|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
18-1035 |
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: 1135.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 18 RFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHPLLFNL 97
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 98 LFNFLQRACFFCHHFMAKPEDVERAVSQLKLIIKGDIVSAKQLESNtptkskssdescesvvttdsseecedsdvedqrw 177
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKLKLLDKGLLVEAAELDFG---------------------------------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 178 tslqfaevtavlknfmrlsskscsrckginpklekpmfgwvrmramkdsdvganvirglklkkstssvenpdgfddsgid 257
Cdd:cd01435 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 258 alsevedgdketrekstevaaefeehnskrdllpsevrnilkhlwqnehefcsfigdlwqsgsekidYSMFFLESVLVPP 337
Cdd:cd01435 127 -------------------------------------------------------------------YDMFFLDVLLVPP 139
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 338 TKFRPPTTGGDSVMEHPQTVGLNKVIESNNILGNACT---------------NKLDQSKVIFRWRNLQESVNVLFDSKTA 402
Cdd:cd01435 140 NRFRPPSFLGDKVFENPQNVLLSKILKDNQQIRDLLAsmrqaesqskldlisGKTNSEKLINAWLQLQSAVNELFDSTKA 219
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 403 TVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIIN 482
Cdd:cd01435 220 PKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVIN 299
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 483 GPDIHPGATHYSDKSSTM-KLPSTEKARRAIARKLLSSRGATTELgktcdiNFEGKTVHRHMRDGDIVLVNRQPTLHKPS 561
Cdd:cd01435 300 GPDVYPGANAIEDEDGRLiLLSALSEERRKALAKLLLLLSSAKLL------LNGPKKVYRHLLDGDVVLLNRQPTLHKPS 373
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 562 LMAHKVRVLKGEKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVL 641
Cdd:cd01435 374 IMAHKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVL 453
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 642 LTKRDTFLDKDHFNQLLFsSGVTDMVLSTFSGRsgkkvmvsasdaeLLTVTPAILKPVPLWTGKQVITAVLNQITKGHPP 721
Cdd:cd01435 454 LTSRDTFFTREEYQQLVY-AALRPLFTSDKDGR-------------IKLLPPAILKPKPLWTGKQVISTILKNLIPGNAP 519
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 722 FTVEkatklpvdffkcrsrevkpNSGDLTKKKEIDESWKQNLNEDKLHIRKNEFVCGVIDKAQFAD--YGLVHTVHELYG 799
Cdd:cd01435 520 LLNL-------------------SGKKKTKKKVGGGKWGGGSEESQVIIRNGELLTGVLDKSQFGAsaYGLVHAVYELYG 580
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 800 SNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENVGERVLRKTFGIdvdvqidpqdmrsrieri 879
Cdd:cd01435 581 GETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEFLGL------------------ 642
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 880 lyedgesalasldrsivnYLNQCSSKgVMNDLLSDGLLKTPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPR 959
Cdd:cd01435 643 ------------------KLNKVTSS-IIKACLPKGLLKPFPENNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPL 703
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063717413 960 MVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1035
Cdd:cd01435 704 MVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
10-1655 |
9.22e-167 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 541.15 E-value: 9.22e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 10 ASQVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPI 89
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 90 YHPLLFNLLFNFLQRACFFCHHFMAKPEDVeravSQLKLIikgdivsakqlesntptkskssdESCESVVTTDSSEECED 169
Cdd:PRK14977 85 IHIAFIDNIKDLLNSTCHKCAKLKLPQEDL----NVFKLI-----------------------EEAHAAARDIPEKRIDD 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 170 SDVEDQRWTSLQFAEvtavlknfmrlSSKSCSRCkginpklekpmfgwvrmramkdsdvGANVIRgLKLKKSTSSVENpd 249
Cdd:PRK14977 138 EIIEEVRDQVKVYAK-----------KAKECPHC-------------------------GAPQHE-LEFEEPTIFIEK-- 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 250 gfddsgidalsevedgdketrekstevaAEFEEHNskrdLLPSEVRNILKHLWQNEHEFCSFigdlwqsGSEKIDYSMFF 329
Cdd:PRK14977 179 ----------------------------TEIEEHR----LLPIEIRDIFEKIIDDDLELIGF-------DPKKARPEWAV 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 330 LESVLVPPTKFRPPT---TGGDSvmEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDSKTATV-- 404
Cdd:PRK14977 220 LQAFLVPPLTARPSIileTGERS--EDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIpq 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 405 ----QSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAI 480
Cdd:PRK14977 298 ahhkGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELV 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 481 INGPDIHPGAtHYSDKSSTMKlpstekarraIARKLLSSRG--ATTELGKTCDInfeGKTVHRHMRDGDIVLVNRQPTLH 558
Cdd:PRK14977 378 INGPDEFPGA-NAIRKGDGTK----------IRLDFLEDKGkdALREAAEQLEI---GDIVERHLADGDIVIFNRQPSLH 443
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 559 KPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVS 638
Cdd:PRK14977 444 KLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITA 522
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 639 SVLLTKRDTFLDKDHFNQLLFSSGVTDMVLStfsgrsgkkvmvsasdaelltvtPAI-LKPVPLWTGKQVITAVlnqitk 717
Cdd:PRK14977 523 AYLITKDDALFDKNEASNIAMLAGITDPLPE-----------------------PAIkTKDGPAWTGKQLFSLF------ 573
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 718 ghppftvekatkLPVDFfkcrSREVKPNSGDLTKKKEIDESWkqnLNEDKLHIRKNEFVCGVIDKAQFADY-----GLVH 792
Cdd:PRK14977 574 ------------LPKDF----NFEGIAKWSAGKAGEAKDPSC---LGDGYVLIKEGELISGVIDDNIIGALveepeSLID 634
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 793 TVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIIlkdMDEERTKQLQECENVGERVLRKTFGIDVDVQIDPQDM 872
Cdd:PRK14977 635 RIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLII---PDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKG 711
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 873 RSRIERILYEDgesalASLDRSIVNYLNQCSSK--GVMNDLLsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGQQ 950
Cdd:PRK14977 712 KEELLRGMKEE-----EALEADIVNELDKARDKagSSANDCI-------DADNAGKIMAKTGARGSMANLAQIAGALGQQ 779
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 951 D--------LEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRC 1022
Cdd:PRK14977 780 KrktrigfvLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRR 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1023 LMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHR---------SSFIEKFKELTINQDMVLQKCSEDMLSGASSYIS 1093
Cdd:PRK14977 860 LANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKldhgeafnlERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNA 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1094 DLPISLkkgAEKFVEAMPMNERIaskfvrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEM 1173
Cdd:PRK14977 940 NLPKLL---ADAIHGAELKEDEL-------EAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAM 1009
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1174 NVTLGIPRLQEiLMTAAANIKTPIMTCpLLKGKTKED---ANDITDRLRKITVADIIKSMElsvvpyTVYENEVCSIhkl 1250
Cdd:PRK14977 1010 DVTHGLERFIE-LVDARAKPSTPTMDI-YLDDECKEDiekAIEIARNLKELKVRALIADSA------IDNANEIKLI--- 1078
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1251 kinlyKPEHypkhtditeedweetmravflRKLEDAIETHMKMLHRIRGIHNDVTGPIagnETDNDdsvsgkqneddgdd 1330
Cdd:PRK14977 1079 -----KPDK---------------------RALENGCIPMERFAEIEAALAKGKKFEM---ELEDD-------------- 1115
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1331 dgegTEVDDLGSDAQKQKKQETdemdyeensedetnepssISGVEDPEMDsenedtevskedtpepqeesmepqKEVKGV 1410
Cdd:PRK14977 1116 ----LIILDLVEAADRDKPLAT------------------LIAIRNKILD------------------------KPVKGV 1149
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1411 KNVKeqskkkrRKFVraksdrhifvkgegekfevhfkfatddphillaQIAQQTAQKVY-IQNSGkierctvancgdpqv 1489
Cdd:PRK14977 1150 PDIE-------RAWV---------------------------------ELVEKDGRDEWiIQTSG--------------- 1174
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1490 iyhgdnpkerreiSNDEKkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGI 1569
Cdd:PRK14977 1175 -------------SNLAA----VLEMKCI------------DIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGL 1225
|
1610 1620 1630 1640 1650 1660 1670 1680
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1570 SVSIRHLNLIADYMTFSG-----GYRPMSRMGGIA-ESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPAL 1643
Cdd:PRK14977 1226 EVDNRYIMLVADIMCSRGtieaiGLQAAGVRHGFAgEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIP 1305
|
1690
....*....|..
