|
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 ... |
1-843 |
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: 1580.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCf 79
Cdd:cd02733 16 MSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGFLTKILKILRCVC- 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 fcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltkekghggcgryqprir 159
Cdd:cd02733 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 160 rsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARN 239
Cdd:cd02733 93 --------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSARS 152
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 240 QDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRG 319
Cdd:cd02733 153 EDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRG 232
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 320 NLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFH 399
Cdd:cd02733 233 NLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGERIDLRYL 312
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 400 PKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETR 479
Cdd:cd02733 313 KKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETR 392
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 480 AEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIF 559
Cdd:cd02733 393 AELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQPAILKPKPLWTGKQIF 472
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 560 SLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDVTRLFYSNI 639
Cdd:cd02733 473 SLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNI 547
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 640 QTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKT 719
Cdd:cd02733 548 QRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKA 627
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 720 GSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLT 799
Cdd:cd02733 628 GKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLT 707
|
810 820 830 840
....*....|....*....|....*....|....*....|....
gi 1958662372 800 PTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 843
Cdd:cd02733 708 PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
1-862 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 968.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCF 79
Cdd:PRK08566 25 MSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIHVGFAKLIYKLLRATCR 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 FCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPegdedltkekgHggCGR 153
Cdd:PRK08566 103 ECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P-----------H--CGE 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 154 YQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVM 233
Cdd:PRK08566 154 KQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITL 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 234 QGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKG 312
Cdd:PRK08566 228 ETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 313 KEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGD 392
Cdd:PRK08566 307 KEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGR 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 393 RIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNL 470
Cdd:PRK08566 387 RIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 471 HLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPR 550
Cdd:PRK08566 466 HVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGK 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 551 PLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHD 630
Cdd:PRK08566 546 PYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPE 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 631 VTRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNR 710
Cdd:PRK08566 624 RARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQ 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 711 ILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFV 790
Cdd:PRK08566 704 VLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFV 783
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958662372 791 ENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDG 862
Cdd:PRK08566 784 RSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
1-864 |
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: 920.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCF 79
Cdd:TIGR02390 20 MSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVHVGFAKEIYKILRATCR 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 FCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPegdedltkekghggcgr 153
Cdd:TIGR02390 98 KCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP----------------- 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 154 yqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVM 233
Cdd:TIGR02390 160 ----------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITL 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 234 QGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGK 313
Cdd:TIGR02390 224 ETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGK 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 314 EGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDR 393
Cdd:TIGR02390 304 EGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRR 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 394 IDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHL 472
Cdd:TIGR02390 384 IKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHV 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 473 PQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLSTWDGKVPQPAILKPRPL 552
Cdd:TIGR02390 464 PQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAGYFGDPPEPAIEKPKEY 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 553 WTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDV 631
Cdd:TIGR02390 543 WTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEA 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 632 TRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRI 711
Cdd:TIGR02390 620 ARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEV 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 712 LNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVE 791
Cdd:TIGR02390 700 LGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVR 779
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958662372 792 NSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLA 864
Cdd:TIGR02390 780 SSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVD 852
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1025-1443 |
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: 820.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1025 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1104
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1105 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1182
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1183 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1262
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1263 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1342
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1343 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1422
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 1958662372 1423 ENIMLGQLAPAGTGCFDLLLD 1443
Cdd:cd02584 390 ENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
797-1394 |
4.85e-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: 544.26 E-value: 4.85e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 797 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 876
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 877 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 956
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 957 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1036
Cdd:pfam04998 120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1037 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1116
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1117 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1188
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1189 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1268
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1269 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1347
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 1958662372 1348 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1394
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
213-513 |
2.83e-172 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 524.78 E-value: 2.83e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 213 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 292
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 293 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 372
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 373 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 451
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958662372 452 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 513
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-321 |
3.80e-132 |
|
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: 415.92 E-value: 3.80e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVC 78
Cdd:pfam04997 20 WSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFHIGFFKKTLKILECVC 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 79 FFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpegdedltkekghGGCGRYQP 156
Cdd:pfam04997 98 KYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------------------GVCGSQQP 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 157 RIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGS 236
Cdd:pfam04997 158 VSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 237 ARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGR 316
Cdd:pfam04997 236 RRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGR 315
|
....*
gi 1958662372 317 VRGNL 321
Cdd:pfam04997 316 FRGNL 320
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
863-1046 |
3.00e-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: 3.00e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 863 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 939
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 940 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1018
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 1958662372 1019 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1046
Cdd:pfam04992 161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1019-1446 |
2.96e-88 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 293.29 E-value: 2.96e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1019 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1098
Cdd:PRK04309 27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1099 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1178
Cdd:PRK04309 107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1179 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1258
Cdd:PRK04309 157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1259 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1338
Cdd:PRK04309 214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1339 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1418
Cdd:PRK04309 275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354
|
410 420
....*....|....*....|....*...
gi 1958662372 1419 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1446
Cdd:PRK04309 355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1021-1443 |
7.25e-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: 283.10 E-value: 7.25e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1021 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1100
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1101 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1180
Cdd:TIGR02389 94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1181 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1258
Cdd:TIGR02389 144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1259 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1338
Cdd:TIGR02389 201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1339 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1418
Cdd:TIGR02389 263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342
|
410 420
....*....|....*....|....*
gi 1958662372 1419 KGVSENIMLGQLAPAGTGCFDLLLD 1443
Cdd:TIGR02389 343 KGVIENIIVGQPIPLGTGDVDLVMD 367
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
52-915 |
1.79e-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: 241.60 E-value: 1.79e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 52 FGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrlthvydlckgk 118
Cdd:COG0086 92 MGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI------------- 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 119 nICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllspervhEIFKRI 195
Cdd:COG0086 159 -LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK--------KLIKRL 211
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 196 SDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVK 275
Cdd:COG0086 212 KVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKR 287
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 276 LLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAan 354
Cdd:COG0086 288 MLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA-- 363
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 355 mtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhmcdgdiVIFNR 427
Cdd:COG0086 364 ---LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------------VLLNR 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 428 QPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNR 499
Cdd:COG0086 416 APTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGK 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 500 PVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ------------IF 559
Cdd:COG0086 488 PIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgkivettvgryLV 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 560 SLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLEMGHDVTRLFY 636
Cdd:COG0086 563 NEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRRCGLKETVIFL 602
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 637 SNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfENQVNRILNDAR 716
Cdd:COG0086 603 DRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTKAS 671
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 717 DKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenSYL 795
Cdd:COG0086 672 LETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS---------------------NFR 730
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 796 AGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedglaGESVEfqnla 874
Cdd:COG0086 731 EGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG-----GEVIE----- 799
|
890 900 910 920
....*....|....*....|....*....|....*....|.
gi 1958662372 875 TLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 915
Cdd:COG0086 800 PLK----------------ERILGRVAAED-VVDPGTGEVL 823
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1821-1926 |
4.73e-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: 4.73e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1898
Cdd:pfam05109 517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
|
90 100
....*....|....*....|....*...
gi 1958662372 1899 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1926
Cdd:pfam05109 597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
731-1084 |
3.84e-12 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 71.95 E-value: 3.84e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 731 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 797
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 798 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 876
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 877 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 956
Cdd:PRK02597 238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 957 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1034
Cdd:PRK02597 257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 1958662372 1035 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1084
Cdd:PRK02597 301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1458-1577 |
2.17e-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: 59.84 E-value: 2.17e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1458 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1530
Cdd:smart01104 15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1958662372 1531 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1577
Cdd:smart01104 91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1820-1930 |
2.64e-06 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 52.45 E-value: 2.64e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1820 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1896
Cdd:COG3469 89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
|
90 100 110
....*....|....*....|....*....|....
gi 1958662372 1897 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISP 1930
Cdd:COG3469 169 TTTTTSASTTPSATTTATATTASGATTPSATTTA 202
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1842-1936 |
4.14e-06 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 51.73 E-value: 4.14e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1842 SPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT--YSPTSPKGSTYSPTSPGYSPTSP 1919
Cdd:PRK14950 370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTpeSAPKLTRAAIPVDEKPKYTPPAP 449
|
90
....*....|....*..
gi 1958662372 1920 TYSLTSPAISPEDSDEE 1936
Cdd:PRK14950 450 PKEEEKALIADGDVLEQ 466
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1823-1927 |
4.72e-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: 44.82 E-value: 4.72e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1823 TSPKYSPTS---PKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTS 1894
Cdd:smart01104 3 RTPAWGASGsktPAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEG 79
|
90 100 110
....*....|....*....|....*....|...
gi 1958662372 1895 PTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1927
Cdd:smart01104 80 SASSWAAGPGGAYGAPTPGYGGTPSAYGPATPG 112
|
|
| rad23 |
TIGR00601 |
UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
1837-1909 |
1.44e-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: 1.44e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958662372 1837 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1909
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 ... |
1-843 |
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: 1580.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCf 79
Cdd:cd02733 16 MSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGFLTKILKILRCVC- 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 fcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltkekghggcgryqprir 159
Cdd:cd02733 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 160 rsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARN 239
Cdd:cd02733 93 --------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSARS 152
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 240 QDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRG 319
Cdd:cd02733 153 EDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRG 232
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 320 NLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFH 399
Cdd:cd02733 233 NLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGERIDLRYL 312
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 400 PKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETR 479
Cdd:cd02733 313 KKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETR 392
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 480 AEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIF 559
Cdd:cd02733 393 AELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQPAILKPKPLWTGKQIF 472
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 560 SLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDVTRLFYSNI 639
Cdd:cd02733 473 SLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNI 547
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 640 QTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKT 719
Cdd:cd02733 548 QRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKA 627
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 720 GSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLT 799
Cdd:cd02733 628 GKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLT 707
|
810 820 830 840
....*....|....*....|....*....|....*....|....
