|
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 ... |
19-876 |
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: 1611.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733 93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733 138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733 298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733 458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733 533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733 613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939 818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd02733 693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
18-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 992.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 97 VGFLVKTMKVLRCVCFFCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPe 170
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 171 gdedltkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:PRK08566 150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 329
Cdd:PRK08566 212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 330 QKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRG 409
Cdd:PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 410 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 487
Cdd:PRK08566 371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 488 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 567
Cdd:PRK08566 450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 568 STWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGT 647
Cdd:PRK08566 530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 648 SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEP 727
Cdd:PRK08566 608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 728 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 807
Cdd:PRK08566 688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 808 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 887
Cdd:PRK08566 768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847
|
....*...
gi 4505939 888 QLRYGEDG 895
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 ... |
18-897 |
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: 940.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:TIGR02390 4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 97 VGFLVKTMKVLRCVCFFCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPe 170
Cdd:TIGR02390 82 VGFAKEIYKILRATCRKCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP- 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 171 gdedltkekghggcgryqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:TIGR02390 160 --------------------------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVL 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:TIGR02390 208 TVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARH 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 331 KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGN 410
Cdd:TIGR02390 288 RSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGP 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 411 SQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVT 489
Cdd:TIGR02390 368 DSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVC 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 490 TPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLST 569
Cdd:TIGR02390 448 PPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAG 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 570 WDGKVPQPAILKPRPLWTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTS 648
Cdd:TIGR02390 527 YFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAE 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:TIGR02390 604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:TIGR02390 684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQ 888
Cdd:TIGR02390 764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843
|
....*....
gi 4505939 889 LRYGEDGLA 897
Cdd:TIGR02390 844 FKYGEDGVD 852
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1058-1476 |
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: 821.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 4505939 1456 ENIMLGQLAPAGTGCFDLLLD 1476
Cdd:cd02584 390 ENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
830-1427 |
3.85e-176 |
|
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 545.03 E-value: 3.85e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 830 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 909
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 910 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 989
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 990 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1069
Cdd:pfam04998 120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1070 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1149
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1150 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1221
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1222 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1301
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1302 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1380
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 4505939 1381 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1427
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
246-546 |
4.54e-172 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 524.78 E-value: 4.54e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 246 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 325
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 326 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 405
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 406 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 484
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939 485 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
15-354 |
3.70e-142 |
|
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: 444.04 E-value: 3.70e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 93 PVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpe 170
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 171 gdedltkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:pfam04997 150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:pfam04997 217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
|
330 340
....*....|....*....|....
gi 4505939 331 KSGRPLKSLKQRLKGKEGRVRGNL 354
Cdd:pfam04997 297 KSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
896-1079 |
3.06e-96 |
|
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: 308.27 E-value: 3.06e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 4505939 1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1052-1479 |
2.20e-88 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 294.06 E-value: 2.20e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1052 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:PRK04309 27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1132 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1211
Cdd:PRK04309 107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1212 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1291
Cdd:PRK04309 157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1292 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:PRK04309 214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:PRK04309 275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354
|
410 420
....*....|....*....|....*...
gi 4505939 1452 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1479
Cdd:PRK04309 355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1054-1476 |
5.76e-85 |
|
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: 283.48 E-value: 5.76e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1213
Cdd:TIGR02389 94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1214 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1291
Cdd:TIGR02389 144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1292 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:TIGR02389 201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:TIGR02389 263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342
|
410 420
....*....|....*....|....*
gi 4505939 1452 KGVSENIMLGQLAPAGTGCFDLLLD 1476
Cdd:TIGR02389 343 KGVIENIIVGQPIPLGTGDVDLVMD 367
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
20-948 |
2.36e-64 |
|
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: 241.22 E-value: 2.36e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 20 RVQFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:COG0086 9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrl 141
Cdd:COG0086 82 VTLSKvrrERMGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI--- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 142 thvydlckgknICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllsp 218
Cdd:COG0086 159 -----------LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK---- 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 219 ervhEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGA 298
Cdd:COG0086 206 ----KLIKRLKVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKA 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 299 AAHVIAEDVKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:COG0086 278 PDIIVRNEKRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 378 VGVPRSIAanmtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhm 450
Cdd:COG0086 356 CGLPKKMA-----LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------- 410
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:COG0086 411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLST 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 523 RMIVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ---- 590
Cdd:COG0086 478 NNILSPANGKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgki 552
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 591 --------IFSLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLE 659
Cdd:COG0086 553 vettvgryLVNEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRR 592
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 660 MGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfEN 739
Cdd:COG0086 593 CGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YN 661
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 740 QVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpe 818
Cdd:COG0086 662 KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS-------------- 727
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 819 srgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedgla 897
Cdd:COG0086 728 -------NFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG----- 794
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|.
gi 4505939 898 GESVEfqnlaTLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 948
Cdd:COG0086 795 GEVIE-----PLK----------------ERILGRVAAED-VVDPGTGEVL 823
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1854-1959 |
4.83e-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: 81.12 E-value: 4.83e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1931
Cdd:pfam05109 517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
|
90 100
....*....|....*....|....*...
gi 4505939 1932 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1959
Cdd:pfam05109 597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
764-1117 |
3.92e-12 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 71.95 E-value: 3.92e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 764 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 830
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 831 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 909
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 910 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 989
Cdd:PRK02597 238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 990 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1067
Cdd:PRK02597 257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 4505939 1068 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1117
Cdd:PRK02597 301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1491-1610 |
3.19e-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: 59.46 E-value: 3.19e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104 15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 4505939 1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104 91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1853-1967 |
1.68e-06 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 52.83 E-value: 1.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1853 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1929
Cdd:COG3469 89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
|
90 100 110
....*....|....*....|....*....|....*...
gi 4505939 1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSD 1967
Cdd:COG3469 169 TTTTTSASTTPSATTTATATTASGATTPSATTTATTTG 206
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1858-1962 |
1.01e-05 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 50.34 E-value: 1.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1858 PKYSPTSPKYSPTSPKYSPTSpTYSPTTPKYSPTSPTYSPTSPvyTPTSPKySPTSPTYSPTSPKYSPTSPTYSPTSPkg 1937
Cdd:PHA03291 181 SADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTP--TPSTTT-SPPSTTIPAPSTTIAAPQAGTTPEAE-- 254
|
90 100
....*....|....*....|....*
gi 4505939 1938 STYSPTSPGYSPTSPTYSLTSPAIS 1962
Cdd:PHA03291 255 GTPAPPTPGGGEAPPANATPAPEAS 279
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1865-1960 |
5.88e-05 |
|
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: 44.43 E-value: 5.88e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1865 PKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTSPTYSPTSPKGST 1939
Cdd:smart01104 15 PAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEGSASSWAAGPGGA 91
|
90 100
....*....|....*....|.
gi 4505939 1940 YSPTSPGYSPTSPTYSLTSPA 1960
Cdd:smart01104 92 YGAPTPGYGGTPSAYGPATPG 112
|
|
| rad23 |
TIGR00601 |
UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
1870-1942 |
1.46e-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: 46.43 E-value: 1.46e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4505939 1870 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:TIGR00601 75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
|
|
| |
|
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 ... |
19-876 |
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: 1611.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733 79 GFLTKILKILRCVC------------------------------------------------------------------ 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733 93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733 138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733 298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733 458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733 533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733 613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939 818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
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 ... |
15-895 |
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: 1006.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKP 93
Cdd:cd02582 1 PKRIKGIKFGLLSPEEIRKMSVVE--IITPDTyDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 94 VFHVGFLVKTMKVLRCVCFFCSKLLV-DSNNPKIKDILAKSKG---QPKKRL-THVYDLCKGKNICeggeemdnkfgveq 168
Cdd:cd02582 79 VIHVGFAKHIYDLLRATCRSCGRILLpEEEIEKYLERIRRLKEkwpELVKRViEKVKKKAKKRKVC-------------- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 169 PegdedltkekgHggCGRYQPRIRrsgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWM 248
Cdd:cd02582 145 P-----------H--CGAPQYKIK---LEKPTTFYEEKEEGEVK---LTPSEIRERLEKIPDEDLELLGIDPKTARPEWM 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 249 IVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRA 328
Cdd:cd02582 206 VLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPA 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 329 MQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRR 408
Cdd:cd02582 286 RHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLN 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 409 GNSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNL 486
Cdd:cd02582 366 GPDKWPGANYVIRPDGRRIRLRYVNR-EELaeRLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 444
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 487 SVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMF 566
Cdd:cd02582 445 AVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSA 524
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 567 LStWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHisPGDTKVVVENGELIMGILCKKSLG 646
Cdd:cd02582 525 AG-YDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEGKAKVCSGCSECKDEDC--PNDGYVVIKNGKLLEGVIDKKAIG 601
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 647 T-SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNEL 725
Cdd:cd02582 602 AeQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGEL 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 726 EPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHR 805
Cdd:cd02582 682 EPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNR 761
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 806 TLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQ 885
Cdd:cd02582 762 TLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGN 841
|
890
....*....|
gi 4505939 886 VVQLRYGEDG 895
Cdd:cd02582 842 IIQFKYGEDG 851
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
18-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 992.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 97 VGFLVKTMKVLRCVCFFCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPe 170
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 171 gdedltkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:PRK08566 150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 329
Cdd:PRK08566 212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 330 QKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRG 409
Cdd:PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 410 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 487
Cdd:PRK08566 371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 488 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 567
Cdd:PRK08566 450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 568 STWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGT 647
Cdd:PRK08566 530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 648 SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEP 727
Cdd:PRK08566 608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 728 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 807
Cdd:PRK08566 688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 808 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 887
Cdd:PRK08566 768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847
|
....*...
gi 4505939 888 QLRYGEDG 895
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 ... |
18-897 |
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: 940.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:TIGR02390 4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 97 VGFLVKTMKVLRCVCFFCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPe 170
Cdd:TIGR02390 82 VGFAKEIYKILRATCRKCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP- 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 171 gdedltkekghggcgryqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:TIGR02390 160 --------------------------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVL 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:TIGR02390 208 TVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARH 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 331 KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGN 410
Cdd:TIGR02390 288 RSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGP 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 411 SQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVT 489
Cdd:TIGR02390 368 DSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVC 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 490 TPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLST 569
Cdd:TIGR02390 448 PPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAG 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 570 WDGKVPQPAILKPRPLWTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTS 648
Cdd:TIGR02390 527 YFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAE 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:TIGR02390 604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:TIGR02390 684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQ 888
Cdd:TIGR02390 764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843
|
....*....