gi 1063717413 1644 SGTGCFDLMQRV 1655
Cdd:PRK14977 1306 IGSGKVDLLMDF 1317
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
12-1062 |
1.79e-165 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 524.42 E-value: 1.79e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 12 QVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYH 91
Cdd:PRK08566 7 KRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 92 PLLFNLLFNFLQRACFFCHHFMAKPEDVERAVSQLKliikgdivsakqlesntptkskssdescesvvttdsseecedsd 171
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLE-------------------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 172 vEDQRWTSLqfaeVTAVLKNFMRLSSK--SCSRC--KGINPKLEKPmfgwvrmramkdsdvganvirglklkksTSSVEN 247
Cdd:PRK08566 123 -RLKEWGSL----ADDLIKEVKKEAAKrmVCPHCgeKQYKIKFEKP----------------------------TTFYEE 169
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 248 pdgfddsgidalsevedgDKETREKstevaaefeehnskrdLLPSEVRNILkhlwqnehefcsfigdlwqsgsEKI---D 324
Cdd:PRK08566 170 ------------------RKEGLVK----------------LTPSDIRERL----------------------EKIpdeD 193
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 325 YSMFFLE-----------SVL-VPPTKFRPPTT---GGDSvmEHPQTVGLNKVIESN-----NILGNACTNKLDQskvif 384
Cdd:PRK08566 194 LELLGINpevarpewmvlTVLpVPPVTVRPSITletGQRS--EDDLTHKLVDIIRINqrlkeNIEAGAPQLIIED----- 266
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 385 RWRNLQESVNVLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFA 459
Cdd:PRK08566 267 LWELLQYHVTTYFDNEIPGIPPARHRSGrplktLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIA 346
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 460 LKLTYPERVTPWNVEKLREAIINGPDIHPGAThYSDKSSTMKLPSTEKARRAIARKLLssrgattelgktcdinfEGKTV 539
Cdd:PRK08566 347 KELTVPERVTEWNIEELREYVLNGPEKHPGAN-YVIRPDGRRIKLTDKNKEELAEKLE-----------------PGWIV 408
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 540 HRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQY 619
Cdd:PRK08566 409 ERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHI 487
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 620 ARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLFSSGVTdmvlstfsgrsgkkvmvsasdaELLTVTPAILKPV 699
Cdd:PRK08566 488 LSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGID----------------------ELPEPEPAIENGK 545
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 700 PLWTGKQVITAVlnqitkghppftvekatkLPVDF-FKCRSrevKPNSGDLTKKKEIDEswkqnlNEDKLHIRKNEFVCG 778
Cdd:PRK08566 546 PYWTGKQIFSLF------------------LPKDLnLEFKA---KICSGCDECKKEDCE------HDAYVVIKNGKLLEG 598
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 779 VIDKAQFADYG--LVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLiilkDMDEERTKQLQECENVGERvlr 856
Cdd:PRK08566 599 VIDKKAIGAEQgsILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDE----DIPEEAKEEIDEIIEEAEK--- 671
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 857 ktfgiDVDvqidpqdmrSRIERilYEDGESALA---SLDRSIVNYLNQCSSKG--VMNDLLSDGLLKTpgrNCISLMTIS 931
Cdd:PRK08566 672 -----RVE---------ELIEA--YENGELEPLpgrTLEETLEMKIMQVLGKArdEAGEIAEKYLGLD---NPAVIMART 732
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 932 GAKGSKVNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAV 1011
Cdd:PRK08566 733 GARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAV 812
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|.
gi 1063717413 1012 KTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHRSSF 1062
Cdd:PRK08566 813 RTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDH 863
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1133-1652 |
7.30e-130 |
|
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: 406.58 E-value: 7.30e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1133 KFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTAAANIKTPIMTCPLLKGKTKEDAN 1212
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1213 DITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinlykpehypkhtditeEDWEETMRAVFLRKLedaiethmk 1292
Cdd:cd02735 81 TLKKRLSRVTLSDVVEKVEV------------------------------------TEILKTIERVFKKLL--------- 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1293 mlhrirgihndvtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssis 1372
Cdd:cd02735 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1373 gvedpemdsenedtevskedtpepqeesmepqkevkgvknvkeqskkkrrkfvraksdrhifvkgeGEKFEVHFKFATDD 1452
Cdd:cd02735 116 ------------------------------------------------------------------GKWCEVTIKLPLSS 129
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1453 PHILLAQIAQQTAQKVYIQNSGKIERCTVANCgdpqviyhgdnpkerreisNDEKKASPALHASGVDFPALWEFQDKLDV 1532
Cdd:cd02735 130 PKLLLLSIVEKLARKAVIREIPGITRCFVVEE-------------------DKGGKTKYLVITEGVNLAALWKFSDILDV 190
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1533 RYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIAESTSPFCRMTFET 1612
Cdd:cd02735 191 NRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRI-GMESSTSPLQKMSFET 269
|
490 500 510 520
....*....|....*....|....*....|....*....|
gi 1063717413 1613 ATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1652
Cdd:cd02735 270 TLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
326-640 |
3.41e-115 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 365.69 E-value: 3.41e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 326 SMFFLESVLVPPTKFRPPTTGGDS-VMEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDS---KT 401
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGrFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNeglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 402 ATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAII 481
Cdd:smart00663 81 ANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 482 NGPdihPGATHYSDKSSTMKlpsTEKARRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPS 561
Cdd:smart00663 161 NGP---NGAKYIIRGKKTNL---KLAKKSKIANHLK-----------------IGDIVERHVIDGDVVLFNRQPTLHRMS 217
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063717413 562 LMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSV 640
Cdd:smart00663 218 IQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
989-1605 |
5.28e-103 |
|
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: 340.49 E-value: 5.28e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 989 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDV----------- 1057
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPlkiekqgrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1058 -HRSSFIEKFKELTINQDMVLQKCSEDMLSGASSYISDLPISLKKGAEKFVEAMPMNE-----RIASKFVRQ-------- 1123
Cdd:pfam04998 81 eFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSKEAQERATLLFElllksGLESKRVRSeltcnska 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1124 -EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTaAANIKTPIMTCPL 1202
Cdd:pfam04998 161 fVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINV-SKNIKSPSLTVYL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1203 L--KGKTKEDANDITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinLYKPehYPKHTDITEEdweetmravfl 1280
Cdd:pfam04998 240 FdeVGRELEKAKKVYGAIEKVTLGSVVESGEI---------------------LYDP--DPFNTPIISD----------- 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1281 rklEDAIETHMKMlhrirgiHNDVTgpiagnETDNDDSVSGKQNEddgdddgegtevddlgsdaqkqkkqetdemdyeeN 1360
Cdd:pfam04998 286 ---VKGVVKFFDI-------IDEVT------NEEEIDPETGLLIL----------------------------------V 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1361 SEDETNEPSSISGVedpemdsenedteVSKEDTPEPQEES-MEPQKEVKGVKNVKEQSKKKRRKfvraksdrhifvKGEG 1439
Cdd:pfam04998 316 IRLLKILNKSIKKV-------------VKSEVIPRSIRNKvDEGRDIAIGEITAFIIKISKKIR------------QDTG 370
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1440 EKFEVHFKFATDDPhiLLAQIAQQTAQKVYIQNSGKIERCTVancgdpqviyhgdnpkerREISNDEKKASPALHASGVD 1519
Cdd:pfam04998 371 GLRRVDELFMEEDP--KLAILVASLLGNITLRGIPGIKRILV------------------NEDDKGKVEPDWVLETEGVN 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1520 FPALWEFQDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIA 1599
Cdd:pfam04998 431 LLRVLLVPGFVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH-GIN 509
|
....*.
