGpLSPAMLAGPQGASQSDYFDTTSIRTGFTPNESSLR-------TGLTPGGGGSMFPAP-SPNT 71
|
|
| 2A1904 |
TIGR00927 |
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1850-1962 |
1.02e-04 |
|
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]
Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 47.68 E-value: 1.02e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1850 EYTPTSPKyspTSPKYSPTSPK--YSPTSPTY------SPTTPKYSPTSptYSPTSPtyTPTSPKYSPTS----PTYSPT 1917
Cdd:TIGR00927 109 ENTPSPPR---RTAKITPTTPKnnYSPTAAGTervkedTPATPSRALNH--YISTSG--RQRVKSYTPKPrgevKSSSPT 181
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1900307341 1918 SPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSPAISPDDSD 1962
Cdd:TIGR00927 182 QTREKVRKYTPSPLGRMVNSYAPSTFMTMPRSHGITPRTTVKDSE 226
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1850-1956 |
1.56e-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: 46.83 E-value: 1.56e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1850 EYTPTSPKYSPT---SPKYSPTSPK--YSPTSPTYSPTTpkySPTSPTYSPTSPTYTPTSPKYSPTSPtysPTSPK---- 1920
Cdd:pfam05109 426 ESTTTSPTLNTTgfaAPNTTTGLPSstHVPTNLTAPAST---GPTVSTADVTSPTPAGTTSGASPVTP---SPSPRdngt 499
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 1900307341 1921 --YSP--TSPTYSPTSPKGSTYSPTSPGYSPTSPTYSPAI 1956
Cdd:pfam05109 500 esKAPdmTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTL 539
|
|
| PHA03269 |
PHA03269 |
envelope glycoprotein C; Provisional |
1856-1955 |
1.65e-04 |
|
envelope glycoprotein C; Provisional
Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 46.65 E-value: 1.65e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1856 PKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKG 1935
Cdd:PHA03269 42 PAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQLAAAPKPDAAEAFTSAAQ 121
|
90 100
....*....|....*....|
gi 1900307341 1936 STYSPTSPGYSPTSPTYSPA 1955
Cdd:PHA03269 122 AHEAPADAGTSAASKKPDPA 141
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1861-1955 |
2.68e-04 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 42.51 E-value: 2.68e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1861 TSPKYSPTSPKysptSPTYSPTTPKYSPTSPTYSPT-SPTYTPT-------SPKYSPTSPTYSPTsPKYSPTS------- 1925
Cdd:smart01104 3 RTPAWGASGSK----TPAWGSRTPGTAAGGAPTARGgSGSRTPAwggagsrTPAWGGAGPTGSRT-PAWGGASawgnkss 77
|
90 100 110
....*....|....*....|....*....|..
gi 1900307341 1926 --PTYSPTSPKGSTYSPTSPGYSPTSPTYSPA 1955
Cdd:smart01104 78 egSASSWAAGPGGAYGAPTPGYGGTPSAYGPA 109
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1851-1945 |
2.86e-04 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 45.90 E-value: 2.86e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1851 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSP 1930
Cdd:COG3469 121 SVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTTTTSASTTPSATTTATATTASGATTPSATT 200
|
90 100
....*....|....*....|
gi 1900307341 1931 TSPKGSTYSPTSP-----GY 1945
Cdd:COG3469 201 TATTTGPPTPGLPkhvlvGY 220
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1429-1468 |
3.26e-04 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 46.09 E-value: 3.26e-04
10 20 30 40
....*....|....*....|....*....|....*....|
gi 1900307341 1429 SFEETVDVLMEASSHGECDPMKGVSENIMLGQLAPAGTGC 1468
Cdd:CHL00117 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
|
|
| PHA03269 |
PHA03269 |
envelope glycoprotein C; Provisional |
1853-1958 |
3.78e-04 |
|
envelope glycoprotein C; Provisional
Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 45.49 E-value: 3.78e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1853 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTySPTSPKYSPtsPTYSPTS 1932
Cdd:PHA03269 46 PHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQLAA-APKPDAAEA--FTSAAQA 122
|
90 100
....*....|....*....|....*.