gi 1958662372 800 PTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 843
Cdd:cd02733 708 PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
1-862 |
0e+00 |
|
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 983.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCF 79
Cdd:cd02582 20 MSVVE--IITPDTyDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHVGFAKHIYDLLRATCR 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 FCSKLLV-DSNNPKIKDILAKSKG---QPKKRL-THVYDLCKGKNICeggeemdnkfgveqPegdedltkekgHggCGRY 154
Cdd:cd02582 98 SCGRILLpEEEIEKYLERIRRLKEkwpELVKRViEKVKKKAKKRKVC--------------P-----------H--CGAP 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 155 QPRIRrsgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQ 234
Cdd:cd02582 151 QYKIK---LEKPTTFYEEKEEGEVK---LTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTVRPSITLE 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 235 GSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKE 314
Cdd:cd02582 225 TGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKE 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 315 GRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRI 394
Cdd:cd02582 305 GRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRPDGRRI 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 395 DLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHL 472
Cdd:cd02582 385 RLRYVNR-EELaeRLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHV 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 473 PQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStWDGKVPQPAILKPRPL 552
Cdd:cd02582 464 PQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAG-YDGLLPEPAILEPKPL 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 553 WTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHisPGDTKVVVENGELIMGILCKKSLGT-SAGSLVHISYLEMGHDV 631
Cdd:cd02582 543 WTGKQLFSLFLPKDLNFEGKAKVCSGCSECKDEDC--PNDGYVVIKNGKLLEGVIDKKAIGAeQPGSLLHRIAKEYGNEV 620
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 632 TRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRI 711
Cdd:cd02582 621 ARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQV 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 712 LNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVE 791
Cdd:cd02582 701 LGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVR 780
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958662372 792 NSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDG 862
Cdd:cd02582 781 SSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDG 851
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
1-862 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 968.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCF 79
Cdd:PRK08566 25 MSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIHVGFAKLIYKLLRATCR 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 FCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPegdedltkekgHggCGR 153
Cdd:PRK08566 103 ECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P-----------H--CGE 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 154 YQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVM 233
Cdd:PRK08566 154 KQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITL 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 234 QGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKG 312
Cdd:PRK08566 228 ETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 313 KEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGD 392
Cdd:PRK08566 307 KEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGR 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 393 RIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNL 470
Cdd:PRK08566 387 RIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 471 HLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPR 550
Cdd:PRK08566 466 HVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGK 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 551 PLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHD 630
Cdd:PRK08566 546 PYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPE 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 631 VTRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNR 710
Cdd:PRK08566 624 RARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQ 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 711 ILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFV 790
Cdd:PRK08566 704 VLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFV 783
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958662372 791 ENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDG 862
Cdd:PRK08566 784 RSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDG 855
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
1-864 |
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: 920.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCF 79
Cdd:TIGR02390 20 MSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVHVGFAKEIYKILRATCR 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 FCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPegdedltkekghggcgr 153
Cdd:TIGR02390 98 KCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP----------------- 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 154 yqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVM 233
Cdd:TIGR02390 160 ----------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITL 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 234 QGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGK 313
Cdd:TIGR02390 224 ETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGK 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 314 EGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDR 393
Cdd:TIGR02390 304 EGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRR 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 394 IDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHL 472
Cdd:TIGR02390 384 IKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHV 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 473 PQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLSTWDGKVPQPAILKPRPL 552
Cdd:TIGR02390 464 PQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAGYFGDPPEPAIEKPKEY 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 553 WTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDV 631
Cdd:TIGR02390 543 WTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEA 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 632 TRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRI 711
Cdd:TIGR02390 620 ARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEV 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 712 LNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVE 791
Cdd:TIGR02390 700 LGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVR 779
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958662372 792 NSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLA 864
Cdd:TIGR02390 780 SSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVD 852
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
8-1448 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 895.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 8 IKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLV 86
Cdd:PRK14977 30 ITAPEAyDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKL 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 87 ---DSNNPK-IKDILAKSKGQPKKRLThvydlckgkniceggEEMDNKFGvEQPEGDEDLTKEKGHggCGRYQPRirrsg 162
Cdd:PRK14977 110 pqeDLNVFKlIEEAHAAARDIPEKRID---------------DEIIEEVR-DQVKVYAKKAKECPH--CGAPQHE----- 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 163 LELYAEWKHVNEDSQEKKILLsPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDD 242
Cdd:PRK14977 167 LEFEEPTIFIEKTEIEEHRLL-PIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDD 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 243 LTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQK-SGRPLKSLKQRLKGKEGRVRGNL 321
Cdd:PRK14977 246 LTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKgSGRPLKSLFQRLKGKEGRFRGNL 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 322 MGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPK 401
Cdd:PRK14977 326 IGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLED 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 402 PSDL-------HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQ 474
Cdd:PRK14977 406 KGKDalreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQ 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 475 SLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMfLSTWDGKVPQPAI-LKPRPLW 553
Cdd:PRK14977 486 IEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAM-LAGITDPLPEPAIkTKDGPAW 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 554 TGKQIFSLIIPGHINCIRThSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAG---SLVHISYLEMGHD 630
Cdd:PRK14977 565 TGKQLFSLFLPKDFNFEGI-AKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEepeSLIDRIAKDYGEA 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 631 VTRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEK--------AHNNELEPTPGNTLRQ 702
Cdd:PRK14977 644 VAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQrkitrkitIYKGKEELLRGMKEEE 723
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 703 TFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVE--------GKRIPFGFKHRTL 774
Cdd:PRK14977 724 ALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKtrigfvltGGRLHEGYKDRAL 803
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 775 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 854
Cdd:PRK14977 804 SHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHII 883
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 855 QLRYGEDGLagesvefqnlatlkpsnkAFEKKFRFDYTN-ERALRRTLQEDLVKDVlSNAHIQnELEREFERMREDRevl 933
Cdd:PRK14977 884 QFKFGEDGI------------------DPQKLDHGEAFNlERIIEKQKIEDRGKGA-SKDEIE-ELAKEYTKTFNAN--- 940
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 934 rvifptgdskvvLPCNLLRMIWNAQkifhinprlPSDlhpikvvEGVKELSKKLvivngddplsrqaqenatllfnihlr 1013
Cdd:PRK14977 941 ------------LPKLLADAIHGAE---------LKE-------DELEAICAEG-------------------------- 966
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1014 stlcsrrmaeefrlsgeafdwLLGeieskFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKE 1093
Cdd:PRK14977 967 ---------------------KEG-----FEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIE 1020
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1094 LINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYdPNPQSTVVAEDQEWVNVYYEMPDFdvar 1173
Cdd:PRK14977 1021 LVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN-ANEIKLIKPDKRALENGCIPMERF---- 1095
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1174 ispwllrVELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeKLVlririmnsdenkmqeeeEVVDKMDDDVFLR 1253
Cdd:PRK14977 1096 -------AEIEAALAKGKKFEMELEDDLIIL----------------DLV-----------------EAADRDKPLATLI 1135
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1254 CIeSNMLTDMTLQGIEQISKVYMHLPQTDNKKkiiitedgefkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIF 1333
Cdd:PRK14977 1136 AI-RNKILDKPVKGVPDIERAWVELVEKDGRD--------------EWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIA 1200
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1334 TVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAI------TRHGVNRQDTGPLMKCSFEETVDVLM 1407
Cdd:PRK14977 1201 GTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglqaagVRHGFAGEKDSPLAKAAFEITTHTIA 1280
|
1450 1460 1470 1480
....*....|....*....|....*....|....*....|.
gi 1958662372 1408 EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK 1448
Cdd:PRK14977 1281 HAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
15-847 |
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: 889.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 15 EGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNnpKIK 94
Cdd:cd02583 23 ETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIINILQCICKTCSRVLLPEE--EKR 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 95 DILAKSKGQPKKRLTH------VYDLCKGKNICeggeemdnkfgveqPEgdedltkekghggCGRYqprirrsglelyae 168
Cdd:cd02583 101 KFLKRLRRPNLDNLQKkalkkkILEKCKKVRKC--------------PH-------------CGLL-------------- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 169 wKHVNEDsqekkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQG-SARNQDDLTHKL 247
Cdd:cd02583 140 -KKAQED-------LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEkSGTNEDDLTVKL 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 248 ADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSgRPLKSLKQRLKGKEGRVRGNLMGKRVD 327
Cdd:cd02583 212 SEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPK-KPIRGFCQRLKGKQGRFRGNLSGKRVD 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 328 FSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYII-RDNGDRIDLRF-HPKPSDL 405
Cdd:cd02583 291 FSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFVIkRDGGKKKFLKYgNRRKIAR 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 406 HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQEL 485
Cdd:cd02583 371 ELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALEL 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 486 AMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwDGK----VPQPAILKPRPLWTGKQIFSL 561
Cdd:cd02583 451 MGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYML--DGEikidLPPPAILKPVELWTGKQIFSL 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 562 II-PGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGT-SAGSLVHISYLEMGHDVTRLFYSNI 639
Cdd:cd02583 529 LLrPNKKSPVLVNLEAKEKSYTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSgSKNSLFYVLLRDYGPEAAAAAMNRL 608
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 640 QTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKT 719
Cdd:cd02583 609 AKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAEQTLEAKISGELSKIREDA 688
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 720 GSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLT 799
Cdd:cd02583 689 GKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLPHFPRNSKTPAAKGFVANSFYSGLT 768
|
810 820 830 840
....*....|....*....|....*....|....*....|....*...
gi 1958662372 800 PTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR 847
Cdd:cd02583 769 PTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1025-1443 |
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: 820.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1025 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1104
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1105 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1182
Cdd:cd02584 81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1183 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1262
Cdd:cd02584 161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1263 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1342
Cdd:cd02584 234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1343 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1422
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389
|
410 420
....*....|....*....|.
gi 1958662372 1423 ENIMLGQLAPAGTGCFDLLLD 1443
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 ... |
1-843 |
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: 617.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCF 79
Cdd:cd01435 13 LSVKE--ITNPVTfDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDLLYKLLRGSCF 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 80 FCSKLLVdsnnPKIKDILAKSKGQPkkrlthvydLCKGKNiceggeemdnkfgveqpegdedltkekghggcgryqprir 159
Cdd:cd01435 91 YCHRFRI----SKWEVKLFVAKLKL---------LDKGLL---------------------------------------- 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 160 rsglelyaewkhvnedsQEKKILLSPervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSVRPAVVMQGSArn 239
Cdd:cd01435 118 -----------------VEAAELDFG--------------------------YDMFFLDVLLVPPNRFRPPSFLGDKV-- 152
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 240 qddLTHK----LADIVKINNQLR------RNEQNGAAAHVIAEDVKL---------LQFHVATMVDNELPGLPRAMQKSG 300
Cdd:cd01435 153 ---FENPqnvlLSKILKDNQQIRdllasmRQAESQSKLDLISGKTNSeklinawlqLQSAVNELFDSTKAPKSGKKSPPG 229
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 301 rplksLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQY 380
Cdd:cd01435 230 -----IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINGPDVY 304
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 381 PGAKYIIRDNGDRIDLRFH--------------PKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPW 446
Cdd:cd01435 305 PGANAIEDEDGRLILLSALseerrkalakllllLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRVLPG 384
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 447 S-TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERG 525
Cdd:cd01435 385 EkTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTFFTRE 464
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 526 EVMNLLMF-LSTWDG-------KVPQPAILKPRPLWTGKQIFSLIIpghINCIRTHStHPDDEDS---------GPYKHI 588
Cdd:cd01435 465 EYQQLVYAaLRPLFTsdkdgriKLLPPAILKPKPLWTGKQVISTIL---KNLIPGNA-PLLNLSGkkktkkkvgGGKWGG 540
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 589 SPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDVTRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQD 668
Cdd:cd01435 541 GSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEK 620
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 669 IQNTIKKAKQDVIEVIEKAhnneleptpgntlrqtFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINI 748
Cdd:cd01435 621 RRKILRKAKKLGLEAAAEF----------------LGLKLNKVTSSIIKACLPKGLLKPFPENNLQLMVQSGAKGSMVNA 684
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 749 SQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQ 828
Cdd:cd01435 685 SQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQ 764
|
890
....*....|....*
gi 1958662372 829 RRLIKSMESVMVKYD 843
Cdd:cd01435 765 RCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
1-843 |
1.28e-177 |
|
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: 548.96 E-value: 1.28e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLvktmkvlrcvc 78
Cdd:cd00399 9 WSVAK--VIKPETIDnrTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFI----------- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 79 ffcskllvdsnnpkikdilakskgqpkkrlTHVYDLCKgkniceggeemdnkfgveqpegdedltkekghggcgryqpri 158
Cdd:cd00399 76 ------------------------------KKVPSFLG------------------------------------------ 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 159 rrsglelyaewkhvnedsqekkillspervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSVRPAVVmqgsar 238
Cdd:cd00399 84 -----------------------------------------------------PEWMILTCLPVPPPCLRPSVI------ 104
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 239 nqddlthkladivkinnqlrrneqngaaahvIAEDVKLLQFHVATMVDNELPGLPRAMqKSGRPLKSLKQRLKGKEGRVR 318
Cdd:cd00399 105 -------------------------------IEERWRLLQEHVDTYLDNGIAGQPQTQ-KSGRPLRSLAQRLKGKEGRFR 152
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 319 GNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMtfaeivtpfnidrlqelvrrgnsqypgakyiirdngdridlrf 398
Cdd:cd00399 153 GNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL------------------------------------------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 399 hpkpsdlhlqtgykverhmcDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLET 478
Cdd:cd00399 190 --------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEA 249
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 479 RAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKrdvflergevmnllmflstwdgkvpqpailkprplwtGKQI 558
Cdd:cd00399 250 RAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL-------------------------------------GKQI 292
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 559 FSLIIPGhincirthsthpddedsgpykhispgdtkvvvengelimgilckkslgtsagSLVHISYLEMGHDVTRLFYSN 638
Cdd:cd00399 293 VSAALPG----------------------------------------------------GLLHTVTRELGPEKAAKLLSN 320
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 639 IQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDK 718
Cdd:cd00399 321 LQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDFLNEARDK 400
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 719 TGSSAQKSL---SEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYL 795
Cdd:cd00399 401 AGSAASVNLdlvSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAKGFIRNSFL 480
|
810 820 830 840
....*....|....*....|....*....|....*....|....*...