gi 1063717413 1600 ESTSPF 1605
Cdd:pfam04998 510 KAELSA 515
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
430-615 |
4.08e-74 |
|
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: 243.75 E-value: 4.08e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 430 GKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGATHYSDKS-STMKLpstEKA 508
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINgARRDL---RYQ 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 509 RRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNA 588
Cdd:pfam00623 78 KRRLDKELE-----------------IGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG-KTFRLNLSVTTPYNA 139
|
170 180
....*....|....*....|....*..
gi 1063717413 589 DFDGDEMNVHFPQDEISRAEAYNIVNA 615
Cdd:pfam00623 140 DFDGDEMNLHVPQSEEARAEAEELMLV 166
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1095-1654 |
8.66e-46 |
|
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: 169.85 E-value: 8.66e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1095 LPISLKKGaekfVEAMPMNERIASKFvRQEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMN 1174
Cdd:TIGR02389 2 LPEKLLKE----LEETVKKREISDKE-ELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELN 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1175 VTLGIPRLQEILmTAAANIKTPIMTCPLLK--GKTKEDANDITDRLRKITVADIIKSMELSVVPYTVyenevcsihklki 1252
Cdd:TIGR02389 77 VTLGLPRLIEIV-DARKTPSTPSMTIYLEDeyEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTV------------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1253 nlykpehypkhtditeedweetmravflrkledAIETHMKMLHRiRGIhndvtgpiagnetdnddsvsgkqneddgdddg 1332
Cdd:TIGR02389 143 ---------------------------------IIELDEEQLKE-RGI-------------------------------- 156
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1333 egtEVDDLGSDAQKQKKQEtdemdyeensedetnepssisgvedpEMDSENEDTEVskedTPEPQEESMepqkevkgvkn 1412
Cdd:TIGR02389 157 ---TVDDVEKAIKKAKLGK--------------------------VIEIDMDNNTI----TIKPGNPSL----------- 192
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1413 vkeqskKKRRKfvRAKSDRHIFVKGegekfevhfkfatddphillaqiaqqtaqkvyIQNsgkIERCTVANCGDPQVIY- 1491
Cdd:TIGR02389 193 ------KELRK--LKEKIKNLHIKG--------------------------------IKG---IKRVVIRKEGDEYVIYt 229
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1492 HGDNPKErreisndekkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISV 1571
Cdd:TIGR02389 230 EGSNLKE-------------VLKLEGV------------DKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDV 284
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1572 SIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDL 1651
Cdd:TIGR02389 285 DIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDL 364
|
...
gi 1063717413 1652 MQR 1654
Cdd:TIGR02389 365 VMD 367
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
387-1248 |
1.45e-43 |
|
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: 174.08 E-value: 1.45e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 387 RNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 462
Cdd:TIGR02386 279 RMLQEAVDALFDNgrrgKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALEL 358
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 463 TYPervtpwnveklreAIINGPDIHPGAthysdksstmklPSTEKARRAIARkllssrgattELGKTCDInFEgKTVHRH 542
Cdd:TIGR02386 359 FKP-------------FIIKRLIDRELA------------ANIKSAKKMIEQ----------EDPEVWDV-LE-DVIKEH 401
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 543 MrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 622
Cdd:TIGR02386 402 P-----VLLNRAPTLHRLGIQAFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNP 475
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 623 SNGEPLRALIQDHIVSSVLLTkrdtfldKDHFNQL----LFSSgVTDMVLSTFSGRSGKKVMVS-ASDAELLTVTPailk 697
Cdd:TIGR02386 476 KDGKPIVTPSQDMVLGLYYLT-------TEKPGAKgegkIFSN-VDEAIRAYDNGKVHLHALIGvRTSGEILETTV---- 543
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 698 pvplwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrsrevkP--NSGDLTKKKEIDEswkqnlnedklhirknef 775
Cdd:TIGR02386 544 ------GR----VIFNEI--------------LPEGF---------PyiNDNEPLSKKEISS------------------ 572
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 776 vcgvidkaqfadygLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECEnvgervl 855
Cdd:TIGR02386 573 --------------LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVA------- 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 856 rktfgidvdvQIDPQdmrsrierilYEDGesALASLDRsivnYLNQCSSKGVMNDLLSDGLLK-----TPGRNCISLMTI 930
Cdd:TIGR02386 632 ----------KIQKF----------YNKG--LITDEER----YRKVVSIWSETKDKVTDAMMKllkkdTYKFNPIFMMAD 685
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 931 SGAKGSKVNFQQISshlGQQDLEGKrvprmVSGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTA 1010
Cdd:TIGR02386 686 SGARGNISQFRQLA---GMRGLMAK-----PSGDIIE-------LP-----IKSSFREGLTVLEYFISTHGARKGLADTA 745
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1011 VKTSRSGYLQRCLMKNLESLKVNY-DC---------TVRDADGSIIQFQYgeDGVdVHRSSfIEKFKElTINQDMVLQkc 1080
Cdd:TIGR02386 746 LKTADSGYLTRRLVDVAQDVVVREeDCgteegieveAIVEGKDEIIESLK--DRI-VGRYS-AEDVYD-PDTGKLIAE-- 818
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1081 SEDMLSGASsyisdlpislkkgAEKFVEAmpmneRIASKFVRQE---ELLKLVKSKFF------ASLAQPGEPVGVLAAQ 1151
Cdd:TIGR02386 819 ANTLITEEI-------------AEKIENS-----GIEKVKVRSVltcESEHGVCQKCYgrdlatGKLVEIGEAVGVIAAQ 880
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1152 SVGEPSTQMTLNTFHL---AGRGEmNVTLGIPRLQEILMTAAANIKTPIMTcplLKGKTKEDANDITDRlRKItvadIIK 1228
Cdd:TIGR02386 881 SIGEPGTQLTMRTFHTggvAGASG-DITQGLPRVKELFEARTPKDKAVIAE---VDGTVEIIEDIVKNK-RVV----VIK 951
|
890 900
....*....|....*....|
gi 1063717413 1229 SMELSVVPYTVYENEVCSIH 1248
Cdd:TIGR02386 952 DENDEEKKYTIPFGAQLRVK 971
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
358-1446 |
7.58e-30 |
|
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: 129.51 E-value: 7.58e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 358 GLNKVIESNNILgnACTNKLDQSKVIFR--WRNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGK 431
Cdd:COG0086 258 LYRRVINRNNRL--KRLLELKAPDIIVRneKRMLQEAVDALFDngrrGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGK 335
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 432 RVNHACRSVISPDPYIAVNDIGIPPCFALKLtyperVTPWNVEKLREAIIngpdihpgathysdkSSTMKlpsteKARRA 511
Cdd:COG0086 336 RVDYSGRSVIVVGPELKLHQCGLPKKMALEL-----FKPFIYRKLEERGL---------------ATTIK-----SAKKM 390
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 512 IARKllssrgaTTELGktcDINFEGKTVHRhmrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFD 591
Cdd:COG0086 391 VERE-------EPEVW---DILEEVIKEHP-------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFD 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 592 GDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKrdtfLDKDHFNQLLFSSGVTDMVLSTF 671
Cdd:COG0086 453 GDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTR----EREGAKGEGMIFADPEEVLRAYE 528
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 672 SGRsgkkvmvsasdAELLTVTPAILKPVPLWTGKQVITAV----LNQItkghppftvekatkLPVDFFKCRSrevkpnsg 747
Cdd:COG0086 529 NGA-----------VDLHARIKVRITEDGEQVGKIVETTVgrylVNEI--------------LPQEVPFYNQ-------- 575
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 748 dLTKKKEIdeswkQNLnedklhIRKNEFVCGVIDKAQFADyglvhtvhelygsnaagNLLSVFSRLFTVflqtHGFTCGV 827
Cdd:COG0086 576 -VINKKHI-----EVI------IRQMYRRCGLKETVIFLD-----------------RLKKLGFKYATR----AGISIGL 622
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 828 DDLIIlkdmDEERTKQLQECEnvgERVlrktfgidvdVQIDPQDMRSRIerilyEDGESALASLDrsIVNYLNQCSSKGV 907