gi 4505939 889 LRYGEDGLA 897
Cdd:TIGR02390 844 FKYGEDGVD 852
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
14-1481 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 914.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 14 PLRTIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAE--ITAPEAyDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 93 PVFHVGFLVKTMKVLRCVCFFCSKLLV---DSNNPK-IKDILAKSKGQPKKRLThvydlckgkniceggEEMDNKFGvEQ 168
Cdd:PRK14977 83 PVIHIAFIDNIKDLLNSTCHKCAKLKLpqeDLNVFKlIEEAHAAARDIPEKRID---------------DEIIEEVR-DQ 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 169 PEGDEDLTKEKGHggCGRYQPRirrsgLELYAEWKHVNEDSQEKKILLsPERVHEIFKRISDEECFVLGMEPRYARPEWM 248
Cdd:PRK14977 147 VKVYAKKAKECPH--CGAPQHE-----LEFEEPTIFIEKTEIEEHRLL-PIEIRDIFEKIIDDDLELIGFDPKKARPEWA 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 249 IVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRA 328
Cdd:PRK14977 219 VLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQA 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 329 MQK-SGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVR 407
Cdd:PRK14977 299 HHKgSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVI 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 408 RGNSQYPGAKYIIRDNGDRIDLRFHPKPSDL-------HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS 480
Cdd:PRK14977 379 NGPDEFPGANAIRKGDGTKIRLDFLEDKGKDalreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGA 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 481 TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEV 560
Cdd:PRK14977 459 TFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEA 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 561 MNLLMfLSTWDGKVPQPAI-LKPRPLWTGKQIFSLIIPGHINCIRThSTHPDDEDSGPYKHISPGDTKVVVENGELIMGI 639
Cdd:PRK14977 539 SNIAM-LAGITDPLPEPAIkTKDGPAWTGKQLFSLFLPKDFNFEGI-AKWSAGKAGEAKDPSCLGDGYVLIKEGELISGV 616
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 640 LCKKSLGTSAG---SLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEV 716
Cdd:PRK14977 617 IDDNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDL 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 717 IEK--------AHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVV 788
Cdd:PRK14977 697 IDQrkitrkitIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGAL 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 789 GQQNVE--------GKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYI 860
Cdd:PRK14977 777 GQQKRKtrigfvltGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYF 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 861 QRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLagesvefqnlatlkpsnkAFEKKFRFDYTN-ERALRRTLQEDLV 939
Cdd:PRK14977 857 QRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGI------------------DPQKLDHGEAFNlERIIEKQKIEDRG 918
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 940 KDVlSNAHIQnELEREFERMREDRevlrvifptgdskvvLPCNLLRMIWNAQkifhinprlPSDlhpikvvEGVKELSKK 1019
Cdd:PRK14977 919 KGA-SKDEIE-ELAKEYTKTFNAN---------------LPKLLADAIHGAE---------LKE-------DELEAICAE 965
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1020 LvivngddplsrqaqenatllfnihlrstlcsrrmaeefrlsgeafdwLLGeieskFNQAIAHPGEMVGALAAQSLGEPA 1099
Cdd:PRK14977 966 G-----------------------------------------------KEG-----FEKAKVEPGQAIGIISAQSIAEPG 993
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1100 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYdP 1179
Cdd:PRK14977 994 TQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN-A 1072
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1180 NPQSTVVAEDQEWVNVYYEMPDFdvarispwllrVELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeKLVlri 1259
Cdd:PRK14977 1073 NEIKLIKPDKRALENGCIPMERF-----------AEIEAALAKGKKFEMELEDDLIIL----------------DLV--- 1122
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1260 rimnsdenkmqeeeEVVDKMDDDVFLRCIeSNMLTDMTLQGIEQISKVYMHLPQTDNKKkiiitedgefkalqEWILETD 1339
Cdd:PRK14977 1123 --------------EAADRDKPLATLIAI-RNKILDKPVKGVPDIERAWVELVEKDGRD--------------EWIIQTS 1173
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1340 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAI----- 1414
Cdd:PRK14977 1174 GSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglqaa 1253
|
1450 1460 1470 1480 1490 1500
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4505939 1415 -TRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK 1481
Cdd:PRK14977 1254 gVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
26-880 |
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: 897.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 26 LSPDELKRMSVTEggIKYPE--TTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKT 103
Cdd:cd02583 1 LSPEDIIRLSEVE--VTNRNlyDIETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 104 MKVLRCVCFFCSKLLVDSNnpKIKDILAKSKGQPKKRLTH------VYDLCKGKNICeggeemdnkfgveqPEgdedltk 177
Cdd:cd02583 79 INILQCICKTCSRVLLPEE--EKRKFLKRLRRPNLDNLQKkalkkkILEKCKKVRKC--------------PH------- 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 178 ekghggCGRYqprirrsglelyaewKHVNEDsqekkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02583 136 ------CGLL---------------KKAQED-------LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPP 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 258 LSVRPAVVMQG-SARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSgRPL 336
Cdd:cd02583 188 LCIRPSVVMDEkSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPK-KPI 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 337 KSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGA 416
Cdd:cd02583 267 RGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGA 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 417 KYII-RDNGDRIDLRF-HPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNA 494
Cdd:cd02583 347 NFVIkRDGGKKKFLKYgNRRKIARELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNA 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 495 DFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwDGK- 573
Cdd:cd02583 427 DFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYML--DGEi 504
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 574 ---VPQPAILKPRPLWTGKQIFSLII-PGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGT-S 648
Cdd:cd02583 505 kidLPPPAILKPVELWTGKQIFSLLLrPNKKSPVLVNLEAKEKSYTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSgS 584
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:cd02583 585 KNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQ 664
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:cd02583 665 PGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLP 744
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939 809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR 880
Cdd:cd02583 745 HFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1058-1476 |
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: 821.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 4505939 1456 ENIMLGQLAPAGTGCFDLLLD 1476
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 ... |
22-876 |
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: 631.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 22 QFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFL 100
Cdd:cd01435 1 SFSFYSAEEIRKLSVKE--ITNPVTfDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFF 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 101 VKTMKVLRCVCFFCSKLLVdsnnPKIKDILAKSKGQPkkrlthvydLCKGKNiceggeemdnkfgveqpegdedltkekg 180
Cdd:cd01435 79 DLLYKLLRGSCFYCHRFRI----SKWEVKLFVAKLKL---------LDKGLL---------------------------- 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 181 hggcgryqprirrsglelyaewkhvnedsQEKKILLSPervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSV 260
Cdd:cd01435 118 -----------------------------VEAAELDFG--------------------------YDMFFLDVLLVPPNRF 142
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 261 RPAVVMQGSArnqddLTHK----LADIVKINNQLR------RNEQNGAAAHVIAEDVKL---------LQFHVATMVDNE 321
Cdd:cd01435 143 RPPSFLGDKV-----FENPqnvlLSKILKDNQQIRdllasmRQAESQSKLDLISGKTNSeklinawlqLQSAVNELFDST 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 322 LPGLPRAMQKSGrplksLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDR 401
Cdd:cd01435 218 KAPKSGKKSPPG-----IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEE 292
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 402 LQELVRRGNSQYPGAKYIIRDNGDRIDLRFH--------------PKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKM 467
Cdd:cd01435 293 LRQAVINGPDVYPGANAIEDEDGRLILLSALseerrkalakllllLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKP 372
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 468 SMMGHRVRILPWS-TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:cd01435 373 SIMAHKVRVLPGEkTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGV 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 547 KFTKRDVFLERGEVMNLLMF-LSTWDG-------KVPQPAILKPRPLWTGKQIFSLIIpghINCIRTHStHPDDEDS--- 615
Cdd:cd01435 453 LLTSRDTFFTREEYQQLVYAaLRPLFTsdkdgriKLLPPAILKPKPLWTGKQVISTIL---KNLIPGNA-PLLNLSGkkk 528
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 616 ------GPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGI 689
Cdd:cd01435 529 tkkkvgGGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGI 608
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 690 GDSIADSKTYQDIQNTIKKAKQDVIEVIEKAhnneleptpgntlrqtFENQVNRILNDARDKTGSSAQKSLSEYNNFKSM 769
Cdd:cd01435 609 EDLLLTPKADEKRRKILRKAKKLGLEAAAEF----------------LGLKLNKVTSSIIKACLPKGLLKPFPENNLQLM 672
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 770 VVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLID 849
Cdd:cd01435 673 VQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLID 752
|
890 900
....*....|....*....|....*..
gi 4505939 850 TAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd01435 753 TAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
26-876 |
2.85e-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: 556.66 E-value: 2.85e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 26 LSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLvkt 103
Cdd:cd00399 1 MSPEEIRKWSVAK--VIKPETIDnrTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFI--- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 104 mkvlrcvcffcskllvdsnnpkikdilakskgqpkkrlTHVYDLCKgkniceggeemdnkfgveqpegdedltkekghgg 183
Cdd:cd00399 76 --------------------------------------KKVPSFLG---------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 184 cgryqprirrsglelyaewkhvnedsqekkillspervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSVRPA 263
Cdd:cd00399 84 -------------------------------------------------------------PEWMILTCLPVPPPCLRPS 102
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 264 VVmqgsarnqddlthkladivkinnqlrrneqngaaahvIAEDVKLLQFHVATMVDNELPGLPRAMqKSGRPLKSLKQRL 343
Cdd:cd00399 103 VI-------------------------------------IEERWRLLQEHVDTYLDNGIAGQPQTQ-KSGRPLRSLAQRL 144
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 344 KGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMtfaeivtpfnidrlqelvrrgnsqypgakyiirdn 423
Cdd:cd00399 145 KGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 424 gdridlrfhpkpsdlhlqtgykverhmcDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNL 503
Cdd:cd00399 190 ----------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNL 241
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 504 HLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKrdvflergevmnllmflstwdgkvpqpailkpr 583
Cdd:cd00399 242 HVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL--------------------------------- 288
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 584 plwtGKQIFSLIIPGhincirthsthpddedsgpykhispgdtkvvvengelimgilckkslgtsagSLVHISYLEMGHD 663
Cdd:cd00399 289 ----GKQIVSAALPG----------------------------------------------------GLLHTVTRELGPE 312
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 664 ITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNR 743
Cdd:cd00399 313 KAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILD 392
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 744 ILNDARDKTGSSAQKSL---SEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESR 820
Cdd:cd00399 393 FLNEARDKAGSAASVNLdlvSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAK 472
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 4505939 821 GFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd00399 473 GFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
830-1427 |
3.85e-176 |
|
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 545.03 E-value: 3.85e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 830 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 909
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 910 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 989
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 990 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1069
Cdd:pfam04998 120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1070 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1149
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1150 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1221
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1222 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1301
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1302 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1380
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 4505939 1381 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1427
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
246-546 |
4.54e-172 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 524.78 E-value: 4.54e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 246 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 325
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 326 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 405
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 406 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 484
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939 485 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
15-354 |
3.70e-142 |
|
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: 444.04 E-value: 3.70e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 93 PVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpe 170
Cdd:pfam04997 79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 171 gdedltkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:pfam04997 150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:pfam04997 217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296
|
330 340
....*....|....*....|....