gi 1900307341 1933 PKGSTYSPTSPGYSPTSPTYSPAISP 1958
Cdd:PHA03269 123 HEAPADAGTSAASKKPDPAAHTQHSP 148
|
|
| rad23 |
TIGR00601 |
UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
1868-1940 |
4.11e-04 |
|
UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 44.89 E-value: 4.11e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1900307341 1868 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1940
Cdd:TIGR00601 75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1855-1955 |
4.53e-04 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 44.56 E-value: 4.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1855 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1934
Cdd:PTZ00436 242 APAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPA 321
|
90 100
....*....|....*....|.
gi 1900307341 1935 GSTYSPTSPGYSPTSPTYSPA 1955
Cdd:PTZ00436 322 KAAAPPAKAATPPAKAAAPPA 342
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1881-1955 |
4.82e-04 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 45.19 E-value: 4.82e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1900307341 1881 PTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSPA 1955
Cdd:PRK14950 364 PAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPV 438
|
|
| PRK14959 |
PRK14959 |
DNA polymerase III subunits gamma and tau; Provisional |
1511-1612 |
5.67e-04 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 184923 [Multi-domain] Cd Length: 624 Bit Score: 45.06 E-value: 5.67e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1511 MSPAMTPWNTgATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPA--WSPTPGSPGSPGPV---SPYIPSPGG 1585
Cdd:PRK14959 361 MLPRLMPVES-LRPSGGGASAPSGSAAEGPASGGAATIPTPGTQGPQGTAPAagMTPSSAAPATPAPSaapSPRVPWDDA 439
|
90 100
....*....|....*....|....*..
gi 1900307341 1586 AMSPNYSPTSPAYEPRSPGgyTPQSPG 1612
Cdd:PRK14959 440 PPAPPRSGIPPRPAPRMPE--ASPVPG 464
|
|
| KAR9 |
pfam08580 |
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ... |
1856-1954 |
6.39e-04 |
|
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.
Pssm-ID: 430088 [Multi-domain] Cd Length: 684 Bit Score: 44.82 E-value: 6.39e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1856 PKYSPTSPKYSpTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTS-PKYSPTSPTYSPTSPkySPTSPTYSPTSPK 1934
Cdd:pfam08580 495 PRASPNHSGFL-STPSNTATSETPTPALRPPSRPQPPPPGNRPRWNASTnTNDLDVGHNFKPLTL--TTPSPTPSRSSRS 571
|
90 100
....*....|....*....|
gi 1900307341 1935 GSTYSPTSPGYSPTSPTYSP 1954
Cdd:pfam08580 572 SSTLPPVSPLSRDKSRSPAP 591
|
|
| Caudal_act |
pfam04731 |
Caudal like protein activation region; This family consists of the amino termini of proteins ... |
1488-1599 |
6.65e-04 |
|
Caudal like protein activation region; This family consists of the amino termini of proteins belonging to the caudal-related homeobox protein family. This region is thought to mediate transcription activation. The level of activation caused by mouse Cdx2 is affected by phosphorylation at serine 60 via the mitogen-activated protein kinase pathway. Caudal family proteins are involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium, and are important in differentiation and maintenance of the intestinal epithelial lining. Caudal proteins always have a homeobox DNA binding domain (pfam00046).
Pssm-ID: 461413 [Multi-domain] Cd Length: 136 Bit Score: 41.66 E-value: 6.65e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1488 IPGISVAGPTGmffGSVPSPMSgmsPAMTPWNTGATPAYGAWSPSVGSGMTPGAAGFSPsaasdasgfsPGYSpawSPTP 1567
Cdd:pfam04731 33 VPGMDPHGQSL---GAWGSPYG---PPREDWNAYGPGPSSTVGTAPMNDASPGQIAYSP----------PDYS---SLHP 93
|
90 100 110
....*....|....*....|....*....|..
gi 1900307341 1568 GSPGSPGPVSPYIPSPGGAMSPNYSPTSPaYE 1599
Cdd:pfam04731 94 PGPSSGLSLPPPLNSSLEQLSPSRQRRSP-YE 124
|
|
| DUF1373 |
pfam07117 |
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ... |
1853-1963 |
7.03e-04 |
|
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.