gi 1958662372 796 AGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 843
Cdd:cd00399 481 EGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
797-1394 |
4.85e-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: 544.26 E-value: 4.85e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 797 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 876
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 877 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 956
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 957 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1036
Cdd:pfam04998 120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1037 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1116
Cdd:pfam04998 166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1117 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1188
Cdd:pfam04998 246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1189 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1268
Cdd:pfam04998 326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1269 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1347
Cdd:pfam04998 403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 1958662372 1348 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1394
Cdd:pfam04998 470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
213-513 |
2.83e-172 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 524.78 E-value: 2.83e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 213 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 292
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 293 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 372
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 373 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 451
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958662372 452 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 513
Cdd:smart00663 234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-321 |
3.80e-132 |
|
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: 415.92 E-value: 3.80e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1 MSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVC 78
Cdd:pfam04997 20 WSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFHIGFFKKTLKILECVC 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 79 FFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpegdedltkekghGGCGRYQP 156
Cdd:pfam04997 98 KYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------------------GVCGSQQP 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 157 RIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGS 236
Cdd:pfam04997 158 VSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 237 ARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGR 316
Cdd:pfam04997 236 RRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGR 315
|
....*
gi 1958662372 317 VRGNL 321
Cdd:pfam04997 316 FRGNL 320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
323-488 |
1.09e-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: 1.09e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 323 GKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKP 402
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 403 SDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEI 482
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 1958662372 483 QELAMV 488
Cdd:pfam00623 161 EELMLV 166
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
863-1046 |
3.00e-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: 3.00e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 863 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 939
Cdd:pfam04992 1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 940 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1018
Cdd:pfam04992 81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160
|
170 180
....*....|....*....|....*...
gi 1958662372 1019 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1046
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 ... |
24-847 |
3.13e-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: 314.73 E-value: 3.13e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 24 LMDPRQGVIERTGRCQTC-AGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCffcskllvdsnnPKIKDILAKSKG 102
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKIC------------PGCKSIKQKKKK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 103 QPKKRLTHVY-DLCKGKniceggeemdnkfgvEQPEGdEDLTKekghggcgryqprirrsglelyaewkhvnedsqekki 181
Cdd:cd10506 88 PPRETLPPDYwDFIPKD---------------GQQEE-SCVTK------------------------------------- 114
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 182 lLSPERVHEIFKRISDEECFVLGMEpRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNE 261
Cdd:cd10506 115 -NLPILSLAQVKKILKEIDPKLIAK-GLPRQEGLFLKCLPVPPNCHRVTEFTHGFSTGSRLIFDERTRAYKKLVDFIGTA 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 262 QNGAAAHviaedvkllqfhvatmvdnelpglpramqKSGrpLKSLKQrlkgkegrvrgNLMGKRVDFSARTVITPDPNLS 341
Cdd:cd10506 193 NESAASK-----------------------------KSG--LKWMKD-----------LLLGKRSGHSFRSVVVGDPYLE 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 342 IDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGnsqyPGAKYII--RDNGDRIDLRFHPKpsdlhLQTGYKVERHMCD 419
Cdd:cd10506 231 LNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLT----LLLKGVIgvRRNGRLVGVRSHNT-----LQIGDVIHRPLVD 301
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 420 GDIVIFNRQPTLHKMSMMGHRVRILPW-STFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSN 498
Cdd:cd10506 302 GDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSG 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 499 RPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTwdgKVPQPAILK--PR--PLWTGKQIFSLIIPGHINCirths 574
Cdd:cd10506 382 QNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKspPSngPLWTGKQLFQMLLPTDLDY----- 453
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 575 thpddedSGPykhispgDTKVVVENGELIMGiLCKKSLGTSAGSLVHISYLEMGHDVTRLFYSNIQTVINNWLLIEGHTI 654
Cdd:cd10506 454 -------SFP-------SNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSV 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 655 GIGD------SIADSKTYQDIQNTIKKAKQ----DVIEV----IEKAHNNELEPTPGNTLRQTFENQVN-RILNDARDK- 718
Cdd:cd10506 519 SLSDlylssdSYSRQKMIEEISLGLREAEIacniKQLLVdsrkDFLSGSGEENDVSSDVERVIYERQKSaALSQASVSAf 598
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 719 ------TGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKrIPFGFKH---------RTLPHFIKDDY- 782
Cdd:cd10506 599 kqvfrdIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVK-LSYRIPRqlscaawnsQKSPRVIEKDGs 677
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 783 ----GPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDtavKTAET-GYIQRRLIKSMESVMVKYDATVR 847
Cdd:cd10506 678 ecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1021-1444 |
2.76e-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: 298.40 E-value: 2.76e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1021 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1100
Cdd:cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1101 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDpnpqstvvaedqewvnvYYEMPdfdvarispwlLR 1180
Cdd:cd06528 90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--D-----------------LFNMR-----------IT 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1181 VELDRKHMTDRKLTMEQIAEKINAGFGDDlncIFNDDNAEKLVLRIrimnsDENKMQEEEEVVDKmdddvflrciesnmL 1260
Cdd:cd06528 140 IELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKA-----EEPSIKELRKLAEK--------------I 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1261 TDMTLQGIEQISKVymhlpqtdnkkkIIITEDGefkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEA 1340
Cdd:cd06528 198 LNTKIKGIKGIKRV------------IVRKEED------EYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEA 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1341 VRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKG 1420
Cdd:cd06528 260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRG 339
|
410 420
....*....|....*....|....
gi 1958662372 1421 VSENIMLGQLAPAGTGCFDLLLDA 1444
Cdd:cd06528 340 VIENIIVGQPIPLGTGDVELTMDP 363
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1019-1446 |
2.96e-88 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 293.29 E-value: 2.96e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1019 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1098
Cdd:PRK04309 27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1099 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1178
Cdd:PRK04309 107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1179 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1258
Cdd:PRK04309 157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1259 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1338
Cdd:PRK04309 214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1339 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1418
Cdd:PRK04309 275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354
|
410 420
....*....|....*....|....*...
gi 1958662372 1419 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1446
Cdd:PRK04309 355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1021-1443 |
7.25e-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: 283.10 E-value: 7.25e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1021 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1100
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1101 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1180
Cdd:TIGR02389 94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1181 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1258
Cdd:TIGR02389 144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1259 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1338
Cdd:TIGR02389 201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1339 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1418
Cdd:TIGR02389 263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342
|
410 420
....*....|....*....|....*
gi 1958662372 1419 KGVSENIMLGQLAPAGTGCFDLLLD 1443
Cdd:TIGR02389 343 KGVIENIIVGQPIPLGTGDVDLVMD 367
|
|
| RNA_pol_Rpb1_7 |
pfam04990 |
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1131-1266 |
2.48e-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: 2.48e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1131 TTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA---RISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFG 1207
Cdd:pfam04990 1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDVEdldRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1958662372 1208 DDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQ 1266
Cdd:pfam04990 81 NDLFVIFSDDNAEKLVIRIRIINDEKEK---DEEQEDKAEDDVFLKRLEANMLDSLTLR 136
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
53-1102 |
1.87e-74 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 272.31 E-value: 1.87e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 53 GHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKI--KDILAkskgqpkkrLTHVYDLCK--- 116
Cdd:TIGR02386 85 GHIELAAPVAHIWYfkglpsrigllLDITAKELESVLYFENYVVLDPGDTKLdkKEVLD---------ETEYREVLKryg 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 117 -GKNICEGGEemdnkfGVEQPEGDEDLTKEkghggcgryqprIRRSGLELyaewKHVNEDSQEKKILlspervheifKRI 195
Cdd:TIGR02386 156 dGFRAGMGAE------AIKELLEKIDLDKE------------IEELKIQL----RESKSDQKRKKLL----------KRL 203
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 196 SDEECFVLGMepryARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVK 275
Cdd:TIGR02386 204 EIVEAFKDSG----NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKR 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 276 LLQFHVATMVDNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAAnm 355
Cdd:TIGR02386 280 MLQEAVDALFDNGRRGKP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMAL-- 356
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 356 tfaEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgykverhmcdgdi 422
Cdd:TIGR02386 357 ---ELFKPFIIKRLIDrelaaniksakkMIEQEDPEvWDVLEDVIKE---------HP---------------------- 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 423 VIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVM 502
Cdd:TIGR02386 403 VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIV 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 503 GIVQDT------LTAVRKFTKRD--VFLERGEVmnllmFLSTWDGKVPQPAILKPRP----LWT--GKQIFSLIIPghin 568
Cdd:TIGR02386 483 TPSQDMvlglyyLTTEKPGAKGEgkIFSNVDEA-----IRAYDNGKVHLHALIGVRTsgeiLETtvGRVIFNEILP---- 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 569 cirthsthpddeDSGPYKHISPgdtkvvvengelimgILCKKSLgtsaGSLVHISYLEMGHDVTRLFYSNIQTVINNWLL 648
Cdd:TIGR02386 554 ------------EGFPYINDNE---------------PLSKKEI----SSLIDLLYEVHGIEETAEMLDKIKALGFKYAT 602
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 649 IEGHTIGIGDSIadskTYQDIQNTIKKAKQDVIEVIEKAHNNELepTPGNTLRQTFEnqvnrILNDARDKTGSSAQKSLS 728
Cdd:TIGR02386 603 KSGTTISASDIV----VPDEKYEILKEADKEVAKIQKFYNKGLI--TDEERYRKVVS-----IWSETKDKVTDAMMKLLK 671
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 729 ----EYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenSYLAGLTPTEF 803
Cdd:TIGR02386 672 kdtyKFNPIFMMADSGARGNISQFRQLAGMRGlMAKPSGDIIELPIKS---------------------SFREGLTVLEY 730
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 804 FFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKY-DATVRNSInQVVQLRYGEDglagESVEfqnlaTLKpsnka 882
Cdd:TIGR02386 731 FISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREeDCGTEEGI-EVEAIVEGKD----EIIE-----SLK----- 795
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 883 fekkfrfdytnERALRRTLQEDLVKDVLSNAHIQ-NELerefermrEDREVLRVIFPTGDSKV----VLPCNLLRMIwnA 957
Cdd:TIGR02386 796 -----------DRIVGRYSAEDVYDPDTGKLIAEaNTL--------ITEEIAEKIENSGIEKVkvrsVLTCESEHGV--C 854
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 958 QKIFHINprlpsdlhpikvvegvkelskklvivngddpLSRQAqenatlLFNIhlrstlcsrrmaeefrlsgeafdwllg 1037
Cdd:TIGR02386 855 QKCYGRD-------------------------------LATGK------LVEI--------------------------- 870
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958662372 1038 eieskfnqaiahpGEMVGALAAQSLGEPATQMTLNTFHYAGVSA--KNVTLGVPRLKELINiSKKPK 1102
Cdd:TIGR02386 871 -------------GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPK 923
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1042-1438 |
4.25e-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: 243.66 E-value: 4.25e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1042 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLgqSARDAERA 1121
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLE--NDRDEKSA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1122 KDILCRLEHTTLRKVTANTAIYYDPNpqstvvaedqewvNVYyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEK 1201
Cdd:cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPD-------------DCY---------------ILIKLDKKIIEKLQLSKSNLYFL 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1202 INagfgddlncifnddnaeklvlririmnsdenkmqeeeevvdkmdddvFLRciesNMLTDMTLQGIEQISKVYMHLPQT 1281
Cdd:cd02736 131 LQ-----------------------------------------------SLK----RKLPDVVVSGIPEVKRAVINKDKK 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1282 DNKKKIIItEDGEFKAlqewILETDGVslmrvlsekdvDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVN 1361
Cdd:cd02736 160 KGKYKLLV-EGYGLRA----VMNTPGV-----------IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSID 223
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958662372 1362 YRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCF 1438
Cdd:cd02736 224 PRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1020-1441 |
5.14e-69 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 242.41 E-value: 5.14e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1020 RMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISK 1099
Cdd:PRK14897 151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1100 KPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVtANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlL 1179
Cdd:PRK14897 231 KPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDV-ADIIT---------------------------DIAEMS---V 279
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1180 RVELDRKHMTDRKLTMEQIAEKInagfgddlncifnddnaEKLVLRIRIMNSDENKMQEEEEVVDKmdddvfLRCIESNm 1259
Cdd:PRK14897 280 VVELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDDGIIRLKPQQPSFKK------LYLLAEK- 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1260 LTDMTLQGIEQISKVymhlpqtdnkkkIIITEDGEfkalQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIE 1339
Cdd:PRK14897 336 VKSLTIKGIKGIKRA------------IARKENDE----RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIE 399
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1340 AVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMK 1419
Cdd:PRK14897 400 AARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLA 479
|
410 420
....*....|....*....|..