Cdd:COG0086 623 DDMVV----PKEKQEIFEEAN---KEV----------KEIEKQYAEGLI-----TEPERYNKVID--GWTKASLETESFL 678
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 908 MNDLlsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGqqdLEGKRvprmvSGKT--LPCFHpwdwspraggfisdR 985
Cdd:COG0086 679 MAAF--------SSQNTTYMMADSGARGSADQLRQLAGMRG---LMAKP-----SGNIieTPIGS--------------N 728
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 986 FLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD---GSIIQFQYGEDGVDVhrssf 1062
Cdd:COG0086 729 FREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVTEEDcgtDRGITVTAIKEGGEV----- 797
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1063 IEKFKE----LTINQDmVLQKCSEDMLSGASSYISDLPISL--KKGAEKFVEAMPMNERIASKFVRQEELLKLVKskffA 1136
Cdd:COG0086 798 IEPLKErilgRVAAED-VVDPGTGEVLVPAGTLIDEEVAEIieEAGIDSVKVRSVLTCETRGGVCAKCYGRDLAR----G 872
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1137 SLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEmnvtlgipRLQEILMTAAANIKTPIMTCPLLKGKTKEDANDITD 1216
Cdd:COG0086 873 HLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS--------RAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSR 944
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1217 RLRKITVADIIKSMELSVVPYTVYENEVCSIHKLKINLYKpEHYPKHTDITEEDWEETMR------AVFLRKLEDAIETH 1290
Cdd:COG0086 945 NSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVA-EWDPHTPPIIEEVGGGVVFddivegGVIVEKTDEETGGL 1023
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1291 MKMLHRIRGIHNDVTGPIAGNETDNDDSVSGKQNEDDGDDDGEGTEVDDLGSDAQKQKKQETDEMDyeensedetnepss 1370
Cdd:COG0086 1024 SIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIAR-------------- 1089
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063717413 1371 ISGVEDPEMDSENEDTEVSKEDTPEPQEESMEPQKEVKGVKNVKEQSKKKRRKFVRAKSDRHIFVKGEGEKFEVHF 1446
Cdd:COG0086 1090 IPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
18-1035 |
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: 1135.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 18 RFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHPLLFNL 97
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 98 LFNFLQRACFFCHHFMAKPEDVERAVSQLKLIIKGDIVSAKQLESNtptkskssdescesvvttdsseecedsdvedqrw 177
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKLKLLDKGLLVEAAELDFG---------------------------------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 178 tslqfaevtavlknfmrlsskscsrckginpklekpmfgwvrmramkdsdvganvirglklkkstssvenpdgfddsgid 257
Cdd:cd01435 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 258 alsevedgdketrekstevaaefeehnskrdllpsevrnilkhlwqnehefcsfigdlwqsgsekidYSMFFLESVLVPP 337
Cdd:cd01435 127 -------------------------------------------------------------------YDMFFLDVLLVPP 139
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 338 TKFRPPTTGGDSVMEHPQTVGLNKVIESNNILGNACT---------------NKLDQSKVIFRWRNLQESVNVLFDSKTA 402
Cdd:cd01435 140 NRFRPPSFLGDKVFENPQNVLLSKILKDNQQIRDLLAsmrqaesqskldlisGKTNSEKLINAWLQLQSAVNELFDSTKA 219
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 403 TVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIIN 482
Cdd:cd01435 220 PKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVIN 299
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 483 GPDIHPGATHYSDKSSTM-KLPSTEKARRAIARKLLSSRGATTELgktcdiNFEGKTVHRHMRDGDIVLVNRQPTLHKPS 561
Cdd:cd01435 300 GPDVYPGANAIEDEDGRLiLLSALSEERRKALAKLLLLLSSAKLL------LNGPKKVYRHLLDGDVVLLNRQPTLHKPS 373
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 562 LMAHKVRVLKGEKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVL 641
Cdd:cd01435 374 IMAHKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVL 453
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 642 LTKRDTFLDKDHFNQLLFsSGVTDMVLSTFSGRsgkkvmvsasdaeLLTVTPAILKPVPLWTGKQVITAVLNQITKGHPP 721
Cdd:cd01435 454 LTSRDTFFTREEYQQLVY-AALRPLFTSDKDGR-------------IKLLPPAILKPKPLWTGKQVISTILKNLIPGNAP 519
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 722 FTVEkatklpvdffkcrsrevkpNSGDLTKKKEIDESWKQNLNEDKLHIRKNEFVCGVIDKAQFAD--YGLVHTVHELYG 799
Cdd:cd01435 520 LLNL-------------------SGKKKTKKKVGGGKWGGGSEESQVIIRNGELLTGVLDKSQFGAsaYGLVHAVYELYG 580
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 800 SNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENVGERVLRKTFGIdvdvqidpqdmrsrieri 879
Cdd:cd01435 581 GETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEFLGL------------------ 642
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 880 lyedgesalasldrsivnYLNQCSSKgVMNDLLSDGLLKTPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPR 959
Cdd:cd01435 643 ------------------KLNKVTSS-IIKACLPKGLLKPFPENNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPL 703
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063717413 960 MVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1035
Cdd:cd01435 704 MVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
321-1035 |
0e+00 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 594.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 321 EKIDYSMFFLESVLVPPTKFRPPTtggdsvmehpqtvglnkviesnnilgnactnkldqsKVIFRWRNLQESVNVLFDSK 400
Cdd:cd00399 80 SFLGPEWMILTCLPVPPPCLRPSV------------------------------------IIEERWRLLQEHVDTYLDNG 123
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 401 TATVQ----SQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLtypervtpwnvekl 476
Cdd:cd00399 124 IAGQPqtqkSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL-------------- 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 477 reaiingpdihpgathysdksstmklpstekarraiarkllssrgattelgktcdinfegktvhrhmrDGDIVLVNRQPT 556
Cdd:cd00399 190 --------------------------------------------------------------------DGDPVLFNRQPS 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 557 LHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHI 636
Cdd:cd00399 202 LHKLSIMAHRVRVLPG-STFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTL 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 637 VSSVLLTKrdtfldkdhfnqllfssgvtdmvlstfsgrsgkkvmvsasdaelltvtpailkpvplwtGKQVITAVLNqit 716
Cdd:cd00399 281 LGAYLLTL-----------------------------------------------------------GKQIVSAALP--- 298
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 717 kghppftvekatklpvdffkcrsrevkpnsgdltkkkeideswkqnlnedklhirknefvcgvidkaqfadYGLVHTVHE 796
Cdd:cd00399 299 -----------------------------------------------------------------------GGLLHTVTR 307
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 797 LYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENVGERVLRKTFGIDVDVQIDPQDMrsri 876
Cdd:cd00399 308 ELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLE---- 383
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 877 erilyedgesalASLDRSIVNYLNQCSSKGVMNDLLSDGLlkTPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKR 956
Cdd:cd00399 384 ------------ESLEDNILDFLNEARDKAGSAASVNLDL--VSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKR 449
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063717413 957 VPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1035
Cdd:cd00399 450 IPRGFSDRTLPHFSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
13-1061 |
7.72e-176 |
|
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: 551.47 E-value: 7.72e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 13 VVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHP 92