Pssm-ID: 462093 [Multi-domain] Cd Length: 212 Bit Score: 43.24 E-value: 7.03e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1853 PTSPKYSPTSPKYSPTSP---KYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1929
Cdd:pfam07117 42 PPRPEEEEGQGGGGGTFPfpgSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSSGSGSGHQGS 121
|
90 100 110
....*....|....*....|....*....|....
gi 1900307341 1930 PTSPKGStyspTSPGYSPTSPTYSPAISPDDSDE 1963
Cdd:pfam07117 122 GGAGAGA----GAPGHQHEQEQESSSSDDDDEDE 151
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1051-1102 |
8.57e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 44.50 E-value: 8.57e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 1900307341 1051 RMTEEFRLSTEAYDWLLGEIETKFNQSIAHPGEMVGALAAQSLGEPATQMTL 1102
Cdd:PRK14898 26 KLSKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1859-1964 |
8.82e-04 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 44.03 E-value: 8.82e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1859 SPTSPKYSPTSPKYSPTSPtysPTTPKYSPTSPTySPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKgsty 1938
Cdd:PRK14950 370 KPTAAAPSPVRPTPAPSTR---PKAAAAANIPPK-EPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPVDEK---- 441
|
90 100
....*....|....*....|....*.
gi 1900307341 1939 sPTSPGYSPTSPTYSPAISPDDSDEE 1964
Cdd:PRK14950 442 -PKYTPPAPPKEEEKALIADGDVLEQ 466
|
|
| Pneumo_att_G |
pfam05539 |
Pneumovirinae attachment membrane glycoprotein G; |
1852-1949 |
8.99e-04 |
|
Pneumovirinae attachment membrane glycoprotein G;
Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 43.88 E-value: 8.99e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1852 TPTSPKYS---PTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSpTYSPTSPTyTPTSPKYSPTSPTYSPTSPKYSPTSPTY 1928
Cdd:pfam05539 226 TSSNPEPQtepPPSQRGPSGSPQHPPSTTSQDQSTTGDGQEH-TQRRKTPP-ATSNRRSPHSTATPPPTTKRQETGRPTP 303
|
90 100
....*....|....*....|.
gi 1900307341 1929 SPTSPKGSTYSPtsPGYSPTS 1949
Cdd:pfam05539 304 RPTATTQSGSSP--PHSSPPG 322
|
|
| Oest_recep |
pfam02159 |
Oestrogen receptor; |
1860-1951 |
9.74e-04 |
|
Oestrogen receptor;
Pssm-ID: 460469 [Multi-domain] Cd Length: 138 Bit Score: 41.51 E-value: 9.74e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1860 PTSPKYSPTSPKYSPTsPTYSPTTPKYSPTSPTYSPTSPT------YTPTSP-KYSPTSPTYSPTSPKYSPTSPTYSPTS 1932
Cdd:pfam02159 14 PEGATYDFAAAAAASA-PVYGSSTLSYSPPSEAFGSNSLGgfhslnSVPPSPlVFLHPPPQLSPFLHPPGQQVPYYLENE 92
|
90 100
....*....|....*....|.
gi 1900307341 1933 PKGSTYSPTSPG--YSPTSPT 1951
Cdd:pfam02159 93 QSGYAVREAAPPafYRPSSDN 113
|
|
| GATA-N |
pfam05349 |
GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell ... |
1859-1949 |
1.13e-03 |
|
GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell differentiation in a diverse range of tissues. Mutation are often associated with certain congenital human disorders. The six classical vertebrate GATA proteins, GATA-1 to GATA-6, are highly homologous and have two tandem zinc fingers. The classical GATA transcription factors function transcription activators. In lower metazoans GATA proteins carry a single canonical zinc finger. This family represents the N-terminal domain of the family of GATA transcription activators.