gi 1958662372 1420 GVSENIMLGQLAPAGTGCFDLL 1441
Cdd:PRK14897 480 GVAENIIVGQPITLGTGAVSLV 501
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
52-915 |
1.79e-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: 241.60 E-value: 1.79e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 52 FGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrlthvydlckgk 118
Cdd:COG0086 92 MGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI------------- 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 119 nICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllspervhEIFKRI 195
Cdd:COG0086 159 -LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK--------KLIKRL 211
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 196 SDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVK 275
Cdd:COG0086 212 KVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKR 287
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 276 LLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAan 354
Cdd:COG0086 288 MLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA-- 363
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 355 mtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhmcdgdiVIFNR 427
Cdd:COG0086 364 ---LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------------VLLNR 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 428 QPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNR 499
Cdd:COG0086 416 APTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGK 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 500 PVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ------------IF 559
Cdd:COG0086 488 PIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgkivettvgryLV 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 560 SLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLEMGHDVTRLFY 636
Cdd:COG0086 563 NEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRRCGLKETVIFL 602
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 637 SNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfENQVNRILNDAR 716
Cdd:COG0086 603 DRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YNKVIDGWTKAS 671
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 717 DKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfvenSYL 795
Cdd:COG0086 672 LETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS---------------------NFR 730
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 796 AGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedglaGESVEfqnla 874
Cdd:COG0086 731 EGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG-----GEVIE----- 799
|
890 900 910 920
....*....|....*....|....*....|....*....|.
gi 1958662372 875 TLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 915
Cdd:COG0086 800 PLK----------------ERILGRVAAED-VVDPGTGEVL 823
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
492-658 |
2.11e-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: 207.10 E-value: 2.11e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 492 IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwdgKVPQPAILKP-RPLWTGKQIFSLIIPGHINCI 570
Cdd:pfam04983 2 ILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 571 RTHSTHPDDEdsgpykhiSPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDVTRLFYSNIQTVINNWLLIE 650
Cdd:pfam04983 78 GKPKTNEEDL--------CENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKS 149
|
....*...
gi 1958662372 651 GHTIGIGD 658
Cdd:pfam04983 150 GFSIGIDD 157
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
211-841 |
3.23e-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: 223.55 E-value: 3.23e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 211 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKladIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMV 285
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGgrfatSDLN--DLYRR---VINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALI 212
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 286 DNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFN 365
Cdd:cd01609 213 DNGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMA-----LELFKPFV 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 366 IdrlQELVRRGNSQYP-GAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRIL 444
Cdd:cd01609 287 I---RELIERGLAPNIkSAKKMIERKDPEV----------------WDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLI 347
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 445 PWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDT------LTAVRKFTKr 518
Cdd:cd01609 348 EGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMvlglyyLTKERKGDK- 426
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 519 dvflerGEVMnllmfLSTWDGKVpqpailkprplwtgkqIFSLIIPghincirthsthpddedsgpykhispgdtkvvvE 598
Cdd:cd01609 427 ------GEGI-----IETTVGRV----------------IFNEILP---------------------------------E 446
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 599 NGELIMGILCKKSLgtsaGSLVHISYLEMGHDVTRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyqdiQNTIKKAK 677
Cdd:cd01609 447 GLPFINKTLKKKVL----KKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDiVVPPEK-----KEIIKEAE 517
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 678 QDVIEvIEKAHNNeleptpGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEY--NNFKSMVVSGAKGSKINISQVIAVV 755
Cdd:cd01609 518 EKVKE-IEKQYEK------GLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDpfNPIYMMADSGARGSKSQIRQLAGMR 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 756 G-QQNVEGKRIPfgfkhrtLPhfIKDdygpesrgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKS 834
Cdd:cd01609 591 GlMAKPSGKIIE-------LP--IKS------------NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDV 649
|
....*..
gi 1958662372 835 MESVMVK 841
Cdd:cd01609 650 AQDVIVT 656
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
165-1083 |
1.77e-59 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 227.88 E-value: 1.77e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 165 LYAEWKHVNEDSQEKKILlspervheifKRISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLT 244
Cdd:PRK09603 1590 LKEEVKDTNSDAKKKKLI----------KRLKVVESFLNSGN----RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVN 1655
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 245 HKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNelpGLPRAMQKSG--RPLKSLKQRLKGKEGRVRGNLM 322
Cdd:PRK09603 1656 ELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDN---GRSTNAVKGAnkRPLKSLSEIIKGKQGRFRQNLL 1732
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 323 GKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQElvrRGN-SQYPGAKYIIRDNGDRIdlrfhpk 401
Cdd:PRK09603 1733 GKRVDFSGRSVIVVGPNLKMDECGLPKNMA-----LELFKPHLLSKLEE---RGYaTTLKQAKRMIEQKSNEV------- 1797
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 402 psdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAE 481
Cdd:PRK09603 1798 ---------WECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAE 1868
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 482 IQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT--KRDVFLER---GEVMNLLMFLST--WDGKVPQPAILKPRPLWT 554
Cdd:PRK09603 1869 CKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSleKSGVKGEHklfSSVNEIITAIDTkeLDIHAKIRVLDQGNIIAT 1948
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 555 --GKQIFSLIIPGHIncirthsthPDDEDSGPYKhispgdtkvvvengelimgilcKKSLGTsagsLVHISYLEMGHDVT 632
Cdd:PRK09603 1949 saGRMIIKSILPDFI---------PTDLWNRPMK----------------------KKDIGV----LVDYVHKVGGIGIT 1993
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 633 RLFYSNIQTVINNWllieGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEViekahnnELEPTPGNTLRQTFENQVNRIL 712
Cdd:PRK09603 1994 ATFLDNLKTLGFRY----ATKAGISISMEDIITPKDKQKMVEKAKVEVKKI-------QQQYDQGLLTDQERYNKIIDTW 2062
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 713 NDARDKTGSSAQKSLSE----YNNFKSMVVSGAKGSKINISQVIAVVGqqnVEGKriPFGFKHRTlphfikddygPESRG 788
Cdd:PRK09603 2063 TEVNDKMSKEMMTAIAKdkegFNSIYMMADSGARGSAAQIRQLSAMRG---LMTK--PDGSIIET----------PIISN 2127
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 789 FVEnsylaGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYdatvrnsinqvvqlrygEDGLAGESV 868
Cdd:PRK09603 2128 FKE-----GLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVS-----------------DDCGTHEGI 2185
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 869 EFQNLATLKPSNKAFEkkfrfdytnERALRRTLQEDLVKDvlsnahIQNElerefermredrevlrvifptgdskVVLPC 948
Cdd:PRK09603 2186 EITDIAVGSELIEPLE---------ERIFGRVLLEDVIDP------ITNE-------------------------ILLYA 2225
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 949 NLLRMIWNAQKIfhinprlpsdlhpikvvegvKELSKKLVIVNgdDPLSRQAQENatllfnihlrstLCSRrmaeefrls 1028
Cdd:PRK09603 2226 DTLIDEEGAKKV--------------------VEAGIKSITIR--TPVTCKAPKG------------VCAK--------- 2262
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*
gi 1958662372 1029 geAFDWLLGEieskfnQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKN 1083
Cdd:PRK09603 2263 --CYGLNLGE------GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1067-1445 |
2.58e-57 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 215.53 E-value: 2.58e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1067 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDP 1146
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI--DL 618
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1147 NPQStvvaedqewvnvyyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRI 1226
Cdd:PRK14898 619 WTQS----------------------------IKVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYL 663
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1227 RImnsdenkmqEEEEVVDkmdddvFLRCIESnmLTDMTLQGIEQISKVYMHLPQTDNKkkiiitedgefkalQEWILETD 1306
Cdd:PRK14898 664 KP---------KTPSYKA------LRKRIPK--IKNIVLKGIPGIERVLVKKEEHEND--------------EEYVLYTQ 712
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1307 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGV 1386
Cdd:PRK14898 713 GSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGV 792
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 1958662372 1387 NRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAE 1445
Cdd:PRK14898 793 AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDRE 851
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1042-1441 |
3.48e-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: 3.48e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1042 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKE-LINISKKPKTPSLTV-FLLGQSARDAE 1119
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREiLMTASKNIKTPSMTLpLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1120 RAK---------DILCRLEHTTLRKVTANTAIyydpnPQStvvaedQEWVNVYYEMPdfdvarispwllrveLDRKhmtd 1190
Cdd:cd02735 81 TLKkrlsrvtlsDVVEKVEVTEILKTIERVFK-----KLL------GKWCEVTIKLP---------------LSSP---- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1191 rKLTMEQIAEKInagfgddlncifnddnAEKLVLRirimnsdenkmqeeeEVvdkmdddvflrciesnmltdmtlQGIEQ 1270
Cdd:cd02735 131 -KLLLLSIVEKL----------------ARKAVIR---------------EI-----------------------PGITR 155
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1271 ISKVYmhlpqTDNKKKiiitedgefkalQEWILETDGVSL--MRVLSEKdVDPVRTTSNDIVEIFTVLGIEAVRKALERE 1348
Cdd:cd02735 156 CFVVE-----EDKGGK------------TKYLVITEGVNLaaLWKFSDI-LDVNRIYTNDIHAMLNTYGIEAARRAIVKE 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1349 LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVnRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLG 1428
Cdd:cd02735 218 ISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVG 296
|
410
....*....|...