gi 4505939 331 KSGRPLKSLKQRLKGKEGRVRGNL 354
Cdd:pfam04997 297 KSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
356-521 |
1.05e-97 |
|
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498 Cd Length: 166 Bit Score: 311.54 E-value: 1.05e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 356 GKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKP 435
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 436 SDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEI 515
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 4505939 516 QELAMV 521
Cdd:pfam00623 161 EELMLV 166
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
896-1079 |
3.06e-96 |
|
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: 308.27 E-value: 3.06e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 4505939 1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
57-880 |
3.96e-91 |
|
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: 314.34 E-value: 3.96e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 57 LMDPRQGVIERTGRCQTC-AGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCffcskllvdsnnPKIKDILAKSKG 135
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKIC------------PGCKSIKQKKKK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 136 QPKKRLTHVY-DLCKGKniceggeemdnkfgvEQPEGdEDLTKekghggcgryqprirrsglelyaewkhvnedsqekki 214
Cdd:cd10506 88 PPRETLPPDYwDFIPKD---------------GQQEE-SCVTK------------------------------------- 114
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 215 lLSPERVHEIFKRISDEECFVLGMEpRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNE 294
Cdd:cd10506 115 -NLPILSLAQVKKILKEIDPKLIAK-GLPRQEGLFLKCLPVPPNCHRVTEFTHGFSTGSRLIFDERTRAYKKLVDFIGTA 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 295 QNGAAAHviaedvkllqfhvatmvdnelpglpramqKSGrpLKSLKQrlkgkegrvrgNLMGKRVDFSARTVITPDPNLS 374
Cdd:cd10506 193 NESAASK-----------------------------KSG--LKWMKD-----------LLLGKRSGHSFRSVVVGDPYLE 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 375 IDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGnsqyPGAKYII--RDNGDRIDLRFHPKpsdlhLQTGYKVERHMCD 452
Cdd:cd10506 231 LNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLT----LLLKGVIgvRRNGRLVGVRSHNT-----LQIGDVIHRPLVD 301
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 453 GDIVIFNRQPTLHKMSMMGHRVRILPW-STFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSN 531
Cdd:cd10506 302 GDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSG 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 532 RPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTwdgKVPQPAILK--PR--PLWTGKQIFSLIIPGHINCirths 607
Cdd:cd10506 382 QNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKspPSngPLWTGKQLFQMLLPTDLDY----- 453
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 608 thpddedSGPykhispgDTKVVVENGELIMGiLCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTI 687
Cdd:cd10506 454 -------SFP-------SNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSV 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 688 GIGD------SIADSKTYQDIQNTIKKAKQ----DVIEV----IEKAHNNELEPTPGNTLRQTFENQVN-RILNDARDK- 751
Cdd:cd10506 519 SLSDlylssdSYSRQKMIEEISLGLREAEIacniKQLLVdsrkDFLSGSGEENDVSSDVERVIYERQKSaALSQASVSAf 598
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 752 ------TGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKrIPFGFKH---------RTLPHFIKDDY- 815
Cdd:cd10506 599 kqvfrdIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVK-LSYRIPRqlscaawnsQKSPRVIEKDGs 677
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 816 ----GPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDtavKTAET-GYIQRRLIKSMESVMVKYDATVR 880
Cdd:cd10506 678 ecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1054-1477 |
2.07e-90 |
|
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: 298.78 E-value: 2.07e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDpnpqstvvaedqewvnvYYEMPdfdvarispwlLR 1213
Cdd:cd06528 90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--D-----------------LFNMR-----------IT 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1214 VELDRKHMTDRKLTMEQIAEKINAGFGDDlncIFNDDNAEKLVLRIrimnsDENKMQEEEEVVDKmdddvflrciesnmL 1293
Cdd:cd06528 140 IELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKA-----EEPSIKELRKLAEK--------------I 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1294 TDMTLQGIEQISKVymhlpqtdnkkkIIITEDGefkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEA 1373
Cdd:cd06528 198 LNTKIKGIKGIKRV------------IVRKEED------EYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEA 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1374 VRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKG 1453
Cdd:cd06528 260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRG 339
|
410 420
....*....|....*....|....
gi 4505939 1454 VSENIMLGQLAPAGTGCFDLLLDA 1477
Cdd:cd06528 340 VIENIIVGQPIPLGTGDVELTMDP 363
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1052-1479 |
2.20e-88 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 294.06 E-value: 2.20e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1052 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:PRK04309 27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1132 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1211
Cdd:PRK04309 107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1212 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1291
Cdd:PRK04309 157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1292 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:PRK04309 214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:PRK04309 275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354
|
410 420
....*....|....*....|....*...
gi 4505939 1452 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1479
Cdd:PRK04309 355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1054-1476 |
5.76e-85 |
|
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: 283.48 E-value: 5.76e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1213
Cdd:TIGR02389 94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1214 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1291
Cdd:TIGR02389 144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1292 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:TIGR02389 201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:TIGR02389 263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342
|
410 420
....*....|....*....|....*
gi 4505939 1452 KGVSENIMLGQLAPAGTGCFDLLLD 1476
Cdd:TIGR02389 343 KGVIENIIVGQPIPLGTGDVDLVMD 367
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
20-1135 |
2.98e-76 |
|
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: 278.09 E-value: 2.98e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 20 RVQFGVLSPDELKRMSvtEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:TIGR02386 1 AIKISIASPDTIRNWS--YGEVKKPETInyRTLKPEKDGLFCEKifgptkdwecycgkykkiryKGVV-----CERCGVE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKI--KDILAkskgqpkkrL 141
Cdd:TIGR02386 74 VTESKvrrERMGHIELAAPVAHIWYfkglpsrigllLDITAKELESVLYFENYVVLDPGDTKLdkKEVLD---------E 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 142 THVYDLCK----GKNICEGGEemdnkfGVEQPEGDEDLTKEkghggcgryqprIRRSGLELyaewKHVNEDSQEKKILls 217
Cdd:TIGR02386 145 TEYREVLKrygdGFRAGMGAE------AIKELLEKIDLDKE------------IEELKIQL----RESKSDQKRKKLL-- 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 218 pervheifKRISDEECFVLGMepryARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNG 297
Cdd:TIGR02386 201 --------KRLEIVEAFKDSG----NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG 268
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 298 AAAHVIAEDVKLLQFHVATMVDNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:TIGR02386 269 APEIIVRNEKRMLQEAVDALFDNGRRGKP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQ 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 378 VGVPRSIAAnmtfaEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgy 444
Cdd:TIGR02386 348 CGLPKKMAL-----ELFKPFIIKRLIDrelaaniksakkMIEQEDPEvWDVLEDVIKE---------HP----------- 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 445 kverhmcdgdiVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRM 524
Cdd:TIGR02386 403 -----------VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNN 471
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 525 IVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVmnllmFLSTWDGKVPQPAILKPRP----LWT--GKQ 590
Cdd:TIGR02386 472 ILNPKDGKPIVTPSQDMvlglyyLTTEKPGAKGEgkIFSNVDEA-----IRAYDNGKVHLHALIGVRTsgeiLETtvGRV 546
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 591 IFSLIIPghincirthsthpddeDSGPYKHISPgdtkvvvengelimgILCKKSLgtsaGSLVHISYLEMGHDITRLFYS 670
Cdd:TIGR02386 547 IFNEILP----------------EGFPYINDNE---------------PLSKKEI----SSLIDLLYEVHGIEETAEMLD 591
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 671 NIQTVINNWLLIEGHTIGIGDSIadskTYQDIQNTIKKAKQDVIEVIEKAHNNELepTPGNTLRQTFEnqvnrILNDARD 750
Cdd:TIGR02386 592 KIKALGFKYATKSGTTISASDIV----VPDEKYEILKEADKEVAKIQKFYNKGLI--TDEERYRKVVS-----IWSETKD 660
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 751 KTGSSAQKSLS----EYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfven 825
Cdd:TIGR02386 661 KVTDAMMKLLKkdtyKFNPIFMMADSGARGNISQFRQLAGMRGlMAKPSGDIIELPIKS--------------------- 719
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 826 SYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKY-DATVRNSInQVVQLRYGEDglagESVEfq 904
Cdd:TIGR02386 720 SFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREeDCGTEEGI-EVEAIVEGKD----EIIE-- 792
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 905 nlaTLKpsnkafekkfrfdytnERALRRTLQEDLVKDVLSNAHIQ-NELerefermrEDREVLRVIFPTGDSKV----VL 979
Cdd:TIGR02386 793 ---SLK----------------DRIVGRYSAEDVYDPDTGKLIAEaNTL--------ITEEIAEKIENSGIEKVkvrsVL 845
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 980 PCNLLRMIwnAQKIFHINprlpsdlhpikvvegvkelskklvivngddpLSRQAqenatlLFNIhlrstlcsrrmaeefr 1059
Cdd:TIGR02386 846 TCESEHGV--CQKCYGRD-------------------------------LATGK------LVEI---------------- 870
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4505939 1060 lsgeafdwllgeieskfnqaiahpGEMVGALAAQSLGEPATQMTLNTFHYAGVSA--KNVTLGVPRLKELINiSKKPK 1135
Cdd:TIGR02386 871 ------------------------GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPK 923
|
|
| RNA_pol_Rpb1_7 |
pfam04990 |
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1164-1299 |
2.04e-75 |
|
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: 246.29 E-value: 2.04e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1164 TTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA---RISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFG 1240
Cdd:pfam04990 1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDVEdldRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939 1241 DDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQ 1299
Cdd:pfam04990 81 NDLFVIFSDDNAEKLVIRIRIINDEKEK---DEEQEDKAEDDVFLKRLEANMLDSLTLR 136
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1075-1471 |
3.71e-72 |
|
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: 244.05 E-value: 3.71e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1075 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLgqSARDAERA 1154
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLE--NDRDEKSA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1155 KDILCRLEHTTLRKVTANTAIYYDPNpqstvvaedqewvNVYyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEK 1234
Cdd:cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPD-------------DCY---------------ILIKLDKKIIEKLQLSKSNLYFL 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1235 INagfgddlncifnddnaeklvlririmnsdenkmqeeeevvdkmdddvFLRciesNMLTDMTLQGIEQISKVYMHLPQT 1314
Cdd:cd02736 131 LQ-----------------------------------------------SLK----RKLPDVVVSGIPEVKRAVINKDKK 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1315 DNKKKIIItEDGEFKAlqewILETDGVslmrvlsekdvDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVN 1394
Cdd:cd02736 160 KGKYKLLV-EGYGLRA----VMNTPGV-----------IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSID 223
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505939 1395 YRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCF 1471
Cdd:cd02736 224 PRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1053-1474 |
4.51e-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: 4.51e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1053 RMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISK 1132
Cdd:PRK14897 151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1133 KPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVtANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlL 1212
Cdd:PRK14897 231 KPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDV-ADIIT---------------------------DIAEMS---V 279
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1213 RVELDRKHMTDRKLTMEQIAEKInagfgddlncifnddnaEKLVLRIRIMNSDENKMQEEEEVVDKmdddvfLRCIESNm 1292
Cdd:PRK14897 280 VVELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDDGIIRLKPQQPSFKK------LYLLAEK- 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1293 LTDMTLQGIEQISKVymhlpqtdnkkkIIITEDGEfkalQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIE 1372
Cdd:PRK14897 336 VKSLTIKGIKGIKRA------------IARKENDE----RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIE 399
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1373 AVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMK 1452
Cdd:PRK14897 400 AARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLA 479
|
410 420
....*....|....*....|..