Pssm-ID: 461628 [Multi-domain] Cd Length: 174 Bit Score: 42.04 E-value: 1.13e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1859 SPTSPKYSPTSPKY---SPTSPTYSPTT--PKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPtsp 1933
Cdd:pfam05349 10 NHGQAAYDHDSGGFlhsAASSPVYVPTTrvPSMLPTLPYLQGCGSSQQSHPVSSHSGWAQAGAESSSYNPGSPHPSP--- 86
|
90
....*....|....*.
gi 1900307341 1934 kGSTYSPTSPGYSPTS 1949
Cdd:pfam05349 87 -RFSYSHSPPGSNGTS 101
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1855-1954 |
1.14e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.40 E-value: 1.14e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1855 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1934
Cdd:PTZ00436 249 APAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPA 328
|
90 100
....*....|....*....|
gi 1900307341 1935 GSTYSPTSPGYSPTSPTYSP 1954
Cdd:PTZ00436 329 KAATPPAKAAAPPAKAAAAP 348
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1855-1935 |
1.18e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.40 E-value: 1.18e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1855 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1934
Cdd:PTZ00436 270 PPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAPV 349
|
.
gi 1900307341 1935 G 1935
Cdd:PTZ00436 350 G 350
|
|
| Endomucin |
pfam07010 |
Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early ... |
1866-1961 |
1.60e-03 |
|
Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Pssm-ID: 429246 [Multi-domain] Cd Length: 260 Bit Score: 42.55 E-value: 1.60e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1866 SPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTS--PKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSp 1943
Cdd:pfam07010 29 ANITLSTTPSTTAETASTPKTTNLNTPTGGTSPVGTTSSelSKTSLVSTTISLTTTKKGVGTTTTDVSKNESSTTKPTV- 107
|
90
....*....|....*...
gi 1900307341 1944 gyspTSPTYSPAISPDDS 1961
Cdd:pfam07010 108 ----TSTPLSNAVSTLQS 121
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1854-1940 |
1.88e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 42.63 E-value: 1.88e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1854 TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1933
Cdd:PTZ00436 262 APPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPP 341
|
....*..
gi 1900307341 1934 KGSTYSP 1940
Cdd:PTZ00436 342 AKAAAAP 348
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1860-1966 |
1.89e-03 |
|
translocon at the inner envelope of chloroplast subunit 62; Provisional
Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 42.99 E-value: 1.89e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1860 PTSP--KYSPTSPkysPTSPtySPTTPKYSPTSPTYSPTSPTyTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKgst 1937
Cdd:PLN03209 437 PLSPyaRYEDLKP---PTSP--SPTAPTGVSPSVSSTSSVPA-VPDTAPATAATDAAAPPPANMRPLSPYAVYDDLK--- 507
|
90 100
....*....|....*....|....*....
gi 1900307341 1938 ySPTSPGYSPTSPTYSPAISPDDSDEENN 1966
Cdd:PLN03209 508 -PPTSPSPAAPVGKVAPSSTNEVVKVGNS 535
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1856-1943 |
3.13e-03 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 39.43 E-value: 3.13e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1856 PKYSPTSPKYSPTSPkysPTSPTYSP-TTPKY----------------SPTSPTYSPTSPTY-----TPTSPKYSPTSPT 1913
Cdd:smart01104 15 PAWGSRTPGTAAGGA---PTARGGSGsRTPAWggagsrtpawggagptGSRTPAWGGASAWGnksseGSASSWAAGPGGA 91
|
90 100 110
....*....|....*....|....*....|
gi 1900307341 1914 YSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1943
Cdd:smart01104 92 YGAPTPGYGGTPSAYGPATPGGGAMAGSAS 121
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1852-1941 |
3.48e-03 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 41.86 E-value: 3.48e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1852 TPTSPKYSPTSPKYSPTSPkySPTSPTySPTTPKYSPTSPTYSPTSPTYTPTSPKysptsptysPTSPKYSPTSPTYSPT 1931
Cdd:PHA03291 207 TPRPTPRTTASPETTPTPS--TTTSPP-STTIPAPSTTIAAPQAGTTPEAEGTPA---------PPTPGGGEAPPANATP 274
|
90
....*....|
gi 1900307341 1932 SPKGSTYSPT 1941
Cdd:PHA03291 275 APEASRYELT 284
|
|
| CTF_NFI |
pfam00859 |
CTF/NF-I family transcription modulation region; |
1853-1958 |
4.15e-03 |
|
CTF/NF-I family transcription modulation region;
Pssm-ID: 459967 [Multi-domain] Cd Length: 288 Bit Score: 41.44 E-value: 4.15e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1853 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPK-----------YSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPtSPKY 1921
Cdd:pfam00859 153 PSSALHFPSSSILQQPSSYFPHPAIRYPPHLPQdplkdlvslacYDPSSQQPSQPNGSGQGKVPGHFISTQMLAP-PPHP 231
|
90 100 110
....*....|....*....|....*....|....*...