gi 1958662372 1429 QLAPAGTGCFDLL 1441
Cdd:cd02735 297 KPVNGGTGLFDLL 309
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
211-1102 |
1.01e-53 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 208.19 E-value: 1.01e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 211 RPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELP 290
Cdd:PRK14906 311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 291 GLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQ 370
Cdd:PRK14906 391 GRP-VTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMA-----LELFKPFVMKRLV 464
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 371 ELVRRGNSQypGAKYIIrdngdridlrfhpkpsDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFR 450
Cdd:PRK14906 465 ELEYAANIK--AAKRAV----------------DRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIK 526
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 451 LNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT-KRDVFLERGEVmn 529
Cdd:PRK14906 527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDGFEGEGRT-- 604
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 530 llmFLSTWDGkvpqpailkprplwtgkqifsliipghincIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMgilCK 609
Cdd:PRK14906 605 ---FADFDDA------------------------------LNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEE---TK 648
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 610 --KSLGTSAGSLV----------HISYLEMGHDVTRLfysnIQTVINNWLLIEGHTI---------------GIGDSIAD 662
Cdd:PRK14906 649 agERIETTVGRIIfnqvlpedypYLNYKMVKKDIGRL----VNDCCNRYSTAEVEPIldgikktgfhyatraGLTVSVYD 724
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 663 SKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPtpgntlrQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAK 742
Cdd:PRK14906 725 ATIPDDKPEILAEADEKVAAIDEDYEDGFLSE-------RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGAR 797
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 743 GSKINISQVIAVVG-QQNVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFHAMGGREGLIDTAVKT 821
Cdd:PRK14906 798 GNIKQIRQLAGMRGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRT 856
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 822 AETGYIQRRLiksmesVMVKYDATVRNsinqvvqlrygEDGLAGESVEfqnlatlkpsnkafekkfrFDYTNERAlrrTL 901
Cdd:PRK14906 857 ADSGYLTRRL------VDVAQDVIVRE-----------EDCGTDEGVT-------------------YPLVKPKG---DV 897
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 902 QEDLVKDVLSNAHIQNELErefermredrevlrVIFPTGDskvvlpcnllrmiwnaqkifhinprlpsdlhpikvvegvk 981
Cdd:PRK14906 898 DTNLIGRCLLEDVCDPNGE--------------VLLSAGD---------------------------------------- 923
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 982 elskklvIVNGDDPLSRQAQENATllfNIHLRSTLCSRrmaEEFRLSGEAFDWLLgeieskfnqAIAHP---GEMVGALA 1058
Cdd:PRK14906 924 -------YIESMDDLKRLVEAGVT---KVQIRTLMTCH---AEYGVCQKCYGWDL---------ATRRPvniGTAVGIIA 981
|
890 900 910 920
....*....|....*....|....*....|....*....|....
gi 1958662372 1059 AQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIsKKPK 1102
Cdd:PRK14906 982 AQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPK 1024
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
211-1104 |
1.22e-53 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 206.84 E-value: 1.22e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 211 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKLadivkI--NNQLRR------------NEQngaaahvia 271
Cdd:PRK00566 223 KPEWMILDVLPVIPPDLRPLVQLDGgrfatSDLN--DLYRRV-----InrNNRLKRllelgapeiivrNEK--------- 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 272 edvKLLQFHVATMVDNELPGlpRAMQ-KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRS 350
Cdd:PRK00566 287 ---RMLQEAVDALFDNGRRG--RPVTgPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKK 361
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 351 IAanmtfAEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgykverhm 417
Cdd:PRK00566 362 MA-----LELFKPFIMKKLVErglattiksakkMVEREDPEvWDVLEEVIKE---------HP----------------- 410
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 418 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPwstfrLnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 489
Cdd:PRK00566 411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHP-----L---VCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSS 477
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 490 RMIVTPQSNRPVmgIV--QD------TLTAVRKFTKrdvflerGEVMnllMFLSTWD-------GKVPQPAILKPRP--- 551
Cdd:PRK00566 478 NNILSPANGKPI--IVpsQDmvlglyYLTREREGAK-------GEGM---VFSSPEEalrayenGEVDLHARIKVRItsk 545
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 552 --LWT--GKQIFSLIIPGHIncirthsthpddedsgPYkhispgdtkvvvENGELIMGilcKKSLgtsaGSLVHISYLEM 627
Cdd:PRK00566 546 klVETtvGRVIFNEILPEGL----------------PF------------INVNKPLK---KKEI----SKIINEVYRRY 590
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 628 GHDVTRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyQDIqntIKKAKQDVIEvIEKAHNNELeptpgntlrQTFE- 705
Cdd:PRK00566 591 GLKETVIFLDKIKDLGFKYATRSGISIGIDDiVIPPEK--KEI---IEEAEKEVAE-IEKQYRRGL---------ITDGe 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 706 --NQVNRILNDARDKTGSSAQKSLSEYNN-FKS---MVVSGAKGSKINISQVIAVVG-QQNVEGKRIPfgfkhrtLPhfI 778
Cdd:PRK00566 656 ryNKVIDIWSKATDEVAKAMMKNLSKDQEsFNPiymMADSGARGSASQIRQLAGMRGlMAKPSGEIIE-------TP--I 726
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 779 KddygpesrgfveNSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLiksmesVMVKYDATVRN----SINQVV 854
Cdd:PRK00566 727 K------------SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVREddcgTDRGIE 788
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 855 QLRYGEDGLAGESVEfqnlatlkpsnkafekkfrfdytnERALRRTLQEDLVKDVLSNahiqnelerefermredrevlr 934
Cdd:PRK00566 789 VTAIIEGGEVIEPLE------------------------ERILGRVLAEDVVDPETGE---------------------- 822
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 935 VIFPTGDskvvlpcnLLRMIWnAQKIfhinprlpsdlhpikVVEGVKElskklvivngddplsrqaqenatllfnIHLRS 1014
Cdd:PRK00566 823 VIVPAGT--------LIDEEI-ADKI---------------EEAGIEE---------------------------VKIRS 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1015 TL-CsrrmaeefrlsgeafdwllgeiESKF---------NQAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVsa 1081
Cdd:PRK00566 852 VLtC----------------------ETRHgvcakcygrDLATGKLvniGEAVGVIAAQSIGEPGTQLTMRTFHTGGV-- 907
|
970 980
....*....|....*....|...
gi 1958662372 1082 kNVTLGVPRLKELINiSKKPKTP 1104
Cdd:PRK00566 908 -DITGGLPRVAELFE-ARKPKGP 928
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
36-1436 |
5.47e-53 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 206.78 E-value: 5.47e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 36 GR-CQTCAGNMTECP---GHFGHIELAKPVFHVGFLvKTMKvlrcvcffcSKL--LVDSNNPKIKDILAKSKGQPKKRLT 109
Cdd:PRK14844 1513 GRiCEKCGVEVTSSKvrrERMGHIELASPVAHIWFL-KSLP---------SRIgaLLDMSLRDIENILYSDNYIVIDPLV 1582
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 110 HVYDlcKGKNICEGG-EEMDNKFGVEQ---PEGDED----LTKEKGHggcgryqpRIRRsglELYAEWKHVNEDSQEKKI 181
Cdd:PRK14844 1583 SPFE--KGEIISEKAyNEAKDSYGIDSfvaMQGVEAirelLTRLDLH--------EIRK---DLRLELESVASEIRRKKI 1649
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 182 LlspervheifKRISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNE 261
Cdd:PRK14844 1650 I----------KRLRIVENFIKSGN----RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLL 1715
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 262 QNGAAAHVIAEDVKLLQFHVATMVDNELPGlpRAMQKSGRP--LKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPN 339
Cdd:PRK14844 1716 SLNPPEIMIRNEKRMLQEAVDSLFDNSRRN--ALVNKAGAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPT 1793
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 340 LSIDQVGVPRSIAanmtfAEIVTPFNIDRLQELVRRGNSQYpgAKYIIRDNgdridlrfHPKPSDLHLQTgykVERHMcd 419
Cdd:PRK14844 1794 LKLNQCGLPKRMA-----LELFKPFVYSKLKMYGMAPTIKF--ASKLIRAE--------KPEVWDMLEEV---IKEHP-- 1853
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 420 gdiVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNR 499
Cdd:PRK14844 1854 ---VLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGR 1930
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 500 PVMGIVQDTLTAVRKFT----KRD---VFLERGEVMNllmflSTWDGKVpqpailkprplwtgkqifsliipgHINC-IR 571
Cdd:PRK14844 1931 PIIVPSKDIVLGIYYLTlqepKEDdlpSFGAFCEVEH-----SLSDGTL------------------------HIHSsIK 1981
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 572 THSTHPDDEDSGPYKHISPGDTKVVV-------EN--GELIMGILCKKSLgtsaGSLVHISYLEMGHDVTRLFYSNIQTV 642
Cdd:PRK14844 1982 YRMEYINSSGETHYKTICTTPGRLILwqifpkhENlgFDLINQVLTVKEI----TSIVDLVYRNCGQSATVAFSDKLMVL 2057
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 643 INNWLLIEGHTIGIGDSIADSKTYQDIQNT---IKKAK---QDVIEVIEKAHNNELEptpgntlrqTFENQVNRILNDAR 716
Cdd:PRK14844 2058 GFEYATFSGVSFSRCDMVIPETKATHVDHArgeIKKFSmqyQDGLITRSERYNKVID---------EWSKCTDMIANDML 2128
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 717 DKTgsSAQKSLSEYNNFKSMVVSGAKGSKiniSQVIAVVGQQNVEGKriPFGFKHRTlphfikddygPESRGFVEnsyla 796
Cdd:PRK14844 2129 KAI--SIYDGNSKYNSVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIISNFRE----- 2186
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 797 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVefqnlat 875
Cdd:PRK14844 2187 GLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDvSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESV------- 2259
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 876 lkpsnkafekkfrfdytnerALRRTLQEDLVKDVlsnahIQNELEREFERMREDRevlrvifptgdskvvlpcnllrmiw 955
Cdd:PRK14844 2260 --------------------VLGRTAANDIYNPV-----TKELLVKAGELIDEDK------------------------- 2289
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 956 naqkifhinprlpsdlhpikvvegVKELS-KKLVIVNGDDPLSRQAQENAtllfnihlrSTLCSRRmaeefrlsgeafDW 1034
Cdd:PRK14844 2290 ------------------------VKQINiAGLDVVKIRSPLTCEISPGV---------CSLCYGR------------DL 2324
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1035 LLGEIESKfnqaiahpGEMVGALAAQSLGEPATQMTLNTFHYAGVsaknVTLGVPRLKELINISKKPKTPSLTVFLLGQS 1114
Cdd:PRK14844 2325 ATGKIVSI--------GEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVESSNIIASINAKIKLNNSNIIIDKNG 2392
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1115 ARDA-ERAKDILC-------RLEHTtlrkVTANTAIYYDPNPQSTVVAEDQEW-------------VNVYYEMPD----- 1168
Cdd:PRK14844 2393 NKIViSRSCEVVLidslgseKLKHS----VPYGAKLYVDEGGSVKIGDKVAEWdpytlpiitektgTVSYQDLKDgisit 2468
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1169 --------------------FDVARISPWLLRVELDRKHMTdrkltmeqIAEKINAGFGDDLNCIFNDDNAEK-----LV 1223
Cdd:PRK14844 2469 evmdestgisskvvkdwklySGGANLRPRIVLLDDNGKVMT--------LASGVEACYFIPIGAVLNVQDGQKvhagdVI 2540
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1224 LRI---------------RIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGI-EQISKVYMHLpqtdNKKKI 1287
Cdd:PRK14844 2541 TRTpresvktrditgglpRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVdEQISPVEYLV----SRSKH 2616
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1288 IITEDGEFkaLQEWILETDGvslmrvlsekdvDPvrttsnDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLAL 1367
Cdd:PRK14844 2617 VIVNEGDF--VRKGDLLMDG------------DP------DLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEV 2676
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1368 LC-------------DTMTCRGHlmAITRHGVNRQDTG------------PLMK---------------CSFEETVDVLM 1407
Cdd:PRK14844 2677 ILkqmlqkveitdpgDTMYLVGE--SIDKLEVDRENDAmsnsgkrpahylPILQgitrasletssfisaASFQETTKVLT 2754
|
1530 1540
....*....|....*....|....*....