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 93 LLFNLLFNFLQRACFFCHHFMAKPEDVERAVSQLKLIIKgdivsakqlesntptkskssdescesvvttdsseecedsdv 172
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKE----------------------------------------- 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 173 edqRWTSLQFAEVTAVLKNFMRlsSKSCSRCKGINPKLekpmfgwvrmramkdsdvganvirglKLKKSTSSVEnpdgfd 252
Cdd:cd02582 122 ---KWPELVKRVIEKVKKKAKK--RKVCPHCGAPQYKI--------------------------KLEKPTTFYE------ 164
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 253 dsgidalsevedgdketrekstevaaEFEEHNSKrdLLPSEVRNILkhlwqnehefcsfigdlwqsgsEKI---DYSMF- 328
Cdd:cd02582 165 --------------------------EKEEGEVK--LTPSEIRERL----------------------EKIpdeDLELLg 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 329 ----------FLESVL-VPPTKFRPPT---TGGDSvmEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVN 394
Cdd:cd02582 195 idpktarpewMVLTVLpVPPVTVRPSItleTGERS--EDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVT 272
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 395 VLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVT 469
Cdd:cd02582 273 TYFDNEIPGIPPARHRSGrplktLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVT 352
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 470 PWNVEKLREAIINGPDIHPGAThYSDKSSTMKLPSTEKARRAIARKLlssrgattelgktcdinfE-GKTVHRHMRDGDI 548
Cdd:cd02582 353 EWNIEKMRKLVLNGPDKWPGAN-YVIRPDGRRIRLRYVNREELAERL------------------EpGWIVERHLIDGDI 413
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 549 VLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPL 628
Cdd:cd02582 414 VLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPI 492
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 629 RALIQDHIVSSVLLTKRDTFLDKDHFNQLLfssgvtdmvlstfsgrsgkkvmvSASDAELLTVTPAILKPVPLWTGKQVI 708
Cdd:cd02582 493 IGGIQDYISGAYLLTRKTTLFTKEEALQLL-----------------------SAAGYDGLLPEPAILEPKPLWTGKQLF 549
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 709 TAVlnqitkghppftvekatkLPVDF-FKCRSrevKPNSGDLTKKKEIDEswkqnlNEDKLHIRKNEFVCGVIDKAQFAD 787
Cdd:cd02582 550 SLF------------------LPKDLnFEGKA---KVCSGCSECKDEDCP------NDGYVVIKNGKLLEGVIDKKAIGA 602
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 788 YG---LVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENvgervlrktfgiDVD 864
Cdd:cd02582 603 EQpgsLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEK------------KVY 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 865 vqidpqdmrSRIERilYEDGE-------SALASLDRSIVNYLNQCSSKGVmnDLLSDGLLKTpgrNCISLMTISGAKGSK 937
Cdd:cd02582 671 ---------ELIEQ--YKNGEleplpgrTLEETLEMKIMQVLGKARDEAG--KVASKYLDPF---NNAVIMARTGARGSM 734
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 938 VNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSG 1017
Cdd:cd02582 735 LNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSG 814
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|....
gi 1063717413 1018 YLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHRSS 1061
Cdd:cd02582 815 YMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSD 858
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
10-1655 |
9.22e-167 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 541.15 E-value: 9.22e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 10 ASQVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPI 89
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 90 YHPLLFNLLFNFLQRACFFCHHFMAKPEDVeravSQLKLIikgdivsakqlesntptkskssdESCESVVTTDSSEECED 169
Cdd:PRK14977 85 IHIAFIDNIKDLLNSTCHKCAKLKLPQEDL----NVFKLI-----------------------EEAHAAARDIPEKRIDD 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 170 SDVEDQRWTSLQFAEvtavlknfmrlSSKSCSRCkginpklekpmfgwvrmramkdsdvGANVIRgLKLKKSTSSVENpd 249
Cdd:PRK14977 138 EIIEEVRDQVKVYAK-----------KAKECPHC-------------------------GAPQHE-LEFEEPTIFIEK-- 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 250 gfddsgidalsevedgdketrekstevaAEFEEHNskrdLLPSEVRNILKHLWQNEHEFCSFigdlwqsGSEKIDYSMFF 329
Cdd:PRK14977 179 ----------------------------TEIEEHR----LLPIEIRDIFEKIIDDDLELIGF-------DPKKARPEWAV 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 330 LESVLVPPTKFRPPT---TGGDSvmEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDSKTATV-- 404
Cdd:PRK14977 220 LQAFLVPPLTARPSIileTGERS--EDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIpq 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 405 ----QSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAI 480
Cdd:PRK14977 298 ahhkGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELV 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 481 INGPDIHPGAtHYSDKSSTMKlpstekarraIARKLLSSRG--ATTELGKTCDInfeGKTVHRHMRDGDIVLVNRQPTLH 558
Cdd:PRK14977 378 INGPDEFPGA-NAIRKGDGTK----------IRLDFLEDKGkdALREAAEQLEI---GDIVERHLADGDIVIFNRQPSLH 443
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 559 KPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVS 638
Cdd:PRK14977 444 KLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITA 522
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 639 SVLLTKRDTFLDKDHFNQLLFSSGVTDMVLStfsgrsgkkvmvsasdaelltvtPAI-LKPVPLWTGKQVITAVlnqitk 717
Cdd:PRK14977 523 AYLITKDDALFDKNEASNIAMLAGITDPLPE-----------------------PAIkTKDGPAWTGKQLFSLF------ 573
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 718 ghppftvekatkLPVDFfkcrSREVKPNSGDLTKKKEIDESWkqnLNEDKLHIRKNEFVCGVIDKAQFADY-----GLVH 792
Cdd:PRK14977 574 ------------LPKDF----NFEGIAKWSAGKAGEAKDPSC---LGDGYVLIKEGELISGVIDDNIIGALveepeSLID 634
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 793 TVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIIlkdMDEERTKQLQECENVGERVLRKTFGIDVDVQIDPQDM 872
Cdd:PRK14977 635 RIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLII---PDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKG 711
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 873 RSRIERILYEDgesalASLDRSIVNYLNQCSSK--GVMNDLLsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGQQ 950
Cdd:PRK14977 712 KEELLRGMKEE-----EALEADIVNELDKARDKagSSANDCI-------DADNAGKIMAKTGARGSMANLAQIAGALGQQ 779
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 951 D--------LEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRC 1022
Cdd:PRK14977 780 KrktrigfvLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRR 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1023 LMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHR---------SSFIEKFKELTINQDMVLQKCSEDMLSGASSYIS 1093
Cdd:PRK14977 860 LANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKldhgeafnlERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNA 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1094 DLPISLkkgAEKFVEAMPMNERIaskfvrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEM 1173
Cdd:PRK14977 940 NLPKLL---ADAIHGAELKEDEL-------EAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAM 1009
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1174 NVTLGIPRLQEiLMTAAANIKTPIMTCpLLKGKTKED---ANDITDRLRKITVADIIKSMElsvvpyTVYENEVCSIhkl 1250
Cdd:PRK14977 1010 DVTHGLERFIE-LVDARAKPSTPTMDI-YLDDECKEDiekAIEIARNLKELKVRALIADSA------IDNANEIKLI--- 1078
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1251 kinlyKPEHypkhtditeedweetmravflRKLEDAIETHMKMLHRIRGIHNDVTGPIagnETDNDdsvsgkqneddgdd 1330
Cdd:PRK14977 1079 -----KPDK---------------------RALENGCIPMERFAEIEAALAKGKKFEM---ELEDD-------------- 1115
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1331 dgegTEVDDLGSDAQKQKKQETdemdyeensedetnepssISGVEDPEMDsenedtevskedtpepqeesmepqKEVKGV 1410
Cdd:PRK14977 1116 ----LIILDLVEAADRDKPLAT------------------LIAIRNKILD------------------------KPVKGV 1149