gi 1900307341 1922 SPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYS-PAISP 1958
Cdd:pfam00859 232 PVARPVPLPMDTKPITTSTEGGASSPTSPTYSaPGTPP 269
|
|
| CytochromB561_N |
pfam09786 |
Cytochrome B561, N terminal; Members of this family are found in the N terminal region of ... |
1853-1964 |
6.11e-03 |
|
Cytochrome B561, N terminal; Members of this family are found in the N terminal region of cytochrome B561, as well as in various other putative uncharacterized proteins.
Pssm-ID: 462899 Cd Length: 579 Bit Score: 41.35 E-value: 6.11e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1853 PTSPKYSPTSPkysptSPKYSPTSPTYSPTT---PKYSPTSPTYSpTSPTYTPTSPKYSPTSP-TYSPTSPKYSPTSPTY 1928
Cdd:pfam09786 129 PPKSKSSPQSP-----SPVLVPLHQSVSPSSsesRKGGDKSPAGS-GKKLRSFSTSSKSPASPsVYLRGSPVPLNSSPLP 202
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 1900307341 1929 SPTSPKGSTYSptSPGYSPTSPT----YSPAISPDDSDEE 1964
Cdd:pfam09786 203 SDRNYENSVQS--SPEIDSAVSTpwsrKRATIGKEIRTEK 240
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1852-1927 |
6.15e-03 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 41.33 E-value: 6.15e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1900307341 1852 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPtyTPTSPKYSPTSPTYSPTSPKYSPTSPT 1927
Cdd:PRK14950 377 SPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPH--TPESAPKLTRAAIPVDEKPKYTPPAPP 450
|
|
| Hamartin |
pfam04388 |
Hamartin protein; This family includes the hamartin protein which is thought to function as a ... |
1874-1953 |
6.44e-03 |
|
Hamartin protein; This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein pfam03542. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin pfam03542. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.
Pssm-ID: 461287 [Multi-domain] Cd Length: 730 Bit Score: 41.58 E-value: 6.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1874 PTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSPKYSPTsPTYSPTSPKGSTYSPTSPGYSPTSPTYS 1953
Cdd:pfam04388 276 PTASPYTDQQSSYGSSTSTPSSTPRLQLSSSSGTSPPYLSPPSIRLKTDSF-PLWSPSSVCGMTTPPTSPGMVPTTPSEL 354
|
|
| PRK12323 |
PRK12323 |
DNA polymerase III subunit gamma/tau; |
1502-1611 |
6.95e-03 |
|
DNA polymerase III subunit gamma/tau;
Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 41.40 E-value: 6.95e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1502 GSVPSPMSgmSPAMTPWNTGATPAYGAWSPSVGSGMTPGAAgfSPSAASDASgfsPGYSPAWSPTPGSPGSPGPVSPYIP 1581
Cdd:PRK12323 445 GGAPAPAP--APAAAPAAAARPAAAGPRPVAAAAAAAPARA--APAAAPAPA---DDDPPPWEELPPEFASPAPAQPDAA 517
|
90 100 110
....*....|....*....|....*....|....
gi 1900307341 1582 SPG----GAMSPNYSPTSPAYEPRSPGGYTPQSP 1611
Cdd:PRK12323 518 PAGwvaeSIPDPATADPDDAFETLAPAPAAAPAP 551
|
|
| KAR9 |
pfam08580 |
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ... |
1851-1953 |
7.19e-03 |
|
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.