gi 4505939 1453 GVSENIMLGQLAPAGTGCFDLL 1474
Cdd:PRK14897 480 GVAENIIVGQPITLGTGAVSLV 501
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
20-948 |
2.36e-64 |
|
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: 241.22 E-value: 2.36e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 20 RVQFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:COG0086 9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrl 141
Cdd:COG0086 82 VTLSKvrrERMGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI--- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 142 thvydlckgknICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllsp 218
Cdd:COG0086 159 -----------LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK---- 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 219 ervhEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGA 298
Cdd:COG0086 206 ----KLIKRLKVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKA 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 299 AAHVIAEDVKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:COG0086 278 PDIIVRNEKRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 378 VGVPRSIAanmtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhm 450
Cdd:COG0086 356 CGLPKKMA-----LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------- 410
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:COG0086 411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLST 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 523 RMIVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ---- 590
Cdd:COG0086 478 NNILSPANGKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgki 552
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 591 --------IFSLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLE 659
Cdd:COG0086 553 vettvgryLVNEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRR 592
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 660 MGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfEN 739
Cdd:COG0086 593 CGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YN 661
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 740 QVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpe 818
Cdd:COG0086 662 KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS-------------- 727
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 819 srgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedgla 897
Cdd:COG0086 728 -------NFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG----- 794
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|.
gi 4505939 898 GESVEfqnlaTLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 948
Cdd:COG0086 795 GEVIE-----PLK----------------ERILGRVAAED-VVDPGTGEVL 823
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
525-691 |
1.67e-61 |
|
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 207.48 E-value: 1.67e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 525 IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwdgKVPQPAILKP-RPLWTGKQIFSLIIPGHINCI 603
Cdd:pfam04983 2 ILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 604 RTHSTHPDDEdsgpykhiSPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIE 683
Cdd:pfam04983 78 GKPKTNEEDL--------CENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKS 149
|
....*...
gi 4505939 684 GHTIGIGD 691
Cdd:pfam04983 150 GFSIGIDD 157
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
244-874 |
2.72e-61 |
|
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: 223.93 E-value: 2.72e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 244 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKladIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMV 318
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGgrfatSDLN--DLYRR---VINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALI 212
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 319 DNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFN 398
Cdd:cd01609 213 DNGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMA-----LELFKPFV 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 399 IdrlQELVRRGNSQYP-GAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRIL 477
Cdd:cd01609 287 I---RELIERGLAPNIkSAKKMIERKDPEV----------------WDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLI 347
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 478 PWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDT------LTAVRKFTKr 551
Cdd:cd01609 348 EGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMvlglyyLTKERKGDK- 426
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 552 dvflerGEVMnllmfLSTWDGKVpqpailkprplwtgkqIFSLIIPghincirthsthpddedsgpykhispgdtkvvvE 631
Cdd:cd01609 427 ------GEGI-----IETTVGRV----------------IFNEILP---------------------------------E 446
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 632 NGELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyqdiQNTIKKAK 710
Cdd:cd01609 447 GLPFINKTLKKKVL----KKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDiVVPPEK-----KEIIKEAE 517
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 711 QDVIEvIEKAHNNeleptpGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEY--NNFKSMVVSGAKGSKINISQVIAVV 788
Cdd:cd01609 518 EKVKE-IEKQYEK------GLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDpfNPIYMMADSGARGSKSQIRQLAGMR 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 789 G-QQNVEGKRIPfgfkhrtLPhfIKDdygpesrgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKS 867
Cdd:cd01609 591 GlMAKPSGKIIE-------LP--IKS------------NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDV 649
|
....*..
gi 4505939 868 MESVMVK 874
Cdd:cd01609 650 AQDVIVT 656
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
22-1116 |
9.11e-60 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 229.04 E-value: 9.11e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 22 QFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLM-------------------DPR-QGViertGRCQTCAGNMT 79
Cdd:PRK09603 1400 QLTLASPEKI--HSWSYGEVKKPETInyRTLKPERDGLFcmkifgptkdyeclcgkykKPRfKDI----GTCEKCGVAIT 1473
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 80 ECP---GHFGHIELAKPVFHVGFL------------VKtMKVLRCVCFFCSKLLV---------DSNNPKIK-DILAKSK 134
Cdd:PRK09603 1474 HSKvrrFRMGHIELATPVAHIWYVnslpsrigtllgVK-MKDLERVLYYEAYIVKepgeaaydnEGTKLVMKyDILNEEQ 1552
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 135 GQP-KKRLTHvydlcKGKNICEGGEEMdnKFGVEQPEGDEDLTKekghggcgryqprirrsgleLYAEWKHVNEDSQEKK 213
Cdd:PRK09603 1553 YQNiSRRYED-----RGFVAQMGGEAI--KDLLEEIDLITLLQS--------------------LKEEVKDTNSDAKKKK 1605
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 214 ILlspervheifKRISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRN 293
Cdd:PRK09603 1606 LI----------KRLKVVESFLNSGN----RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRL 1671
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 294 EQNGAAAHVIAEDVKLLQFHVATMVDNelpGLPRAMQKSG--RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDP 371
Cdd:PRK09603 1672 MELGAPEIIVRNEKRMLQEAVDVLFDN---GRSTNAVKGAnkRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGP 1748
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 372 NLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQElvrRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHM 450
Cdd:PRK09603 1749 NLKMDECGLPKNMA-----LELFKPHLLSKLEE---RGYaTTLKQAKRMIEQKSNEV----------------WECLQEI 1804
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 451 CDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQS 530
Cdd:PRK09603 1805 TEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPAS 1884
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 531 NRPVMGIVQDTLTAVRKFT--KRDVFLER---GEVMNLLMFLST--WDGKVPQPAILKPRPLWT--GKQIFSLIIPGHIn 601
Cdd:PRK09603 1885 GKAVAIPSQDMVLGLYYLSleKSGVKGEHklfSSVNEIITAIDTkeLDIHAKIRVLDQGNIIATsaGRMIIKSILPDFI- 1963
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 602 cirthsthPDDEDSGPYKhispgdtkvvvengelimgilcKKSLGTsagsLVHISYLEMGHDITRLFYSNIQTVINNWll 681
Cdd:PRK09603 1964 --------PTDLWNRPMK----------------------KKDIGV----LVDYVHKVGGIGITATFLDNLKTLGFRY-- 2007
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 682 ieGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEViekahnnELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLS 761
Cdd:PRK09603 2008 --ATKAGISISMEDIITPKDKQKMVEKAKVEVKKI-------QQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIA 2078
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 762 E----YNNFKSMVVSGAKGSKINISQVIAVVGqqnVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFF 837
Cdd:PRK09603 2079 KdkegFNSIYMMADSGARGSAAQIRQLSAMRG---LMTK--PDGSIIET----------PIISNFKE-----GLNVLEYF 2138
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 838 FHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYdatvrnsinqvvqlrygEDGLAGESVEFQNLATLKPSNKAFE 917
Cdd:PRK09603 2139 NSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVS-----------------DDCGTHEGIEITDIAVGSELIEPLE 2201
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 918 kkfrfdytnERALRRTLQEDLVKDvlsnahIQNElerefermredrevlrvifptgdskVVLPCNLLRMIWNAQKIfhin 997
Cdd:PRK09603 2202 ---------ERIFGRVLLEDVIDP------ITNE-------------------------ILLYADTLIDEEGAKKV---- 2237
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 998 prlpsdlhpikvvegvKELSKKLVIVNgdDPLSRQAQENatllfnihlrstLCSRrmaeefrlsgeAFDWLLGEieskfn 1077
Cdd:PRK09603 2238 ----------------VEAGIKSITIR--TPVTCKAPKG------------VCAK-----------CYGLNLGE------ 2270
|
1130 1140 1150
....*....|....*....|....*....|....*....
gi 4505939 1078 QAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKN 1116
Cdd:PRK09603 2271 GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1100-1478 |
2.65e-57 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 215.53 E-value: 2.65e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1100 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDP 1179
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI--DL 618
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1180 NPQStvvaedqewvnvyyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRI 1259
Cdd:PRK14898 619 WTQS----------------------------IKVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYL 663
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1260 RImnsdenkmqEEEEVVDkmdddvFLRCIESnmLTDMTLQGIEQISKVYMHLPQTDNKkkiiitedgefkalQEWILETD 1339
Cdd:PRK14898 664 KP---------KTPSYKA------LRKRIPK--IKNIVLKGIPGIERVLVKKEEHEND--------------EEYVLYTQ 712
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1340 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGV 1419
Cdd:PRK14898 713 GSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGV 792
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939 1420 NRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAE 1478
Cdd:PRK14898 793 AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDRE 851
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1075-1474 |
3.10e-55 |
|
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: 195.49 E-value: 3.10e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1075 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKE-LINISKKPKTPSLTV-FLLGQSARDAE 1152
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREiLMTASKNIKTPSMTLpLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1153 RAK---------DILCRLEHTTLRKVTANTAIyydpnPQStvvaedQEWVNVYYEMPdfdvarispwllrveLDRKhmtd 1223
Cdd:cd02735 81 TLKkrlsrvtlsDVVEKVEVTEILKTIERVFK-----KLL------GKWCEVTIKLP---------------LSSP---- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1224 rKLTMEQIAEKInagfgddlncifnddnAEKLVLRirimnsdenkmqeeeEVvdkmdddvflrciesnmltdmtlQGIEQ 1303
Cdd:cd02735 131 -KLLLLSIVEKL----------------ARKAVIR---------------EI-----------------------PGITR 155
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1304 ISKVYmhlpqTDNKKKiiitedgefkalQEWILETDGVSL--MRVLSEKdVDPVRTTSNDIVEIFTVLGIEAVRKALERE 1381
Cdd:cd02735 156 CFVVE-----EDKGGK------------TKYLVITEGVNLaaLWKFSDI-LDVNRIYTNDIHAMLNTYGIEAARRAIVKE 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1382 LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVnRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLG 1461
Cdd:cd02735 218 ISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVG 296
|
410
....*....|...