gi 1958662372 1408 EAAAHGESDPMKGVSENIMLGQLAPAGTG 1436
Cdd:PRK14844 2755 EAAFCGKSDPLSGLKENVIVGRLIPAGTG 2783
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
684-790 |
2.56e-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: 159.07 E-value: 2.56e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 684 IEKA-HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEG 762
Cdd:pfam05000 1 ITDAeRYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 1958662372 763 KRIPFGFKHRTLPHFIKDDYGPESRGFV 790
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
210-507 |
4.42e-42 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 165.31 E-value: 4.42e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 210 ARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNEL 289
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 290 PGlPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRl 369
Cdd:PRK02625 320 RG-RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMA-----IELFQPFVIHR- 392
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 370 qeLVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST 448
Cdd:PRK02625 393 --LIRQGIvNNIKAAKKLIQRADPEV----------------WQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 1958662372 449 FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD 507
Cdd:PRK02625 455 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
53-481 |
7.32e-40 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 159.30 E-value: 7.32e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 53 GHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNpkiKDILAKSKGqpkkrlTHVYDLCKGKNIc 121
Cdd:CHL00018 105 GYIKLACPVTHVWYlkrlpsyianlLDKPLKELEGLVYCDFSFARPIAK---KPTFLRLRG------LFEYEIQSWKYS- 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 122 eggeemDNKFgVEQPEGDEDLTKEKGHGGcgryqPRIRR--SGLEL-------YAEWKHVNEDSQ------EKKILLspe 186
Cdd:CHL00018 175 ------IPLF-FSTQGFDTFRNREISTGA-----GAIREqlADLDLriiidnsLVEWKELGEEGStgneweDRKIGR--- 239
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 187 RVHEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRR--NEQNG 264
Cdd:CHL00018 240 RKDFLVRRIKLAKHFIR----TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDllTTSRS 315
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 265 AAAHVIAEDVKLLQFHVATMVDNELPGLPraMQKS-GRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSID 343
Cdd:CHL00018 316 TPGELVMCQKKLLQEAVDALLDNGIRGQP--MRDGhNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLH 393
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 344 QVGVPRSIAanmtfAEIVTPFNIdrlQELVRRGNSQYPG-AKYIIRDNGDRIDlrfhpkpsdlhlqtgyKVERHMCDGDI 422
Cdd:CHL00018 394 QCGLPREIA-----IELFQPFVI---RGLIRQHLASNIRaAKSKIREKEPIVW----------------EILQEVMQGHP 449
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958662372 423 VIFNRQPTLHKMSMM--------GHRVRILPwstfrlnlSVTTPYNADFDGDEMNLHLPQSLETRAE 481
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 ... |
1328-1437 |
1.61e-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: 1.61e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1328 DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM 1407
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 1958662372 1408 EAAAHGESDPMKGVSENIMLGQLAPAGTGC 1437
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 ... |
1051-1098 |
4.37e-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: 4.37e-21
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1958662372 1051 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1098
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1821-1926 |
4.73e-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: 4.73e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TP--TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1898
Cdd:pfam05109 517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596
|
90 100
....*....|....*....|....*...
gi 1958662372 1899 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1926
Cdd:pfam05109 597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1821-1937 |
4.68e-14 |
|
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: 78.03 E-value: 4.68e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TP--TSPKYSPTSPKYSP------------TSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPT 1886
Cdd:pfam05109 477 TPagTTSGASPVTPSPSPrdngteskapdmTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNAT 556
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1958662372 1887 SPKYSPTSPTYSPTSPkgsTYSPTSPGYSPTSPTYSLTSPAISpEDSDEEN 1937
Cdd:pfam05109 557 SPTPAVTTPTPNATIP---TLGKTSPTSAVTTPTPNATSPTVG-ETSPQAN 603
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
731-1084 |
3.84e-12 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 71.95 E-value: 3.84e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 731 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 797
Cdd:PRK02597 111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 798 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 876
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 877 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 956
Cdd:PRK02597 238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 957 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1034
Cdd:PRK02597 257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 1958662372 1035 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1084
Cdd:PRK02597 301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
731-1201 |
7.19e-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: 7.19e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 731 NNFKSMVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFH 806
Cdd:TIGR02388 119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 807 AMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqvvQLRYGEDGlaGESVEFQNlatlkpsnkafek 885
Cdd:TIGR02388 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTERSI----VVRAMTEG--DKKISLGD------------- 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 886 kfrfdytneRALRRTLQEDLVkdvlsnaHIQNElerefermredrevlrVIFPTGDSkvvlpcnllrmiwnaqkifhINP 965
Cdd:TIGR02388 236 ---------RLLGRLVAEDVL-------HPEGE----------------VIVPKNTA--------------------IDP 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 966 RLPSDLHPIKVVEgvkelskklviVNGDDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDWllgeieskfnq 1045
Cdd:TIGR02388 264 DLAKTIETAGISE-----------VVVRSPLTCEAA-----------RS-VCRK-----------CYGW----------- 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1046 AIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGV-PRLKELINISKKPKT-PSLTVFllGQSARDA 1118
Cdd:TIGR02388 299 SLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVrSKIDGTVEFGKKLRTrGYRTRH--GEDAKQV 376
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1119 ERAKDILCRlehttLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDF--------------DVA-RISPWLLRVEL 1183
Cdd:TIGR02388 377 EVAGLLIIK-----PTGSITNKAQEIEVTQGSLLFVEDGQTVDAGQLLAEIalgavrkstekatkDVAsDLAGEVKFDKV 451
|
490
....*....|....*...
gi 1958662372 1184 DRKHMTDRKLTMEQIAEK 1201
Cdd:TIGR02388 452 VPEEKTDRQGNTTRIAQR 469
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1051-1094 |
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 1958662372 1051 GEMVGALAAQSLGEPATQMTLNTFHYAGVsAKNVTLGVPRLKEL 1094
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 ... |
1051-1442 |
6.02e-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: 6.02e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1051 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAknvtlgVPRLKELI--NISKKPKTPSLTVFL---LGQSARDAE---RAK 1122
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESSP------LELLKEVLecRSKSKSKENDRRVILslhLCKCDHGFEyerAAL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1123 DILCRLEHTTLRKVTANTAIYYDPNPQstvvaedqewvnvyyEMPDFDVARISPWLLRVELDRKHMTDRKLTmeqiaeKI 1202
Cdd:cd02737 75 EVKNHLERVTLEDLATTSMIKYSPQAT---------------EAIVGEIGDQLNTKKKGKKKAIFSTSLKIT------KF 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1203 NAGfgddlNCIFNDDNAEKLVLR---IRIMNSDENKmQEEEEVVDKMDDDVFlrciesNMLTDMTLQGIEQISKVYMhLP 1279
Cdd:cd02737 134 SPW-----VCHFHLDKECQKLSDgpcLTFSVSKEVS-KSSEELLDVLRDRII------PFLLETVIKGDERIKSVNI-LW 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1280 QTDNKKKIIITEDGEFKAlqEWILETdGVSLMRVLSEKD---------------VDPVRTTSNDIVEIFTVLGIEAVRKA 1344
Cdd:cd02737 201 EDSPSTSWVKSVGKSSRG--ELVLEV-TVEESCKKTRGNawnvvmdacipvmdlIDWERSMPYSIQQIKSVLGIDAAFEQ 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1345 LERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDT-----GPLMKCSFEETVDVLMEAAAHGESDPMK 1419
Cdd:cd02737 278 FVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRslkisAPFTEACFSSPIKCFLKAAKKGASDSLS 357
|
410 420
....*....|....*....|....
gi 1958662372 1420 GVSENIMLGQLAPAGTGC-FDLLL 1442
Cdd:cd02737 358 GVLDACAWGKEAPVGTGSkFEILW 381
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1458-1577 |
2.17e-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: 59.84 E-value: 2.17e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1458 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1530
Cdd:smart01104 15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1958662372 1531 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1577
Cdd:smart01104 91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
|
|
| PARM |
pfam17061 |
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present ... |
1821-1935 |
6.47e-09 |
|
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: 59.49 E-value: 6.47e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKY--SPTSPKYSPTSPKySPTSPTYSPTTPKYSPTSPT----------YSPTSPV-------YTPTSPKYSPTS- 1880
Cdd:pfam17061 22 TPPTATWtsSPQNTAAVTASPT-SGTHNNSVLPVTASAPTSPLpknvsvepreEESTSPAsnwegtsTDPSPPGLSPTSs 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958662372 1881 -----PT---YSPTSPKYS-PT----SPTYSP--TSPKGSTYSPTSPGYSPT-SPTYSLTSPAISPEDSDE 1935
Cdd:pfam17061 101 gvhltPTpeeHSSGTPETSvPAtgsqSPAESPtlTSPQAPASSPSSPSTSPPeVSSASVTTNHSSTETSTQ 171
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1398-1436 |
3.53e-07 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 55.77 E-value: 3.53e-07
10 20 30
....*....|....*....|....*....|....*....
gi 1958662372 1398 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTG 1436
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1051-1079 |
8.72e-07 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 54.56 E-value: 8.72e-07
10 20
....*....|....*....|....*....
gi 1958662372 1051 GEMVGALAAQSLGEPATQMTLNTFHYAGV 1079
Cdd:CHL00117 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
728-832 |
1.77e-06 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 53.40 E-value: 1.77e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 728 SEY------NNFKS---------MVVSGAKGskiNISQVIAVVG--------QqnveGKRIpfgfkhrTLPhfIKddygp 784
Cdd:CHL00117 108 SEYlkqemnPNFRMtdplnpvymMSFSGARG---NASQVHQLVGmrglmsdpQ----GQII-------DLP--IQ----- 166
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1958662372 785 esRGFVEnsylaGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLI 832
Cdd:CHL00117 167 --SNFRE-----GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1820-1930 |
2.64e-06 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 52.45 E-value: 2.64e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1820 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1896
Cdd:COG3469 89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168
|
90 100 110
....*....|....*....|....*....|....
gi 1958662372 1897 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISP 1930
Cdd:COG3469 169 TTTTTSASTTPSATTTATATTASGATTPSATTTA 202
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1842-1936 |
4.14e-06 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 51.73 E-value: 4.14e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1842 SPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT--YSPTSPKGSTYSPTSPGYSPTSP 1919
Cdd:PRK14950 370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTpeSAPKLTRAAIPVDEKPKYTPPAP 449
|
90
....*....|....*..
gi 1958662372 1920 TYSLTSPAISPEDSDEE 1936
Cdd:PRK14950 450 PKEEEKALIADGDVLEQ 466
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1825-1936 |
6.86e-06 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 50.72 E-value: 6.86e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1825 PKYSPTSPKYSPTSPKYSPTSpTYSPTTPKYSPTSPTYSPTSPvyTPTSPKySPTSPTYSPTSPKYSPTSPTYSPTSPkg 1904
Cdd:PHA03291 181 SADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTP--TPSTTT-SPPSTTIPAPSTTIAAPQAGTTPEAE-- 254
|
90 100 110
....*....|....*....|....*....|..
gi 1958662372 1905 STYSPTSPGYSPTSPtyslTSPAISPEDSDEE 1936
Cdd:PHA03291 255 GTPAPPTPGGGEAPP----ANATPAPEASRYE 282
|
|
| Herpes_BLLF1 |
pfam05109 |
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
1838-1930 |
8.00e-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: 8.00e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1838 SPKYSPTSPTYSpTTPKYSPTSPTYSP------------------------TSPVYTPTSPKYSPTSPTYSP-------- 1885
Cdd:pfam05109 424 APESTTTSPTLN-TTGFAAPNTTTGLPssthvptnltapastgptvstadvTSPTPAGTTSGASPVTPSPSPrdngtesk 502
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 1958662372 1886 ----TSPKYSPTSPTYSPTSPKGSTYSP----TSPGYSPTSPTYSLTSP---AISP 1930
Cdd:pfam05109 503 apdmTSPTSAVTTPTPNATSPTPAVTTPtpnaTSPTLGKTSPTSAVTTPtpnATSP 558
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1398-1437 |
1.86e-05 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 49.94 E-value: 1.86e-05
10 20 30 40
....*....|....*....|....*....|....*....|
gi 1958662372 1398 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGC 1437
Cdd:CHL00117 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1823-1927 |
4.72e-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: 44.82 E-value: 4.72e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1823 TSPKYSPTS---PKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTS 1894
Cdd:smart01104 3 RTPAWGASGsktPAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEG 79
|
90 100 110
....*....|....*....|....*....|...