Pssm-ID: 430088 [Multi-domain] Cd Length: 684 Bit Score: 41.35 E-value: 7.19e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1851 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTP---------------KYSPTSPT-YSPTSPTYTPTSPKYSPTSP-- 1912
Cdd:pfam08580 503 GFLSTPSNTATSETPTPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTtPSPTPSRSSRSSSTLPPVSPls 582
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1900307341 1913 ---TYSPTSPKYSPTSPTYSPTSPKGS-TYSPTSPGYSPTSPTYS 1953
Cdd:pfam08580 583 rdkSRSPAPTCRSVSRASRRRASRKPTrIGSPNSRTSLLDEPPYP 627
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|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1851-1948 |
7.37e-03 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 41.09 E-value: 7.37e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1851 YTPTSPKYSPTSPKYSPTSpKYSPTSPTYSP--------TTPKYSPTSPTySPTSPTYTPTSPKYSPTSPTYSPTSPKys 1922
Cdd:PHA03291 183 DGSCDPALPLSAPRLGPAD-VFVPATPRPTPrttaspetTPTPSTTTSPP-STTIPAPSTTIAAPQAGTTPEAEGTPA-- 258
|
90 100
....*....|....*....|....*.
gi 1900307341 1923 PTSPTYSPTSPKGSTYSPTSPGYSPT 1948
Cdd:PHA03291 259 PPTPGGGEAPPANATPAPEASRYELT 284
|
|
| PHA03255 |
PHA03255 |
BDLF3; Provisional |
1852-1960 |
7.44e-03 |
|
BDLF3; Provisional
Pssm-ID: 165513 [Multi-domain] Cd Length: 234 Bit Score: 40.27 E-value: 7.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1852 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSP-TSPKYSPTSPTYSP 1930
Cdd:PHA03255 63 TTSAPITTTAILSTNTTTVTSTGTTVTPVPTTSNASTINVTTKVTAQNITATEAGTGTSTGVTSNvTTRSSSTTSATTRI 142
|
90 100 110
....*....|....*....|....*....|
gi 1900307341 1931 TSPKGSTYSPTSPGYSPTSPTYSPAISPDD 1960
Cdd:PHA03255 143 TNATTLAPTLSSKGTSNATKTTAELPTVPD 172
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1852-1934 |
8.96e-03 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 41.21 E-value: 8.96e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1852 TPTSPKYSPTSPKYSPTSPKYSPTSP----TYSPTTPKYSPTSPTYSPTSPTYTPTSPKYSPTSPTYSPTSP-KYSPTSP 1926
Cdd:PTZ00449 728 DEEFPFEPIGDPDAEQPDDIEFFTPPeeerTFFHETPADTPLPDILAEEFKEEDIHAETGEPDEAMKRPDSPsEHEDKPP 807
|
....*...
gi 1900307341 1927 TYSPTSPK 1934
Cdd:PTZ00449 808 GDHPSLPK 815
|
|
| TYA |
pfam01021 |
Ty transposon capsid protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a ... |
1850-1966 |
9.03e-03 |
|
Ty transposon capsid protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles. This entry corresponds to the capsid protein from Ty1 and Ty2 transposons.
Pssm-ID: 425992 Cd Length: 384 Bit Score: 40.71 E-value: 9.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1850 EYTPTSPKYSPTSPKYSP-TSPKYSPTSPTYSP---TTPKYSPTS--PTYS-PTSPTYTP--TSPKYSPTSPTYSptSPK 1920
Cdd:pfam01021 39 TTTPGSSAVPENHHHASPqPASVPPPQNGPYSQqcmMTPNQANPSgwPFYGhPSMMPYTPyqMSPMYFPPGPQSQ--FPQ 116
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1900307341 1921 YSPT--SPTYSPTSPKGSTYSPTSPGYSPTSPTYSPAISPDDSDEENN 1966
Cdd:pfam01021 117 YPSSvgTPLSTPSPESGNTFTDSSSAKSDMTSTNKYVRPPPILTSPND 164
|
|
| PHA03247 |
PHA03247 |
large tegument protein UL36; Provisional |
1505-1611 |
9.38e-03 |
|
large tegument protein UL36; Provisional
Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 41.08 E-value: 9.38e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1900307341 1505 PSPMSGMSPAMTPWNTGATPAYGAWSPSVGSGMTPGAAGFSPSAASD-ASGFSPGYSPA-WSPTPGSP---GSPGPVSPY 1579
Cdd:PHA03247 2767 PAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLApAAALPPAASPAgPLPPPTSAqptAPPPPPGPP 2846
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 1900307341 1580 IPS--------PGGAMS----PNYSPTSPAYEPRSPGGYTPQSP 1611
Cdd:PHA03247 2847 PPSlplggsvaPGGDVRrrppSRSPAAKPAAPARPPVRRLARPA 2890
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