gi 4505939 1462 QLAPAGTGCFDLL 1474
Cdd:cd02735 297 KPVNGGTGLFDLL 309
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
16-1469 |
3.11e-54 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 211.02 E-value: 3.11e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 16 RTIKRVQFGVLSPDELKRMS------VTEGGIKYPETTEGGR--PKLGGLMDPRQGVIER------TGR-CQTCAGNMTE 80
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSygeiedVSTANYRTFKVEKGGLfcPKIFGPVNDDECLCGKykkrrhRGRiCEKCGVEVTS 1525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 81 CP---GHFGHIELAKPVFHVGFLvKTMKvlrcvcffcSKL--LVDSNNPKIKDILAKSKGQPKKRLTHVYDlcKGKNICE 155
Cdd:PRK14844 1526 SKvrrERMGHIELASPVAHIWFL-KSLP---------SRIgaLLDMSLRDIENILYSDNYIVIDPLVSPFE--KGEIISE 1593
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 156 GG-EEMDNKFGVEQ---PEGDED----LTKEKGHggcgryqpRIRRsglELYAEWKHVNEDSQEKKILlspervheifKR 227
Cdd:PRK14844 1594 KAyNEAKDSYGIDSfvaMQGVEAirelLTRLDLH--------EIRK---DLRLELESVASEIRRKKII----------KR 1652
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 228 ISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDV 307
Cdd:PRK14844 1653 LRIVENFIKSGN----RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEK 1728
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 308 KLLQFHVATMVDNELPGlpRAMQKSGRP--LKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIA 385
Cdd:PRK14844 1729 RMLQEAVDSLFDNSRRN--ALVNKAGAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMA 1806
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 386 anmtfAEIVTPFNIDRLQELVRRGNSQYpgAKYIIRDNgdridlrfHPKPSDLHLQTgykVERHMcdgdiVIFNRQPTLH 465
Cdd:PRK14844 1807 -----LELFKPFVYSKLKMYGMAPTIKF--ASKLIRAE--------KPEVWDMLEEV---IKEHP-----VLLNRAPTLH 1863
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 466 KMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAV 545
Cdd:PRK14844 1864 RLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGI 1943
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 546 RKFT----KRD---VFLERGEVMNllmflSTWDGKVpqpailkprplwtgkqifsliipgHINC-IRTHSTHPDDEDSGP 617
Cdd:PRK14844 1944 YYLTlqepKEDdlpSFGAFCEVEH-----SLSDGTL------------------------HIHSsIKYRMEYINSSGETH 1994
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 618 YKHISPGDTKVVV-------EN--GELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIG 688
Cdd:PRK14844 1995 YKTICTTPGRLILwqifpkhENlgFDLINQVLTVKEI----TSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFS 2070
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 689 IGDSIADSKTYQDIQNT---IKKAK---QDVIEVIEKAHNNELEptpgntlrqTFENQVNRILNDARDKTgsSAQKSLSE 762
Cdd:PRK14844 2071 RCDMVIPETKATHVDHArgeIKKFSmqyQDGLITRSERYNKVID---------EWSKCTDMIANDMLKAI--SIYDGNSK 2139
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 763 YNNFKSMVVSGAKGSKiniSQVIAVVGQQNVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFFFHAMG 842
Cdd:PRK14844 2140 YNSVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIISNFRE-----GLNVFEYFNSTHG 2199
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 843 GREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVefqnlatlkpsnkafekkfr 921
Cdd:PRK14844 2200 ARKGLADTALKTANSGYLTRRLVDvSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESV-------------------- 2259
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 922 fdytnerALRRTLQEDLVKDVlsnahIQNELEREFERMREDRevlrvifptgdskvvlpcnllrmiwnaqkifhinprlp 1001
Cdd:PRK14844 2260 -------VLGRTAANDIYNPV-----TKELLVKAGELIDEDK-------------------------------------- 2289
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1002 sdlhpikvvegVKELS-KKLVIVNGDDPLSRQAQENAtllfnihlrSTLCSRRmaeefrlsgeafDWLLGEIESKfnqai 1080
Cdd:PRK14844 2290 -----------VKQINiAGLDVVKIRSPLTCEISPGV---------CSLCYGR------------DLATGKIVSI----- 2332
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1081 ahpGEMVGALAAQSLGEPATQMTLNTFHYAGVsaknVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDA-ERAKDILC 1159
Cdd:PRK14844 2333 ---GEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIViSRSCEVVL 2405
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1160 -------RLEHTtlrkVTANTAIYYDPNPQSTVVAEDQEW-------------VNVYYEMPD------------------ 1201
Cdd:PRK14844 2406 idslgseKLKHS----VPYGAKLYVDEGGSVKIGDKVAEWdpytlpiitektgTVSYQDLKDgisitevmdestgisskv 2481
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1202 -------FDVARISPWLLRVELDRKHMTdrkltmeqIAEKINAGFGDDLNCIFNDDNAEK-----LVLRI---------- 1259
Cdd:PRK14844 2482 vkdwklySGGANLRPRIVLLDDNGKVMT--------LASGVEACYFIPIGAVLNVQDGQKvhagdVITRTpresvktrdi 2553
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1260 -----RIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGI-EQISKVYMHLpqtdNKKKIIITEDGEFkaLQE 1333
Cdd:PRK14844 2554 tgglpRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVdEQISPVEYLV----SRSKHVIVNEGDF--VRK 2627
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1334 WILETDGvslmrvlsekdvDPvrttsnDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLC----------- 1402
Cdd:PRK14844 2628 GDLLMDG------------DP------DLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILkqmlqkveitd 2689
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1403 --DTMTCRGHlmAITRHGVNRQDTG------------PLMK---------------CSFEETVDVLMEAAAHGESDPMKG 1453
Cdd:PRK14844 2690 pgDTMYLVGE--SIDKLEVDRENDAmsnsgkrpahylPILQgitrasletssfisaASFQETTKVLTEAAFCGKSDPLSG 2767
|
1610
....*....|....*.
gi 4505939 1454 VSENIMLGQLAPAGTG 1469
Cdd:PRK14844 2768 LKENVIVGRLIPAGTG 2783
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
244-1135 |
9.82e-54 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 208.19 E-value: 9.82e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 244 RPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELP 323
Cdd:PRK14906 311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 324 GLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQ 403
Cdd:PRK14906 391 GRP-VTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMA-----LELFKPFVMKRLV 464
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 404 ELVRRGNSQypGAKYIIrdngdridlrfhpkpsDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFR 483
Cdd:PRK14906 465 ELEYAANIK--AAKRAV----------------DRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIK 526
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 484 LNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT-KRDVFLERGEVmn 562
Cdd:PRK14906 527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDGFEGEGRT-- 604
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 563 llmFLSTWDGkvpqpailkprplwtgkqifsliipghincIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMgilCK 642
Cdd:PRK14906 605 ---FADFDDA------------------------------LNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEE---TK 648
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 643 --KSLGTSAGSLV----------HISYLEMGHDITRLfysnIQTVINNWLLIEGHTI---------------GIGDSIAD 695
Cdd:PRK14906 649 agERIETTVGRIIfnqvlpedypYLNYKMVKKDIGRL----VNDCCNRYSTAEVEPIldgikktgfhyatraGLTVSVYD 724
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 696 SKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPtpgntlrQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAK 775
Cdd:PRK14906 725 ATIPDDKPEILAEADEKVAAIDEDYEDGFLSE-------RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGAR 797
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 776 GSKINISQVIAVVG-QQNVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFHAMGGREGLIDTAVKT 854
Cdd:PRK14906 798 GNIKQIRQLAGMRGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRT 856
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 855 AETGYIQRRLiksmesVMVKYDATVRNsinqvvqlrygEDGLAGESVEfqnlatlkpsnkafekkfrFDYTNERAlrrTL 934
Cdd:PRK14906 857 ADSGYLTRRL------VDVAQDVIVRE-----------EDCGTDEGVT-------------------YPLVKPKG---DV 897
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 935 QEDLVKDVLSNAHIQNELErefermredrevlrVIFPTGDskvvlpcnllrmiwnaqkifhinprlpsdlhpikvvegvk 1014
Cdd:PRK14906 898 DTNLIGRCLLEDVCDPNGE--------------VLLSAGD---------------------------------------- 923
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1015 elskklvIVNGDDPLSRQAQENATllfNIHLRSTLCSRrmaEEFRLSGEAFDWLLgeieskfnqAIAHP---GEMVGALA 1091
Cdd:PRK14906 924 -------YIESMDDLKRLVEAGVT---KVQIRTLMTCH---AEYGVCQKCYGWDL---------ATRRPvniGTAVGIIA 981
|
890 900 910 920
....*....|....*....|....*....|....*....|....
gi 4505939 1092 AQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIsKKPK 1135
Cdd:PRK14906 982 AQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPK 1024
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
244-1137 |
1.33e-53 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 206.84 E-value: 1.33e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 244 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKLadivkI--NNQLRR------------NEQngaaahvia 304
Cdd:PRK00566 223 KPEWMILDVLPVIPPDLRPLVQLDGgrfatSDLN--DLYRRV-----InrNNRLKRllelgapeiivrNEK--------- 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 305 edvKLLQFHVATMVDNELPGlpRAMQ-KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRS 383
Cdd:PRK00566 287 ---RMLQEAVDALFDNGRRG--RPVTgPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKK 361
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 384 IAanmtfAEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgykverhm 450
Cdd:PRK00566 362 MA-----LELFKPFIMKKLVErglattiksakkMVEREDPEvWDVLEEVIKE---------HP----------------- 410
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPwstfrLnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:PRK00566 411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHP-----L---VCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSS 477
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 523 RMIVTPQSNRPVmgIV--QD------TLTAVRKFTKrdvflerGEVMnllMFLSTWD-------GKVPQPAILKPRP--- 584
Cdd:PRK00566 478 NNILSPANGKPI--IVpsQDmvlglyYLTREREGAK-------GEGM---VFSSPEEalrayenGEVDLHARIKVRItsk 545
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 585 --LWT--GKQIFSLIIPGHIncirthsthpddedsgPYkhispgdtkvvvENGELIMGilcKKSLgtsaGSLVHISYLEM 660
Cdd:PRK00566 546 klVETtvGRVIFNEILPEGL----------------PF------------INVNKPLK---KKEI----SKIINEVYRRY 590
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 661 GHDITRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyQDIqntIKKAKQDVIEvIEKAHNNELeptpgntlrQTFE- 738
Cdd:PRK00566 591 GLKETVIFLDKIKDLGFKYATRSGISIGIDDiVIPPEK--KEI---IEEAEKEVAE-IEKQYRRGL---------ITDGe 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 739 --NQVNRILNDARDKTGSSAQKSLSEYNN-FKS---MVVSGAKGSKINISQVIAVVG-QQNVEGKRIPfgfkhrtLPhfI 811
Cdd:PRK00566 656 ryNKVIDIWSKATDEVAKAMMKNLSKDQEsFNPiymMADSGARGSASQIRQLAGMRGlMAKPSGEIIE-------TP--I 726
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 812 KddygpesrgfveNSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLiksmesVMVKYDATVRN----SINQVV 887
Cdd:PRK00566 727 K------------SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVREddcgTDRGIE 788
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 888 QLRYGEDGLAGESVEfqnlatlkpsnkafekkfrfdytnERALRRTLQEDLVKDVLSNahiqnelerefermredrevlr 967
Cdd:PRK00566 789 VTAIIEGGEVIEPLE------------------------ERILGRVLAEDVVDPETGE---------------------- 822
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 968 VIFPTGDskvvlpcnLLRMIWnAQKIfhinprlpsdlhpikVVEGVKElskklvivngddplsrqaqenatllfnIHLRS 1047
Cdd:PRK00566 823 VIVPAGT--------LIDEEI-ADKI---------------EEAGIEE---------------------------VKIRS 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1048 TL-CsrrmaeefrlsgeafdwllgeiESKF---------NQAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVsa 1114
Cdd:PRK00566 852 VLtC----------------------ETRHgvcakcygrDLATGKLvniGEAVGVIAAQSIGEPGTQLTMRTFHTGGV-- 907
|
970 980
....*....|....*....|...