gi 1958662372 1895 PTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1927
Cdd:smart01104 80 SASSWAAGPGGAYGAPTPGYGGTPSAYGPATPG 112
|
|
| Endomucin |
pfam07010 |
Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early ... |
1835-1933 |
4.93e-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: 47.17 E-value: 4.93e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1835 SPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTS--PKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1912
Cdd:pfam07010 29 ANITLSTTPSTTAETASTPKTTNLNTPTGGTSPVGTTSSelSKTSLVSTTISLTTTKKGVGTTTTDVSKNESSTTKPTVT 108
|
90 100
....*....|....*....|.
gi 1958662372 1913 GYSPTSPTYSLTSPAISPEDS 1933
Cdd:pfam07010 109 STPLSNAVSTLQSSQHKTENQ 129
|
|
| PRK14950 |
PRK14950 |
DNA polymerase III subunits gamma and tau; Provisional |
1821-1905 |
5.58e-05 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 48.27 E-value: 5.58e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPkySPTSPTYSPTSPKYSPTSPTYSPT 1900
Cdd:PRK14950 370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPH--TPESAPKLTRAAIPVDEKPKYTPP 447
|
....*
gi 1958662372 1901 SPKGS 1905
Cdd:PRK14950 448 APPKE 452
|
|
| DUF1373 |
pfam07117 |
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ... |
1822-1935 |
6.00e-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: 6.00e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSPKYSPTSPKYSPTSPKY----SPTSP-TYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT 1896
Cdd:pfam07117 33 PLPPGQEPEPPRPEEEEGQGggggTFPFPgSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSS 112
|
90 100 110
....*....|....*....|....*....|....*....
gi 1958662372 1897 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPEDSDE 1935
Cdd:pfam07117 113 GSGSGHQGSGGAGAGAGAPGHQHEQEQESSSSDDDDEDE 151
|
|
| Chi1 |
COG3469 |
Chitinase [Carbohydrate transport and metabolism]; |
1819-1924 |
6.14e-05 |
|
Chitinase [Carbohydrate transport and metabolism];
Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 47.83 E-value: 6.14e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1819 EYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS------PTSPVYTPTSPKYSPTSPTYSPTSPKYSP 1892
Cdd:COG3469 109 TSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVsgtetaTGGTTTTSTTTTTTSASTTPSATTTATAT 188
|
90 100 110
....*....|....*....|....*....|..
gi 1958662372 1893 TSPTYSPTSPKGSTysPTSPGYSPTSPTYSLT 1924
Cdd:COG3469 189 TASGATTPSATTTA--TTTGPPTPGLPKHVLV 218
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1821-1927 |
1.06e-04 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 46.87 E-value: 1.06e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPT 1900
Cdd:PTZ00436 232 AAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAA 311
|
90 100 110
....*....|....*....|....*....|.
gi 1958662372 1901 SPKGSTYSP----TSPGYSPTSPTYSLTSPA 1927
Cdd:PTZ00436 312 APAKAAAPPakaaAPPAKAATPPAKAAAPPA 342
|
|
| PLN02217 |
PLN02217 |
probable pectinesterase/pectinesterase inhibitor |
1836-1933 |
1.13e-04 |
|
probable pectinesterase/pectinesterase inhibitor
Pssm-ID: 215130 [Multi-domain] Cd Length: 670 Bit Score: 47.01 E-value: 1.13e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1836 PTSPKYSPTSPTYSPTTPKYS--PTSPTYSPTSPVyTPTSPKYSPtsPTYSPTSPKYSPT---SPTYSPtsPKGSTYSPT 1910
Cdd:PLN02217 556 PYIPGLFAGNPGSTNSTPTGSaaSSNTTFSSDSPS-TVVAPSTSP--PAGHLGSPPATPSkivSPSTSP--PASHLGSPS 630
|
90 100
....*....|....*....|...
gi 1958662372 1911 SPGYSPTSPTYSLTSPAISPEDS 1933
Cdd:PLN02217 631 TTPSSPESSIKVASTETASPESS 653
|
|
| rad23 |
TIGR00601 |
UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
1837-1909 |
1.44e-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: 1.44e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958662372 1837 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1909
Cdd:TIGR00601 75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1822-1933 |
1.55e-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: 1.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSPkySPTSPKYSPTSPKYSPTSPTySPTTPKYSPTSPTYSPTSPVYTPTSPKY------SPTSPTYSPTSPKYSPTSP 1895
Cdd:PLN03209 450 PTSP--SPTAPTGVSPSVSSTSSVPA-VPDTAPATAATDAAAPPPANMRPLSPYAvyddlkPPTSPSPAAPVGKVAPSST 526
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1958662372 1896 TYSPtsPKGSTYSPTS---------PGYSPTSP--TYSLTSPAISPEDS 1933
Cdd:PLN03209 527 NEVV--KVGNSAPPTAladeqhhaqPKPRPLSPytMYEDLKPPTSPTPS 573
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1820-1928 |
1.72e-04 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 46.10 E-value: 1.72e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1820 YTPTSPKYSPTSPKYSPTSpKYSPTSPTYSP--------TTPKYSPTSPTysptspvyTPTSPKYSPTSPTYSPTSPKYS 1891
Cdd:PHA03291 183 DGSCDPALPLSAPRLGPAD-VFVPATPRPTPrttaspetTPTPSTTTSPP--------STTIPAPSTTIAAPQAGTTPEA 253
|
90 100 110
....*....|....*....|....*....|....*..
gi 1958662372 1892 PTSPtySPTSPKGSTYSPTSPGYSPTSPTYSLTSPAI 1928
Cdd:PHA03291 254 EGTP--APPTPGGGEAPPANATPAPEASRYELTVTQI 288
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1027-1071 |
1.84e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 46.42 E-value: 1.84e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 1958662372 1027 LSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTL 1071
Cdd:PRK14898 33 VTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1832-1919 |
2.30e-04 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 45.72 E-value: 2.30e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1832 PKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSpVYTPTSPKYSPTSPTySP--TSPKYSPTSPTYSPTSPKGSTYSP 1909
Cdd:PHA03291 167 PAEGTLAAPPLGEGSADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTA-SPetTPTPSTTTSPPSTTIPAPSTTIAA 244
|
90
....*....|
gi 1958662372 1910 TSPGYSPTSP 1919
Cdd:PHA03291 245 PQAGTTPEAE 254
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1482-1588 |
4.27e-04 |
|
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pssm-ID: 215026 [Multi-domain] Cd Length: 121 Bit Score: 42.12 E-value: 4.27e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1482 PAMTP-WNQGA--TPAYGAWSPSVGSGMTPGAAGFSPSAASdASGFSPGYSPAWSPTpgspgspgpsspyipSPGGAMSP 1558
Cdd:smart01104 1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRTP-AWGGAGSRTPAWGGA---------------GPTGSRTP 64
|
90 100 110
....*....|....*....|....*....|
gi 1958662372 1559 SYSPTSPAYEPRSPGGYTPQSPSYSPTSPS 1588
Cdd:smart01104 65 AWGGASAWGNKSSEGSASSWAAGPGGAYGA 94
|
|
| GATA-N |
pfam05349 |
GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell ... |
1828-1936 |
4.66e-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: 43.19 E-value: 4.66e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1828 SPTSPKYSPTSPKY---SPTSPTYSPTT--PKYSPTSPtYSPTSPVYTPTSPKYS-PTSPTYSPTSPKYSPTSPTYSPts 1901
Cdd:pfam05349 10 NHGQAAYDHDSGGFlhsAASSPVYVPTTrvPSMLPTLP-YLQGCGSSQQSHPVSShSGWAQAGAESSSYNPGSPHPSP-- 86
|
90 100 110
....*....|....*....|....*....|....*
gi 1958662372 1902 pkGSTYSPTSPGYSPTSPTYSLTSPAISPEDSDEE 1936
Cdd:pfam05349 87 --RFSYSHSPPGSNGTSRDAAYQSPLLISAGGREQ 119
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1822-1932 |
6.42e-04 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 44.68 E-value: 6.42e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSPKY--SPTSPKySPTSPKySPTSP-----TYSPTTPKySPTSPTySPTSP-----VYTPTSPKYSPTSPTYS----- 1884
Cdd:PTZ00449 621 PKSPKRpeSPKSPK-RPPPPQ-RPSSPerpegPKIIKSPK-PPKSPK-PPFDPkfkekFYDDYLDAAAKSKETKTtvvld 696
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1958662372 1885 -----------PTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPED 1932
Cdd:PTZ00449 697 esfesilketlPETPGTPFTTPRPLPPKLPRDEEFPFEPIGDPDAEQPDDIEFFTPPEE 755
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1821-1903 |
6.87e-04 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 44.68 E-value: 6.87e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKYSPTS-PKYSPTSPKySPTSPTYSPTTPKYSPTSPTYSPTS--------PVYTP--------------TSPKYS 1877
Cdd:PTZ00449 710 TPGTPFTTPRPlPPKLPRDEE-FPFEPIGDPDAEQPDDIEFFTPPEEertffhetPADTPlpdilaeefkeediHAETGE 788
|
90 100
....*....|....*....|....*..
gi 1958662372 1878 PTSPTYSPTSP-KYSPTSPTYSPTSPK 1903
Cdd:PTZ00449 789 PDEAMKRPDSPsEHEDKPPGDHPSLPK 815
|
|
| Pneumo_att_G |
pfam05539 |
Pneumovirinae attachment membrane glycoprotein G; |
1821-1937 |
7.70e-04 |
|
Pneumovirinae attachment membrane glycoprotein G;
Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 44.27 E-value: 7.70e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKysptsPKYSPTSPKYSPT-SPTYSPTTPkySPTSPTySPTSPVYTPTspkysPTSPTySPTSPKYSPTSPTYSP 1899
Cdd:pfam05539 226 TSSNPE-----PQTEPPPSQRGPSgSPQHPPSTT--SQDQST-TGDGQEHTQR-----RKTPP-ATSNRRSPHSTATPPP 291
|
90 100 110
....*....|....*....|....*....|....*...
gi 1958662372 1900 TSPKGSTYSPTspgYSPTSPTYSLTSPAISPEDSDEEN 1937
Cdd:pfam05539 292 TTKRQETGRPT---PRPTATTQSGSSPPHSSPPGVQAN 326
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1824-1926 |
8.18e-04 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.79 E-value: 8.18e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1824 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1903
Cdd:PTZ00436 249 APAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPA 328
|
90 100
....*....|....*....|...