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1411 KNVKeqskkkrRKFVraksdrhifvkgegekfevhfkfatddphillaQIAQQTAQKVY-IQNSGkierctvancgdpqv 1489
Cdd:PRK14977 1150 PDIE-------RAWV---------------------------------ELVEKDGRDEWiIQTSG--------------- 1174
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1490 iyhgdnpkerreiSNDEKkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGI 1569
Cdd:PRK14977 1175 -------------SNLAA----VLEMKCI------------DIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGL 1225
|
1610 1620 1630 1640 1650 1660 1670 1680
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1570 SVSIRHLNLIADYMTFSG-----GYRPMSRMGGIA-ESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPAL 1643
Cdd:PRK14977 1226 EVDNRYIMLVADIMCSRGtieaiGLQAAGVRHGFAgEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIP 1305
|
1690
....*....|..
gi 1063717413 1644 SGTGCFDLMQRV 1655
Cdd:PRK14977 1306 IGSGKVDLLMDF 1317
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
22-1039 |
1.27e-166 |
|
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: 525.58 E-value: 1.27e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 22 MTEQDVRKHSFLKVTSPILHDNV-GNPFPGGLYDLKLGPKDDKQACNSCGqLKLA-CPGHCGHIELVFPIYHPLLFNLLF 99
Cdd:cd02583 1 LSPEDIIRLSEVEVTNRNLYDIEtRKPLPYGVLDPRLGTSDKDGICETCG-LNLAdCVGHFGYIKLELPVFHIGYFKAII 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 100 NFLQRACFFCHHFMAKPEdvERAVSQLKLIIKGDIVSAKQLesntptKSKSSDESCESVvttdsseecedsdvedqrwts 179
Cdd:cd02583 80 NILQCICKTCSRVLLPEE--EKRKFLKRLRRPNLDNLQKKA------LKKKILEKCKKV--------------------- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 180 lqfaevtavlknfmrlssKSCSRCkginpklekpmfgwvrmramkdsdvganvirglklkkstssvenpdgfddsgiDAL 259
Cdd:cd02583 131 ------------------RKCPHC-----------------------------------------------------GLL 139
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 260 SEVEDgdketrekstevaaefeehnskrDLLPSEVRNILKhlwQNEHEFCSFIGDLwqsgSEKIDYSMFFLESVLVPPTK 339
Cdd:cd02583 140 KKAQE-----------------------DLNPLKVLNLFK---NIPPEDVELLLMN----PLAGRPENLILTRIPVPPLC 189
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 340 FRPPTTGGDSVM--EHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDSKT----ATVQSQRDSSGI 413
Cdd:cd02583 190 IRPSVVMDEKSGtnEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELpglpLSMQPKKPIRGF 269
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 414 CQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGATHY 493
Cdd:cd02583 270 CQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFV 349
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 494 SDKSSTMKlpsteKARRAIARKLLSSRGAttelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGe 573
Cdd:cd02583 350 IKRDGGKK-----KFLKYGNRRKIARELK------------IGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPW- 411
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 574 KTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDH 653
Cdd:cd02583 412 RTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQ 491
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 654 FNQLL--FSSGVTDMVLstfsgrsgkkvmvsasdaelltVTPAILKPVPLWTGKQVITAVLnqitkghppftvEKATKLP 731
Cdd:cd02583 492 FCQLCsyMLDGEIKIDL----------------------PPPAILKPVELWTGKQIFSLLL------------RPNKKSP 537
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 732 VDF-FKCRSREVKPNSGDLTkkkeIDESWkqnlnedkLHIRKNEFVCGVIDKAQFAD---YGLVHTVHELYGSNAAGNLL 807
Cdd:cd02583 538 VLVnLEAKEKSYTKKSPDMC----PNDGY--------VVIRNSELLCGRLDKSTLGSgskNSLFYVLLRDYGPEAAAAAM 605
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 808 SVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENV--------GERVLRKTFGIDVDvqidpQDMRSRIERI 879
Cdd:cd02583 606 NRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKcdeyikqyKKGKLELQPGCTAE-----QTLEAKISGE 680
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 880 LyedgeSALasldRsivnylNQCSSkgVMNDLLSDgllktpgRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPR 959
Cdd:cd02583 681 L-----SKI----R------EDAGK--ACLKELHK-------SNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPN 736
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 960 MVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYDCTVR 1039
Cdd:cd02583 737 GFEDRTLPHFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
12-1062 |
1.79e-165 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 524.42 E-value: 1.79e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 12 QVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYH 91
Cdd:PRK08566 7 KRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 92 PLLFNLLFNFLQRACFFCHHFMAKPEDVERAVSQLKliikgdivsakqlesntptkskssdescesvvttdsseecedsd 171
Cdd:PRK08566 87 VGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLE-------------------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 172 vEDQRWTSLqfaeVTAVLKNFMRLSSK--SCSRC--KGINPKLEKPmfgwvrmramkdsdvganvirglklkksTSSVEN 247
Cdd:PRK08566 123 -RLKEWGSL----ADDLIKEVKKEAAKrmVCPHCgeKQYKIKFEKP----------------------------TTFYEE 169
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 248 pdgfddsgidalsevedgDKETREKstevaaefeehnskrdLLPSEVRNILkhlwqnehefcsfigdlwqsgsEKI---D 324
Cdd:PRK08566 170 ------------------RKEGLVK----------------LTPSDIRERL----------------------EKIpdeD 193
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 325 YSMFFLE-----------SVL-VPPTKFRPPTT---GGDSvmEHPQTVGLNKVIESN-----NILGNACTNKLDQskvif 384
Cdd:PRK08566 194 LELLGINpevarpewmvlTVLpVPPVTVRPSITletGQRS--EDDLTHKLVDIIRINqrlkeNIEAGAPQLIIED----- 266
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 385 RWRNLQESVNVLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFA 459
Cdd:PRK08566 267 LWELLQYHVTTYFDNEIPGIPPARHRSGrplktLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIA 346
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 460 LKLTYPERVTPWNVEKLREAIINGPDIHPGAThYSDKSSTMKLPSTEKARRAIARKLLssrgattelgktcdinfEGKTV 539
Cdd:PRK08566 347 KELTVPERVTEWNIEELREYVLNGPEKHPGAN-YVIRPDGRRIKLTDKNKEELAEKLE-----------------PGWIV 408
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 540 HRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQY 619
Cdd:PRK08566 409 ERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHI 487
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 620 ARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLFSSGVTdmvlstfsgrsgkkvmvsasdaELLTVTPAILKPV 699
Cdd:PRK08566 488 LSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGID----------------------ELPEPEPAIENGK 545
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 700 PLWTGKQVITAVlnqitkghppftvekatkLPVDF-FKCRSrevKPNSGDLTKKKEIDEswkqnlNEDKLHIRKNEFVCG 778
Cdd:PRK08566 546 PYWTGKQIFSLF------------------LPKDLnLEFKA---KICSGCDECKKEDCE------HDAYVVIKNGKLLEG 598
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 779 VIDKAQFADYG--LVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLiilkDMDEERTKQLQECENVGERvlr 856
Cdd:PRK08566 599 VIDKKAIGAEQgsILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDE----DIPEEAKEEIDEIIEEAEK--- 671
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 857 ktfgiDVDvqidpqdmrSRIERilYEDGESALA---SLDRSIVNYLNQCSSKG--VMNDLLSDGLLKTpgrNCISLMTIS 931
Cdd:PRK08566 672 -----RVE---------ELIEA--YENGELEPLpgrTLEETLEMKIMQVLGKArdEAGEIAEKYLGLD---NPAVIMART 732
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 932 GAKGSKVNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAV 1011
Cdd:PRK08566 733 GARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAV 812
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|.