gi 4505939 1115 kNVTLGVPRLKELINiSKKPKTP 1137
Cdd:PRK00566 908 -DITGGLPRVAELFE-ARKPKGP 928
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
717-823 |
2.50e-45 |
|
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 159.45 E-value: 2.50e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 717 IEKA-HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEG 795
Cdd:pfam05000 1 ITDAeRYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 4505939 796 KRIPFGFKHRTLPHFIKDDYGPESRGFV 823
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
243-540 |
4.52e-42 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 165.31 E-value: 4.52e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 243 ARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNEL 322
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 323 PGlPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRl 402
Cdd:PRK02625 320 RG-RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMA-----IELFQPFVIHR- 392
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 403 qeLVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST 481
Cdd:PRK02625 393 --LIRQGIvNNIKAAKKLIQRADPEV----------------WQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 4505939 482 FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD 540
Cdd:PRK02625 455 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
86-514 |
7.16e-40 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 159.30 E-value: 7.16e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 86 GHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNpkiKDILAKSKGqpkkrlTHVYDLCKGKNIc 154
Cdd:CHL00018 105 GYIKLACPVTHVWYlkrlpsyianlLDKPLKELEGLVYCDFSFARPIAK---KPTFLRLRG------LFEYEIQSWKYS- 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 155 eggeemDNKFgVEQPEGDEDLTKEKGHGGcgryqPRIRR--SGLEL-------YAEWKHVNEDSQ------EKKILLspe 219
Cdd:CHL00018 175 ------IPLF-FSTQGFDTFRNREISTGA-----GAIREqlADLDLriiidnsLVEWKELGEEGStgneweDRKIGR--- 239
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 220 RVHEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRR--NEQNG 297
Cdd:CHL00018 240 RKDFLVRRIKLAKHFIR----TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDllTTSRS 315
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 298 AAAHVIAEDVKLLQFHVATMVDNELPGLPraMQKS-GRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSID 376
Cdd:CHL00018 316 TPGELVMCQKKLLQEAVDALLDNGIRGQP--MRDGhNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLH 393
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 377 QVGVPRSIAanmtfAEIVTPFNIdrlQELVRRGNSQYPG-AKYIIRDNGDRIDlrfhpkpsdlhlqtgyKVERHMCDGDI 455
Cdd:CHL00018 394 QCGLPREIA-----IELFQPFVI---RGLIRQHLASNIRaAKSKIREKEPIVW----------------EILQEVMQGHP 449
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505939 456 VIFNRQPTLHKMSMM--------GHRVRILPwstfrlnlSVTTPYNADFDGDEMNLHLPQSLETRAE 514
Cdd:CHL00018 450 VLLNRAPTLHRLGIQafqpilveGRAICLHP--------LVCKGFNADFDGDQMAVHVPLSLEAQAE 508
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1361-1470 |
1.59e-38 |
|
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: 141.79 E-value: 1.59e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1361 DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM 1440
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 4505939 1441 EAAAHGESDPMKGVSENIMLGQLAPAGTGC 1470
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 ... |
1084-1131 |
4.41e-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: 4.41e-21
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 4505939 1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1854-1959 |
4.83e-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: 81.12 E-value: 4.83e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1931
Cdd:pfam05109 517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
|
90 100
....*....|....*....|....*...
gi 4505939 1932 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1959
Cdd:pfam05109 597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
764-1117 |
3.92e-12 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 71.95 E-value: 3.92e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 764 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 830
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 831 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 909
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 910 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 989
Cdd:PRK02597 238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 990 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1067
Cdd:PRK02597 257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 4505939 1068 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1117
Cdd:PRK02597 301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
764-1234 |
6.98e-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: 71.03 E-value: 6.98e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 764 NNFKSMVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFH 839
Cdd:TIGR02388 119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 840 AMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqvvQLRYGEDGlaGESVEFQNlatlkpsnkafek 918
Cdd:TIGR02388 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTERSI----VVRAMTEG--DKKISLGD------------- 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 919 kfrfdytneRALRRTLQEDLVkdvlsnaHIQNElerefermredrevlrVIFPTGDSkvvlpcnllrmiwnaqkifhINP 998
Cdd:TIGR02388 236 ---------RLLGRLVAEDVL-------HPEGE----------------VIVPKNTA--------------------IDP 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 999 RLPSDLHPIKVVEgvkelskklviVNGDDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDWllgeieskfnq 1078
Cdd:TIGR02388 264 DLAKTIETAGISE-----------VVVRSPLTCEAA-----------RS-VCRK-----------CYGW----------- 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1079 AIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGV-PRLKELINISKKPKT-PSLTVFllGQSARDA 1151
Cdd:TIGR02388 299 SLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVrSKIDGTVEFGKKLRTrGYRTRH--GEDAKQV 376
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1152 ERAKDILCRlehttLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDF--------------DVA-RISPWLLRVEL 1216
Cdd:TIGR02388 377 EVAGLLIIK-----PTGSITNKAQEIEVTQGSLLFVEDGQTVDAGQLLAEIalgavrkstekatkDVAsDLAGEVKFDKV 451
|
490
....*....|....*...
gi 4505939 1217 DRKHMTDRKLTMEQIAEK 1234
Cdd:TIGR02388 452 VPEEKTDRQGNTTRIAQR 469
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1084-1127 |
5.94e-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: 5.94e-11
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 4505939 1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVsAKNVTLGVPRLKEL 1127
Cdd:cd02655 6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEEL 48
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1084-1475 |
6.13e-11 |
|
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: 66.68 E-value: 6.13e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAknvtlgVPRLKELI--NISKKPKTPSLTVFL---LGQSARDAE---RAK 1155
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESSP------LELLKEVLecRSKSKSKENDRRVILslhLCKCDHGFEyerAAL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1156 DILCRLEHTTLRKVTANTAIYYDPNPQstvvaedqewvnvyyEMPDFDVARISPWLLRVELDRKHMTDRKLTmeqiaeKI 1235
Cdd:cd02737 75 EVKNHLERVTLEDLATTSMIKYSPQAT---------------EAIVGEIGDQLNTKKKGKKKAIFSTSLKIT------KF 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1236 NAGfgddlNCIFNDDNAEKLVLR---IRIMNSDENKmQEEEEVVDKMDDDVFlrciesNMLTDMTLQGIEQISKVYMhLP 1312
Cdd:cd02737 134 SPW-----VCHFHLDKECQKLSDgpcLTFSVSKEVS-KSSEELLDVLRDRII------PFLLETVIKGDERIKSVNI-LW 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1313 QTDNKKKIIITEDGEFKAlqEWILETdGVSLMRVLSEKD---------------VDPVRTTSNDIVEIFTVLGIEAVRKA 1377
Cdd:cd02737 201 EDSPSTSWVKSVGKSSRG--ELVLEV-TVEESCKKTRGNawnvvmdacipvmdlIDWERSMPYSIQQIKSVLGIDAAFEQ 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1378 LERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDT-----GPLMKCSFEETVDVLMEAAAHGESDPMK 1452
Cdd:cd02737 278 FVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRslkisAPFTEACFSSPIKCFLKAAKKGASDSLS 357
|
410 420
....*....|....*....|....
gi 4505939 1453 GVSENIMLGQLAPAGTGC-FDLLL 1475
Cdd:cd02737 358 GVLDACAWGKEAPVGTGSkFEILW 381
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1491-1610 |
3.19e-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: 59.46 E-value: 3.19e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104 15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 4505939 1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104 91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
|
|
| PARM |
pfam17061 |
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present ... |
1854-1970 |
1.30e-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: 58.72 E-value: 1.30e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKY--SPTSPKYSPTSPKySPTSPTYSPTTPKYSPTSPT----------YSPTSPV-------YTPTSPKYSPTS- 1913
Cdd:pfam17061 22 TPPTATWtsSPQNTAAVTASPT-SGTHNNSVLPVTASAPTSPLpknvsvepreEESTSPAsnwegtsTDPSPPGLSPTSs 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4505939 1914 -----PT---YSPTSPKYS-PT----SPTYSP--TSPKGSTYSPTSPgysPTSPTySLTSPAISPDDSDEEN 1970
Cdd:pfam17061 101 gvhltPTpeeHSSGTPETSvPAtgsqSPAESPtlTSPQAPASSPSSP---STSPP-EVSSASVTTNHSSTET 168
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1431-1469 |
3.60e-07 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 55.77 E-value: 3.60e-07
10 20 30
....*....|....*....|....*....|....*....
gi 4505939 1431 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTG 1469
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1084-1112 |
8.89e-07 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 54.56 E-value: 8.89e-07
10 20
....*....|....*....|....*....
gi 4505939 1084 GEMVGALAAQSLGEPATQMTLNTFHYAGV 1112
Cdd:CHL00117 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1853-1967 |
1.68e-06 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 52.83 E-value: 1.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1853 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1929
Cdd:COG3469 89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
|
90 100 110
....*....|....*....|....*....|....*...