gi 1958662372 1904 GSTyspTSPGYSPTSPTYSLTSP 1926
Cdd:PTZ00436 329 KAA---TPPAKAAAPPAKAAAAP 348
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1822-1935 |
9.19e-04 |
|
translocon at the inner envelope of chloroplast subunit 62; Provisional
Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 44.15 E-value: 9.19e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSPkySPTSPKYSPTSPKysPTSPTYSPTTPKYSPTSPTYS----------------PTSPvYT-------PTSPkySP 1878
Cdd:PLN03209 383 PTSP--IPTPPSSSPASSK--SVDAVAKPAEPDVVPSPGSASnvpevepaqveakktrPLSP-YAryedlkpPTSP--SP 455
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958662372 1879 TSPTYSPTSPKYS--------------------PTSPTYSPTSPkgstYSPTSPGYSPTSPTYSLTSPAISPEDSDE 1935
Cdd:PLN03209 456 TAPTGVSPSVSSTssvpavpdtapataatdaaaPPPANMRPLSP----YAVYDDLKPPTSPSPAAPVGKVAPSSTNE 528
|
|
| PLN03209 |
PLN03209 |
translocon at the inner envelope of chloroplast subunit 62; Provisional |
1822-1927 |
9.59e-04 |
|
translocon at the inner envelope of chloroplast subunit 62; Provisional
Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 44.15 E-value: 9.59e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSP--KYSPTSPkysPTSPKYSPTSPTYSPTTpkySPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPK------YSPT 1893
Cdd:PLN03209 437 PLSPyaRYEDLKP---PTSPSPTAPTGVSPSVS---STSSVPAVPDTAPATAATDAAAPPPANMRPLSPYavyddlKPPT 510
|
90 100 110
....*....|....*....|....*....|....
gi 1958662372 1894 SPTysPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1927
Cdd:PLN03209 511 SPS--PAAPVGKVAPSSTNEVVKVGNSAPPTALA 542
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1824-1927 |
1.02e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.79 E-value: 1.02e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1824 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1903
Cdd:PTZ00436 228 APAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPA 307
|
90 100
....*....|....*....|....*...
gi 1958662372 1904 GSTYSP----TSPGYSPTSPTYSLTSPA 1927
Cdd:PTZ00436 308 KAAAAPakaaAPPAKAAAPPAKAATPPA 335
|
|
| rad23 |
TIGR00601 |
UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
1829-1910 |
1.11e-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: 43.35 E-value: 1.11e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1829 PTSPKYSPTSPKYSPTS-PTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTY 1907
Cdd:TIGR00601 77 PKTGTGKVAPPAATPTSaPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSER 156
|
...
gi 1958662372 1908 SPT 1910
Cdd:TIGR00601 157 ETT 159
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1824-1904 |
1.21e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.40 E-value: 1.21e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1824 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1903
Cdd:PTZ00436 270 PPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAPV 349
|
.
gi 1958662372 1904 G 1904
Cdd:PTZ00436 350 G 350
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1824-1927 |
1.22e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 43.40 E-value: 1.22e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1824 SPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPK 1903
Cdd:PTZ00436 221 APAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPA 300
|
90 100
....*....|....*....|....*...
gi 1958662372 1904 GSTYSP----TSPGYSPTSPTYSLTSPA 1927
Cdd:PTZ00436 301 KAAAAPakaaAAPAKAAAPPAKAAAPPA 328
|
|
| KAR9 |
pfam08580 |
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ... |
1820-1929 |
1.46e-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: 1.46e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1820 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTP---------------KYSPTSPT-YSPTSPVYTPTSPKYSPTSPTY 1883
Cdd:pfam08580 503 GFLSTPSNTATSETPTPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTtPSPTPSRSSRSSSTLPPVSPLS 582
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1958662372 1884 SPTSPKYSPTSPTYSPTSPKGSTYSPTSPGySPTSPTYSLTSPAIS 1929
Cdd:pfam08580 583 RDKSRSPAPTCRSVSRASRRRASRKPTRIG-SPNSRTSLLDEPPYP 627
|
|
| PHA03269 |
PHA03269 |
envelope glycoprotein C; Provisional |
1822-1926 |
1.54e-03 |
|
envelope glycoprotein C; Provisional
Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 43.56 E-value: 1.54e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTySPTSPKYSPtsPTYSPTS 1901
Cdd:PHA03269 46 PHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQLAA-APKPDAAEA--FTSAAQA 122
|
90 100
....*....|....*....|....*.
gi 1958662372 1902 PKGSTYSPTSP-GYSPTSPTYSLTSP 1926
Cdd:PHA03269 123 HEAPADAGTSAaSKKPDPAAHTQHSP 148
|
|
| PHA03291 |
PHA03291 |
envelope glycoprotein I; Provisional |
1846-1931 |
1.63e-03 |
|
envelope glycoprotein I; Provisional
Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 43.02 E-value: 1.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1846 PTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSpTYSPTSPKYSPTSPTySP--TSPKGSTYSPTSPGYSPTSPTYSL 1923
Cdd:PHA03291 167 PAEGTLAAPPLGEGSADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTA-SPetTPTPSTTTSPPSTTIPAPSTTIAA 244
|
....*...
gi 1958662372 1924 TSPAISPE 1931
Cdd:PHA03291 245 PQAGTTPE 252
|
|
| PTZ00436 |
PTZ00436 |
60S ribosomal protein L19-like protein; Provisional |
1823-1909 |
1.93e-03 |
|
60S ribosomal protein L19-like protein; Provisional
Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 42.63 E-value: 1.93e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1823 TSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1902
Cdd:PTZ00436 262 APPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPP 341
|
....*..
gi 1958662372 1903 KGSTYSP 1909
Cdd:PTZ00436 342 AKAAAAP 348
|
|
| 2A1904 |
TIGR00927 |
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ... |
1819-1934 |
1.94e-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: 43.45 E-value: 1.94e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1819 EYTPTSPKyspTSPKYSPTSPK--YSPTSPTY------SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKY 1890
Cdd:TIGR00927 109 ENTPSPPR---RTAKITPTTPKnnYSPTAAGTervkedTPATPSRALNHYISTSGRQRVKSYTPKPRGEVKSSSPTQTRE 185
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 1958662372 1891 SPTSPTYSPTSPKGSTYSPTSPGYSPTSPTyslTSPAISPEDSD 1934
Cdd:TIGR00927 186 KVRKYTPSPLGRMVNSYAPSTFMTMPRSHG---ITPRTTVKDSE 226
|
|
| KAR9 |
pfam08580 |
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ... |
1821-1937 |
2.25e-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: 2.25e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKYSPTSPKYSPTSP---------------KYSPTSPTY-SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPT----- 1879
Cdd:pfam08580 518 TPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTTpSPTPSRSSRSSSTLPPVSPLSRDKSRSPAPTcrsvs 597
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958662372 1880 SPTYSPTSPK----YSPTSPTY--SPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPEDSDEEN 1937
Cdd:pfam08580 598 RASRRRASRKptriGSPNSRTSllDEPPYPKLTLSKGLPRTPRNRQSYAGTSPSRSVSVSSGLG 661
|
|
| PHA03247 |
PHA03247 |
large tegument protein UL36; Provisional |
1821-1933 |
2.33e-03 |
|
large tegument protein UL36; Provisional
Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 43.39 E-value: 2.33e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKYSPTSPkySPTSPKySPTSPTYSPTTPKYSPTSPTYSPTSPVyTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPT 1900
Cdd:PHA03247 2750 TPGGPARPARPP--TTAGPP-APAPPAAPAAGPPRRLTRPAVASLSES-RESLPSPWDPADPPAAVLAPAAALPPAASPA 2825
|
90 100 110
....*....|....*....|....*....|...
gi 1958662372 1901 SPKGstySPTSPGYSPTSPTYSLTSPAISPEDS 1933
Cdd:PHA03247 2826 GPLP---PPTSAQPTAPPPPPGPPPPSLPLGGS 2855
|
|
| CytochromB561_N |
pfam09786 |
Cytochrome B561, N terminal; Members of this family are found in the N terminal region of ... |
1822-1908 |
2.46e-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: 2.46e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSPKYSPTSPKYSPTSPKYSP--TSPTYSPTTPKYSPTSP-TYSPTSPVYTPTSPkySPTSPTYSpTSPKYSP--TSPT 1896
Cdd:pfam09786 145 PLHQSVSPSSSESRKGGDKSPAgsGKKLRSFSTSSKSPASPsVYLRGSPVPLNSSP--LPSDRNYE-NSVQSSPeiDSAV 221
|
90
....*....|..
gi 1958662372 1897 YSPTSPKGSTYS 1908
Cdd:pfam09786 222 STPWSRKRATIG 233
|
|
| Pneumo_att_G |
pfam05539 |
Pneumovirinae attachment membrane glycoprotein G; |
1822-1918 |
3.33e-03 |
|
Pneumovirinae attachment membrane glycoprotein G;
Pssm-ID: 114270 [Multi-domain] Cd Length: 408 Bit Score: 41.96 E-value: 3.33e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1822 PTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS-PTSPVYTPTSPKYSPTSPTYSPTspkYSPTSPTYSPT 1900
Cdd:pfam05539 237 PPSQRGPSGSPQHPPSTTSQDQSTTGDGQEHTQRRKTPPATSnRRSPHSTATPPPTTKRQETGRPT---PRPTATTQSGS 313
|
90
....*....|....*...
gi 1958662372 1901 SPKGStySPTSPGYSPTS 1918
Cdd:pfam05539 314 SPPHS--SPPGVQANPTT 329
|
|
| CTD |
smart01104 |
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ... |
1821-1912 |
3.93e-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: 3.93e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TP----TSPKYSPTSPkysPTSPKYSP-TSPTYSPT---TP------KYSPTSPTYSPTSPVY-----TPTSPKYSPTSP 1881
Cdd:smart01104 14 TPawgsRTPGTAAGGA---PTARGGSGsRTPAWGGAgsrTPawggagPTGSRTPAWGGASAWGnksseGSASSWAAGPGG 90
|
90 100 110
....*....|....*....|....*....|.
gi 1958662372 1882 TYSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1912
Cdd:smart01104 91 AYGAPTPGYGGTPSAYGPATPGGGAMAGSAS 121
|
|
| Hamartin |
pfam04388 |
Hamartin protein; This family includes the hamartin protein which is thought to function as a ... |
1843-1922 |
5.30e-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: 5.30e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1843 PTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTsPTYSPTSPKGSTYSPTSPGYSPTSPTYS 1922
Cdd:pfam04388 276 PTASPYTDQQSSYGSSTSTPSSTPRLQLSSSSGTSPPYLSPPSIRLKTDSF-PLWSPSSVCGMTTPPTSPGMVPTTPSEL 354
|
|
| PHA02682 |
PHA02682 |
ORF080 virion core protein; Provisional |
1821-1935 |
7.19e-03 |
|
ORF080 virion core protein; Provisional
Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 40.61 E-value: 7.19e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKYSPTSPKYSPTSPkySPTSPTYSPTTPKYSPTSPtySPTSPVYTPTSPKySPTSPTYSPtspkysptSPTYSPT 1900
Cdd:PHA02682 99 APAAPAPAVTCPAPAPACP--PATAPTCPPPAVCPAPARP--APACPPSTRQCPP-APPLPTPKP--------APAAKPI 165
|
90 100 110
....*....|....*....|....*....|....*.
gi 1958662372 1901 SPKGSTYSPTSPGYS-PTSPTYSLTSPAISPEDSDE 1935
Cdd:PHA02682 166 FLHNQLPPPDYPAAScPTIETAPAASPVLEPRIPDK 201
|
|
| PTZ00449 |
PTZ00449 |
104 kDa microneme/rhoptry antigen; Provisional |
1821-1919 |
8.45e-03 |
|
104 kDa microneme/rhoptry antigen; Provisional
Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 41.21 E-value: 8.45e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662372 1821 TPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKyspTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTyspt 1900
Cdd:PTZ00449 728 DEEFPFEPIGDPDAEQPDDIEFFTPPEEERTFFH---ETPADTPLPDILAEEFKEEDIHAETGEPDEAMKRPDSPS---- 800
|
90
....*....|....*....
gi 1958662372 1901 spkgsTYSPTSPGYSPTSP 1919
Cdd:PTZ00449 801 -----EHEDKPPGDHPSLP 814
|
|
| |