gi 1063717413 1012 KTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHRSSF 1062
Cdd:PRK08566 813 RTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDH 863
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
286-1035 |
5.31e-145 |
|
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: 464.70 E-value: 5.31e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 286 KRDLLPSEVRNILKHLwqnEHEFCSFIG-DLwqsgsekiDYS---MFFLESVLVPPTKFRPP-TTGGDSVMEHPQTVGLN 360
Cdd:cd02733 93 KRELSAERVLEIFKRI---SDEDCRILGfDP--------KFSrpdWMILTVLPVPPPAVRPSvVMDGSARSEDDLTHKLA 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 361 KVIESNNILgNACTNKLDQSKVIFRWRN-LQESVNVLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVN 434
Cdd:cd02733 162 DIIKANNQL-KRQEQNGAPAHIIEEDEQlLQFHVATYMDNEIPGLPQATQKSGrplksIRQRLKGKEGRIRGNLMGKRVD 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 435 HACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGAThYSDKSSTMKlpstekarraIAR 514
Cdd:cd02733 241 FSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK-YIIRDDGER----------IDL 309
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 515 KLLSSRGattelgktcDINFE-GKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGD 593
Cdd:cd02733 310 RYLKKAS---------DLHLQyGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPY-STFRLNLSVTTPYNADFDGD 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 594 EMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLfssgvtdMVLSTFSG 673
Cdd:cd02733 380 EMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLL-------MWLPDWDG 452
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 674 RSGKkvmvsasdaelltvtPAILKPVPLWTGKQVITAVLNQITKghppftvekatklpvdffkcrsrEVKPNSGDLTKKK 753
Cdd:cd02733 453 KIPQ---------------PAILKPKPLWTGKQIFSLIIPKINN-----------------------LIRSSSHHDGDKK 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 754 EIdeswkqNLNEDKLHIRKNEFVCGVIDKAQFADY--GLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLI 831
Cdd:cd02733 495 WI------SPGDTKVIIENGELLSGILCKKTVGASsgGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTI 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 832 ILKDMDEERTKQLQECENVGERVLRKtfGIDVDVQIDP-QDMR----SRIERIL----YEDGESALASLDRSivnylnqc 902
Cdd:cd02733 569 ADKETMKKIQETIKKAKRDVIKLIEK--AQNGELEPQPgKTLResfeNKVNRILnkarDKAGKSAQKSLSED-------- 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 903 sskgvmndllsdgllktpgrNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFI 982
Cdd:cd02733 639 --------------------NNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFV 698
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|...
gi 1063717413 983 SDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1035
Cdd:cd02733 699 ENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1133-1652 |
7.30e-130 |
|
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: 406.58 E-value: 7.30e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1133 KFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTAAANIKTPIMTCPLLKGKTKEDAN 1212
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1213 DITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinlykpehypkhtditeEDWEETMRAVFLRKLedaiethmk 1292
Cdd:cd02735 81 TLKKRLSRVTLSDVVEKVEV------------------------------------TEILKTIERVFKKLL--------- 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1293 mlhrirgihndvtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssis 1372
Cdd:cd02735 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1373 gvedpemdsenedtevskedtpepqeesmepqkevkgvknvkeqskkkrrkfvraksdrhifvkgeGEKFEVHFKFATDD 1452
Cdd:cd02735 116 ------------------------------------------------------------------GKWCEVTIKLPLSS 129
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1453 PHILLAQIAQQTAQKVYIQNSGKIERCTVANCgdpqviyhgdnpkerreisNDEKKASPALHASGVDFPALWEFQDKLDV 1532
Cdd:cd02735 130 PKLLLLSIVEKLARKAVIREIPGITRCFVVEE-------------------DKGGKTKYLVITEGVNLAALWKFSDILDV 190
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1533 RYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIAESTSPFCRMTFET 1612
Cdd:cd02735 191 NRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRI-GMESSTSPLQKMSFET 269
|
490 500 510 520
....*....|....*....|....*....|....*....|
gi 1063717413 1613 ATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1652
Cdd:cd02735 270 TLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
326-640 |
3.41e-115 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 365.69 E-value: 3.41e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 326 SMFFLESVLVPPTKFRPPTTGGDS-VMEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDS---KT 401
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGrFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNeglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 402 ATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAII 481
Cdd:smart00663 81 ANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 482 NGPdihPGATHYSDKSSTMKlpsTEKARRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPS 561
Cdd:smart00663 161 NGP---NGAKYIIRGKKTNL---KLAKKSKIANHLK-----------------IGDIVERHVIDGDVVLFNRQPTLHRMS 217
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063717413 562 LMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSV 640
Cdd:smart00663 218 IQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
989-1605 |
5.28e-103 |
|
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: 340.49 E-value: 5.28e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 989 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDV----------- 1057
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPlkiekqgrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1058 -HRSSFIEKFKELTINQDMVLQKCSEDMLSGASSYISDLPISLKKGAEKFVEAMPMNE-----RIASKFVRQ-------- 1123
Cdd:pfam04998 81 eFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSKEAQERATLLFElllksGLESKRVRSeltcnska 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1124 -EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTaAANIKTPIMTCPL 1202
Cdd:pfam04998 161 fVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINV-SKNIKSPSLTVYL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1203 L--KGKTKEDANDITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinLYKPehYPKHTDITEEdweetmravfl 1280
Cdd:pfam04998 240 FdeVGRELEKAKKVYGAIEKVTLGSVVESGEI---------------------LYDP--DPFNTPIISD----------- 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1281 rklEDAIETHMKMlhrirgiHNDVTgpiagnETDNDDSVSGKQNEddgdddgegtevddlgsdaqkqkkqetdemdyeeN 1360
Cdd:pfam04998 286 ---VKGVVKFFDI-------IDEVT------NEEEIDPETGLLIL----------------------------------V 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1361 SEDETNEPSSISGVedpemdsenedteVSKEDTPEPQEES-MEPQKEVKGVKNVKEQSKKKRRKfvraksdrhifvKGEG 1439
Cdd:pfam04998 316 IRLLKILNKSIKKV-------------VKSEVIPRSIRNKvDEGRDIAIGEITAFIIKISKKIR------------QDTG 370
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1440 EKFEVHFKFATDDPhiLLAQIAQQTAQKVYIQNSGKIERCTVancgdpqviyhgdnpkerREISNDEKKASPALHASGVD 1519
Cdd:pfam04998 371 GLRRVDELFMEEDP--KLAILVASLLGNITLRGIPGIKRILV------------------NEDDKGKVEPDWVLETEGVN 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1520 FPALWEFQDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIA 1599
Cdd:pfam04998 431 LLRVLLVPGFVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH-GIN 509
|
....*.