gi 4505939 1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSD 1967
Cdd:COG3469 169 TTTTTSASTTPSATTTATATTASGATTPSATTTATTTG 206
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
761-865 |
1.80e-06 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 53.40 E-value: 1.80e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 761 SEY------NNFKS---------MVVSGAKGskiNISQVIAVVG--------QqnveGKRIpfgfkhrTLPhfIKddygp 817
Cdd:CHL00117 108 SEYlkqemnPNFRMtdplnpvymMSFSGARG---NASQVHQLVGmrglmsdpQ----GQII-------DLP--IQ----- 166
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 4505939 818 esRGFVEnsylaGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLI 865
Cdd:CHL00117 167 --SNFRE-----GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1871-1963 |
8.15e-06 |
|
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: 51.07 E-value: 8.15e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1871 SPKYSPTSPTYSpTTPKYSPTSPTYSP------------------------TSPVYTPTSPKYSPTSPTYSP-------- 1918
Cdd:pfam05109 424 APESTTTSPTLN-TTGFAAPNTTTGLPssthvptnltapastgptvstadvTSPTPAGTTSGASPVTPSPSPrdngtesk 502
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 4505939 1919 ----TSPKYSPTSPTYSPTSPKGSTYSP----TSPGYSPTSPTYSLTSP---AISP 1963
Cdd:pfam05109 503 apdmTSPTSAVTTPTPNATSPTPAVTTPtpnaTSPTLGKTSPTSAVTTPtpnATSP 558
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1858-1962 |
1.01e-05 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 50.34 E-value: 1.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1858 PKYSPTSPKYSPTSPKYSPTSpTYSPTTPKYSPTSPTYSPTSPvyTPTSPKySPTSPTYSPTSPKYSPTSPTYSPTSPkg 1937
Cdd:PHA03291 181 SADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTP--TPSTTT-SPPSTTIPAPSTTIAAPQAGTTPEAE-- 254
|
90 100
....*....|....*....|....*
gi 4505939 1938 STYSPTSPGYSPTSPTYSLTSPAIS 1962
Cdd:PHA03291 255 GTPAPPTPGGGEAPPANATPAPEAS 279
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1875-1969 |
1.15e-05 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 50.19 E-value: 1.15e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1875 SPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT--YSPTSPKGSTYSPTSPGYSPTSP 1952
Cdd:PRK14950 370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTpeSAPKLTRAAIPVDEKPKYTPPAP 449
|
90
....*....|....*..
gi 4505939 1953 TYSLTSPAISPDDSDEE 1969
Cdd:PRK14950 450 PKEEEKALIADGDVLEQ 466
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1431-1470 |
1.88e-05 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 49.94 E-value: 1.88e-05
10 20 30 40
....*....|....*....|....*....|....*....|
gi 4505939 1431 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGC 1470
Cdd:CHL00117 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
|
|
| DUF1373 |
pfam07117 |
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ... |
1855-1968 |
5.57e-05 |
|
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: 46.32 E-value: 5.57e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1855 PTSPKYSPTSPKYSPTSPKY----SPTSP-TYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT 1929
Cdd:pfam07117 33 PLPPGQEPEPPRPEEEEGQGggggTFPFPgSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSS 112
|
90 100 110
....*....|....*....|....*....|....*....
gi 4505939 1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDE 1968
Cdd:pfam07117 113 GSGSGHQGSGGAGAGAGAPGHQHEQEQESSSSDDDDEDE 151
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1854-1938 |
5.69e-05 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 48.27 E-value: 5.69e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPkySPTSPTYSPTSPKYSPTSPTYSPT 1933
Cdd:PRK14950 370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPH--TPESAPKLTRAAIPVDEKPKYTPP 447
|
....*
gi 4505939 1934 SPKGS 1938
Cdd:PRK14950 448 APPKE 452
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1865-1960 |
5.88e-05 |
|
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: 44.43 E-value: 5.88e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1865 PKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTSPTYSPTSPKGST 1939
Cdd:smart01104 15 PAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEGSASSWAAGPGGA 91
|
90 100
....*....|....*....|.
gi 4505939 1940 YSPTSPGYSPTSPTYSLTSPA 1960
Cdd:smart01104 92 YGAPTPGYGGTPSAYGPATPG 112
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1852-1957 |
6.25e-05 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 47.83 E-value: 6.25e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1852 EYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS------PTSPVYTPTSPKYSPTSPTYSPTSPKYSP 1925
Cdd:COG3469 109 TSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVsgtetaTGGTTTTSTTTTTTSASTTPSATTTATAT 188
|
90 100 110
....*....|....*....|....*....|..
gi 4505939 1926 TSPTYSPTSPKGSTysPTSPGYSPTSPTYSLT 1957
Cdd:COG3469 189 TASGATTPSATTTA--TTTGPPTPGLPKHVLV 218
|
|
| Endomucin |
pfam07010 |
Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early ... |
1868-1959 |
8.31e-05 |
|
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: 46.40 E-value: 8.31e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1868 SPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTS--PKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1945
Cdd:pfam07010 29 ANITLSTTPSTTAETASTPKTTNLNTPTGGTSPVGTTSSelSKTSLVSTTISLTTTKKGVGTTTTDVSKNESSTTKPTVT 108
|
90
....*....|....
gi 4505939 1946 GYSPTSPTYSLTSP 1959
Cdd:pfam07010 109 STPLSNAVSTLQSS 122
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1854-1960 |
1.08e-04 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 46.87 E-value: 1.08e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPT 1933
Cdd:PTZ00436 232 AAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAA 311
|
90 100 110
....*....|....*....|....*....|.
gi 4505939 1934 SPKGSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436 312 APAKAAAPPakaaAPPAKAATPPAKAAAPPA 342
|
|
| rad23 |
TIGR00601 |
UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
1870-1942 |
1.46e-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: 46.43 E-value: 1.46e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4505939 1870 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:TIGR00601 75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1855-1966 |
1.79e-04 |
|
translocon at the inner envelope of chloroplast subunit 62; Provisional
Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 46.46 E-value: 1.79e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1855 PTSPkySPTSPKYSPTSPKYSPTSPTySPTTPKYSPTSPTYSPTSPVYTPTSPKY------SPTSPTYSPTSPKYSPTSP 1928
Cdd:PLN03209 450 PTSP--SPTAPTGVSPSVSSTSSVPA-VPDTAPATAATDAAAPPPANMRPLSPYAvyddlkPPTSPSPAAPVGKVAPSST 526
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 4505939 1929 TYSPtsPKGSTYSPTS---------PGYSPTSP--TYSLTSPAISPDDS 1966
Cdd:PLN03209 527 NEVV--KVGNSAPPTAladeqhhaqPKPRPLSPytMYEDLKPPTSPTPS 573
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1060-1104 |
1.87e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 46.42 E-value: 1.87e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 4505939 1060 LSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTL 1104
Cdd:PRK14898 33 VTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1853-1961 |
1.94e-04 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 46.10 E-value: 1.94e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1853 YTPTSPKYSPTSPKYSPTSpKYSPTSPTYSP--------TTPKYSPTSPTysptspvyTPTSPKYSPTSPTYSPTSPKYS 1924
Cdd:PHA03291 183 DGSCDPALPLSAPRLGPAD-VFVPATPRPTPrttaspetTPTPSTTTSPP--------STTIPAPSTTIAAPQAGTTPEA 253
|
90 100 110
....*....|....*....|....*....|....*..
gi 4505939 1925 PTSPtySPTSPKGSTYSPTSPGYSPTSPTYSLTSPAI 1961
Cdd:PHA03291 254 EGTP--APPTPGGGEAPPANATPAPEASRYELTVTQI 288
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1865-1952 |
2.55e-04 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 45.72 E-value: 2.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1865 PKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSpVYTPTSPKYSPTSPTySP--TSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:PHA03291 167 PAEGTLAAPPLGEGSADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTA-SPetTPTPSTTTSPPSTTIPAPSTTIAA 244
|
90
....*....|
gi 4505939 1943 TSPGYSPTSP 1952
Cdd:PHA03291 245 PQAGTTPEAE 254
|
|
| PLN02217 |
PLN02217 |
probable pectinesterase/pectinesterase inhibitor |
1869-1966 |
3.33e-04 |
|
probable pectinesterase/pectinesterase inhibitor
Pssm-ID: 215130 [Multi-domain] Cd Length: 670 Bit Score: 45.85 E-value: 3.33e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1869 PTSPKYSPTSPTYSPTTPKYS--PTSPTYSPTSPVyTPTSPKYSPtsPTYSPTSPKYSPT---SPTYSPtsPKGSTYSPT 1943
Cdd:PLN02217 556 PYIPGLFAGNPGSTNSTPTGSaaSSNTTFSSDSPS-TVVAPSTSP--PAGHLGSPPATPSkivSPSTSP--PASHLGSPS 630
|
90 100
....*....|....*....|...
gi 4505939 1944 SPGYSPTSPTYSLTSPAISPDDS 1966
Cdd:PLN02217 631 TTPSSPESSIKVASTETASPESS 653
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1515-1621 |
5.37e-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: 41.74 E-value: 5.37e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1515 PAMTP-WNQGA--TPAYGAWSPSVGSGMTPGAAGFSPSAASdASGFSPGYSPAWSPTpgspgspgpsspyipSPGGAMSP 1591
Cdd:smart01104 1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRTP-AWGGAGSRTPAWGGA---------------GPTGSRTP 64
|
90 100 110
....*....|....*....|....*....|
gi 4505939 1592 SYSPTSPAYEPRSPGGYTPQSPSYSPTSPS 1621
Cdd:smart01104 65 AWGGASAWGNKSSEGSASSWAAGPGGAYGA 94
|
|
| GATA-N |
pfam05349 |
GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell ... |
1861-1969 |
5.40e-04 |
|
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: 42.81 E-value: 5.40e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1861 SPTSPKYSPTSPKY---SPTSPTYSPTT--PKYSPTSPtYSPTSPVYTPTSPKYS-PTSPTYSPTSPKYSPTSPTYSPts 1934
Cdd:pfam05349 10 NHGQAAYDHDSGGFlhsAASSPVYVPTTrvPSMLPTLP-YLQGCGSSQQSHPVSShSGWAQAGAESSSYNPGSPHPSP-- 86
|
90 100 110
....*....|....*....|....*....|....*
gi 4505939 1935 pkGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEE 1969
Cdd:pfam05349 87 --RFSYSHSPPGSNGTSRDAAYQSPLLISAGGREQ 119
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1854-1936 |
7.05e-04 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 44.68 E-value: 7.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKYSPTS-PKYSPTSPKySPTSPTYSPTTPKYSPTSPTYSPTS--------PVYTP--------------TSPKYS 1910
Cdd:PTZ00449 710 TPGTPFTTPRPlPPKLPRDEE-FPFEPIGDPDAEQPDDIEFFTPPEEertffhetPADTPlpdilaeefkeediHAETGE 788
|
90 100
....*....|....*....|....*..
gi 4505939 1911 PTSPTYSPTSP-KYSPTSPTYSPTSPK 1936
Cdd:PTZ00449 789 PDEAMKRPDSPsEHEDKPPGDHPSLPK 815
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1857-1959 |
8.33e-04 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.79 E-value: 8.33e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436 249 APAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPA 328
|
90 100
....*....|....*....|...
gi 4505939 1937 GSTyspTSPGYSPTSPTYSLTSP 1959
Cdd:PTZ00436 329 KAA---TPPAKAAAPPAKAAAAP 348
|
|
| Pneumo_att_G |
pfam05539 |
Pneumovirinae attachment membrane glycoprotein G; |
1854-1970 |
9.16e-04 |
|
Pneumovirinae attachment membrane glycoprotein G;
Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 43.88 E-value: 9.16e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKysptsPKYSPTSPKYSPT-SPTYSPTTPkySPTSPTySPTSPVYTPTspkysPTSPTySPTSPKYSPTSPTYSP 1932
Cdd:pfam05539 226 TSSNPE-----PQTEPPPSQRGPSgSPQHPPSTT--SQDQST-TGDGQEHTQR-----RKTPP-ATSNRRSPHSTATPPP 291
|
90 100 110
....*....|....*....|....*....|....*...
gi 4505939 1933 TSPKGSTYSPTspgYSPTSPTYSLTSPAISPDDSDEEN 1970
Cdd:pfam05539 292 TTKRQETGRPT---PRPTATTQSGSSPPHSSPPGVQAN 326
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1855-1960 |
1.03e-03 |
|
translocon at the inner envelope of chloroplast subunit 62; Provisional
Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 44.15 E-value: 1.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1855 PTSP--KYSPTSPkysPTSPKYSPTSPTYSPTTpkySPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPK------YSPT 1926
Cdd:PLN03209 437 PLSPyaRYEDLKP---PTSPSPTAPTGVSPSVS---STSSVPAVPDTAPATAATDAAAPPPANMRPLSPYavyddlKPPT 510
|
90 100 110
....*....|....*....|....*....|....
gi 4505939 1927 SPTysPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1960
Cdd:PLN03209 511 SPS--PAAPVGKVAPSSTNEVVKVGNSAPPTALA 542
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1857-1960 |
1.03e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.79 E-value: 1.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436 228 APAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPA 307
|
90 100
....*....|....*....|....*...
gi 4505939 1937 GSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436 308 KAAAAPakaaAPPAKAAAPPAKAATPPA 335
|
|
| rad23 |
TIGR00601 |
UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
1862-1943 |
1.12e-03 |
|
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: 43.73 E-value: 1.12e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1862 PTSPKYSPTSPKYSPTS-PTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTY 1940
Cdd:TIGR00601 77 PKTGTGKVAPPAATPTSaPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSER 156
|
...
gi 4505939 1941 SPT 1943
Cdd:TIGR00601 157 ETT 159
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1857-1937 |
1.23e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.40 E-value: 1.23e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436 270 PPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAPV 349
|
.
gi 4505939 1937 G 1937
Cdd:PTZ00436 350 G 350
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1857-1960 |
1.24e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.40 E-value: 1.24e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1857 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1936
Cdd:PTZ00436 221 APAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPA 300
|
90 100
....*....|....*....|....*...
gi 4505939 1937 GSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436 301 KAAAAPakaaAAPAKAAAPPAKAAAPPA 328
|
|
| KAR9 |
pfam08580 |
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ... |
1853-1962 |
1.50e-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: 43.67 E-value: 1.50e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1853 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTP---------------KYSPTSPT-YSPTSPVYTPTSPKYSPTSPTY 1916
Cdd:pfam08580 503 GFLSTPSNTATSETPTPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTtPSPTPSRSSRSSSTLPPVSPLS 582
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 4505939 1917 SPTSPKYSPTSPTYSPTSPKGSTYSPTSPGySPTSPTYSLTSPAIS 1962
Cdd:pfam08580 583 RDKSRSPAPTCRSVSRASRRRASRKPTRIG-SPNSRTSLLDEPPYP 627
|
|
| PHA03269 |
PHA03269 |
envelope glycoprotein C; Provisional |
1855-1959 |
1.59e-03 |
|
envelope glycoprotein C; Provisional
Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 43.56 E-value: 1.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1855 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTySPTSPKYSPtsPTYSPTS 1934
Cdd:PHA03269 46 PHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQLAA-APKPDAAEA--FTSAAQA 122
|
90 100
....*....|....*....|....*.
gi 4505939 1935 PKGSTYSPTSP-GYSPTSPTYSLTSP 1959
Cdd:PHA03269 123 HEAPADAGTSAaSKKPDPAAHTQHSP 148
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1856-1942 |
1.97e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 42.63 E-value: 1.97e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1856 TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1935
Cdd:PTZ00436 262 APPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPP 341
|
....*..
gi 4505939 1936 KGSTYSP 1942
Cdd:PTZ00436 342 AKAAAAP 348
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1855-1959 |
2.19e-03 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 43.14 E-value: 2.19e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1855 PTSPKY--SPTSPKySPTSPKySPTSP-----TYSPTTPKySPTSPTySPTSP-----VYTPTSPKYSPTSPT------- 1915
Cdd:PTZ00449 621 PKSPKRpeSPKSPK-RPPPPQ-RPSSPerpegPKIIKSPK-PPKSPK-PPFDPkfkekFYDDYLDAAAKSKETkttvvld 696
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 4505939 1916 ------------YSPTSPKYSPTS-PTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSP 1959
Cdd:PTZ00449 697 esfesilketlpETPGTPFTTPRPlPPKLPRDEEFPFEPIGDPDAEQPDDIEFFTPP 753
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1854-1968 |
2.31e-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: 2.31e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKYSPTSPK-----YSPTSPKYSPTSPTYS----------------PTTP--KYS----PTSPTYSPTSPVYTPTS 1906
Cdd:PLN03209 387 IPTPPSSSPASSKsvdavAKPAEPDVVPSPGSASnvpevepaqveakktrPLSPyaRYEdlkpPTSPSPTAPTGVSPSVS 466
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4505939 1907 pkySPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP---TSPGYSPTSPTYSLTSPAISPDDSDE 1968
Cdd:PLN03209 467 ---STSSVPAVPDTAPATAATDAAAPPPANMRPLSPyavYDDLKPPTSPSPAAPVGKVAPSSTNE 528
|
|
| KAR9 |
pfam08580 |
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ... |
1854-1970 |
2.39e-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: 42.89 E-value: 2.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKYSPTSPKYSPTSP---------------KYSPTSPTY-SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPT----- 1912
Cdd:pfam08580 518 TPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTTpSPTPSRSSRSSSTLPPVSPLSRDKSRSPAPTcrsvs 597
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4505939 1913 SPTYSPTSPK----YSPTSPTY--SPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN 1970
Cdd:pfam08580 598 RASRRRASRKptriGSPNSRTSllDEPPYPKLTLSKGLPRTPRNRQSYAGTSPSRSVSVSSGLG 661
|
|
| CytochromB561_N |
pfam09786 |
Cytochrome B561, N terminal; Members of this family are found in the N terminal region of ... |
1855-1941 |
2.52e-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: 42.89 E-value: 2.52e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1855 PTSPKYSPTSPKYSPTSPKYSP--TSPTYSPTTPKYSPTSP-TYSPTSPVYTPTSPkySPTSPTYSpTSPKYSP--TSPT 1929
Cdd:pfam09786 145 PLHQSVSPSSSESRKGGDKSPAgsGKKLRSFSTSSKSPASPsVYLRGSPVPLNSSP--LPSDRNYE-NSVQSSPeiDSAV 221
|
90
....*....|..
gi 4505939 1930 YSPTSPKGSTYS 1941
Cdd:pfam09786 222 STPWSRKRATIG 233
|
|
| 2A1904 |
TIGR00927 |
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1852-1967 |
2.99e-03 |
|
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]
Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 42.68 E-value: 2.99e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1852 EYTPTSPKyspTSPKYSPTSPK--YSPTSPTY------SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKY 1923
Cdd:TIGR00927 109 ENTPSPPR---RTAKITPTTPKnnYSPTAAGTervkedTPATPSRALNHYISTSGRQRVKSYTPKPRGEVKSSSPTQTRE 185
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 4505939 1924 SPTSPTYSPTSPKGSTYSPTSPGYSPTSPTyslTSPAISPDDSD 1967
Cdd:TIGR00927 186 KVRKYTPSPLGRMVNSYAPSTFMTMPRSHG---ITPRTTVKDSE 226
|
|
| Pneumo_att_G |
pfam05539 |
Pneumovirinae attachment membrane glycoprotein G; |
1855-1951 |
3.73e-03 |
|
Pneumovirinae attachment membrane glycoprotein G;
Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 41.96 E-value: 3.73e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1855 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS-PTSPVYTPTSPKYSPTSPTYSPTspkYSPTSPTYSPT 1933
Cdd:pfam05539 237 PPSQRGPSGSPQHPPSTTSQDQSTTGDGQEHTQRRKTPPATSnRRSPHSTATPPPTTKRQETGRPT---PRPTATTQSGS 313
|
90
....*....|....*...
gi 4505939 1934 SPKGStySPTSPGYSPTS 1951
Cdd:pfam05539 314 SPPHS--SPPGVQANPTT 329
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1854-1945 |
5.18e-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: 39.04 E-value: 5.18e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TP----TSPKYSPTSPkysPTSPKYSP-TSPTYSPT---TP------KYSPTSPTYSPTSPVY-----TPTSPKYSPTSP 1914
Cdd:smart01104 14 TPawgsRTPGTAAGGA---PTARGGSGsRTPAWGGAgsrTPawggagPTGSRTPAWGGASAWGnksseGSASSWAAGPGG 90
|
90 100 110
....*....|....*....|....*....|.
gi 4505939 1915 TYSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1945
Cdd:smart01104 91 AYGAPTPGYGGTPSAYGPATPGGGAMAGSAS 121
|
|
| Hamartin |
pfam04388 |
Hamartin protein; This family includes the hamartin protein which is thought to function as a ... |
1876-1955 |
5.49e-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: 5.49e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1876 PTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTsPTYSPTSPKGSTYSPTSPGYSPTSPTYS 1955
Cdd:pfam04388 276 PTASPYTDQQSSYGSSTSTPSSTPRLQLSSSSGTSPPYLSPPSIRLKTDSF-PLWSPSSVCGMTTPPTSPGMVPTTPSEL 354
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1854-1952 |
8.61e-03 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 41.21 E-value: 8.61e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505939 1854 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKyspTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTyspt 1933
Cdd:PTZ00449 728 DEEFPFEPIGDPDAEQPDDIEFFTPPEEERTFFH---ETPADTPLPDILAEEFKEEDIHAETGEPDEAMKRPDSPS---- 800
|
90
....*....|....*....
gi 4505939 1934 spkgsTYSPTSPGYSPTSP 1952
Cdd:PTZ00449 801 -----EHEDKPPGDHPSLP 814
|
|
| |