gi 1063717413 1600 ESTSPF 1605
Cdd:pfam04998 510 KAELSA 515
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
430-615 |
4.08e-74 |
|
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: 243.75 E-value: 4.08e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 430 GKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGATHYSDKS-STMKLpstEKA 508
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINgARRDL---RYQ 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 509 RRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNA 588
Cdd:pfam00623 78 KRRLDKELE-----------------IGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG-KTFRLNLSVTTPYNA 139
|
170 180
....*....|....*....|....*..
gi 1063717413 589 DFDGDEMNVHFPQDEISRAEAYNIVNA 615
Cdd:pfam00623 140 DFDGDEMNLHVPQSEEARAEAEELMLV 166
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1124-1652 |
2.93e-56 |
|
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: 201.66 E-value: 2.93e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1124 EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILmTAAANIKTPIMTCPLL 1203
Cdd:cd02584 9 DWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII-NVAKNIKTPSLTVYLE 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1204 KG--KTKEDANDITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinLYKPEhyPKHTDItEEDwEETMRAVF-L 1280
Cdd:cd02584 88 PGfaKDEEKAKKIQSRLEHTTLKDVTAATEI---------------------YYDPD--PQNTVI-EED-KEFVESYFeF 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1281 RKLEDAIETHMKMLHRIrgihndvtgpiagnETDNDDSVSGKQneddgdddgegtevdDLGSDAQKQKkqetdemdyeEN 1360
Cdd:cd02584 143 PDEDVEQDRLSPWLLRI--------------ELDRKKMTDKKL---------------SMEQIAKKIK----------EE 183
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1361 SEDETNEPSSISGVEDPEM-----DSENEDTEVSKEDTPEPQEES-MEPQKEVKGVKNVkeqskkkRRKFVRaKSDRHIF 1434
Cdd:cd02584 184 FKDDLNVIFSDDNAEKLVIririiNDDEEKEEDSEDDVFLKKIESnMLSDMTLKGIEGI-------RKVFIR-EENKKKV 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1435 VKGEGEkfevhfkFATDDPHILlaqiaqQTaqkvyiqnsgkierctvancgdpqviyhgdnpkerrEISNDEKkaspALH 1514
Cdd:cd02584 256 DIETGE-------FKKREEWVL------ET------------------------------------DGVNLRE----VLS 282
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1515 ASGVDFpalwefqdkldVRyLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSR 1594
Cdd:cd02584 283 HPGVDP-----------TR-TTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITR 350
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 1063717413 1595 MGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1652
Cdd:cd02584 351 HGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLL 408
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
328-1039 |
2.98e-56 |
|
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: 210.34 E-value: 2.98e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 328 FFLESVLVPPTKFRPPTtggdsvMEHPQTVGlnkvieSNNILGNacTNKLDQSKVIFRWRnlqesvnvlfdsktatvqSQ 407
Cdd:cd10506 146 LFLKCLPVPPNCHRVTE------FTHGFSTG------SRLIFDE--RTRAYKKLVDFIGT------------------AN 193
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 408 RDSSGICQLLEKkeglFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIingpDIH 487
Cdd:cd10506 194 ESAASKKSGLKW----MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERLQEYC----DLT 265
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 488 PGathysdksstmklpstEKARRAIARK--LLSSRGaTTELGKtcdinfeGKTVHRHMRDGDIVLVNRQPTLHKPSLMAH 565
Cdd:cd10506 266 LL----------------LKGVIGVRRNgrLVGVRS-HNTLQI-------GDVIHRPLVDGDVVLVNRPPSIHQHSLIAL 321
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 566 KVRVLKGEKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKR 645
Cdd:cd10506 322 SVKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTER 401
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 646 DTFLDKDHFNQLlfssgvtdMVLSTFSgrsgkkvmvsasdaellTVTPAILK----PVPLWTGKQvitavLNQITkghpp 721
Cdd:cd10506 402 GVFLDKAQMQQL--------QMLCPSQ-----------------LPPPAIIKsppsNGPLWTGKQ-----LFQML----- 446
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 722 ftvekatkLPVDF-FKCRSREVKPNSGDLTKKKEIDeSWKQNLNedklhirknefvcgvidkaqfadyGLVHTVHELYGS 800
Cdd:cd10506 447 --------LPTDLdYSFPSNLVFISDGELISSSGGS-SWLRDSE------------------------GNLFSILVKHGP 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 801 NAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIIL------KDMDEERTKQLQECENVG--ERVLRKTFGIDVDVQIDPQDM 872
Cdd:cd10506 494 GKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSsdsysrQKMIEEISLGLREAEIACniKQLLVDSRKDFLSGSGEENDV 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 873 RSRIERILYEdgESALASLDRSIVnylnqCSSKGVMNDLLSDGLLKTPGRNCISLMTISGAKGSKVNFQQISSHLG-QQD 951
Cdd:cd10506 574 SSDVERVIYE--RQKSAALSQASV-----SAFKQVFRDIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGlQLS 646
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 952 LEGK----------------RVPRMVSGKTLPCFHPWDwsprAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTsr 1015
Cdd:cd10506 647 LVKLsyriprqlscaawnsqKSPRVIEKDGSECTESYI----PYGVVESSFLDGLNPLECFVHSITSRDSSFSSNADL-- 720
|
730 740
....*....|....*....|....
gi 1063717413 1016 SGYLQRCLMKNLESLKVNYDCTVR 1039
Cdd:cd10506 721 PGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1539-1648 |
4.33e-52 |
|
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: 180.31 E-value: 4.33e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1539 SIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIV 1618
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 1063717413 1619 QAATYGEKDTLETPSARICLGLPALSGTGC 1648
Cdd:cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1124-1654 |
1.22e-49 |
|
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: 180.91 E-value: 1.22e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1124 EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILmTAAANIKTPIMTCPlL 1203
Cdd:cd06528 22 EEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV-DARKEPSTPTMTIY-L 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1204 KGKTKED---ANDITDRLRKITVADIIKSMELSVVPYTVyenevcsihklKINLYKpehypkhtditeedweetmravfl 1280
Cdd:cd06528 100 EEEYKYDrekAEEVARKIEETTLENLAEDISIDLFNMRI-----------TIELDE------------------------ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1281 RKLEDaiethmkmlhriRGIhndvtgpiagnetdnddsvsgkqneddgdddgegtEVDDLGSDAQKQKKQEtdemdyeen 1360
Cdd:cd06528 145 EMLED------------RGI-----------------------------------TVDDVLKAIEKLKKGK--------- 168
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1361 sedetnepssisgvedpEMDSENEDTEVSKEDTPEPQE-ESMEPQ---KEVKGVKNVKeqskkkrrkfvraksdRHIFVK 1436
Cdd:cd06528 169 -----------------VGEEGDVTLIVLKAEEPSIKElRKLAEKilnTKIKGIKGIK----------------RVIVRK 215
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1437 GEGEkfevhfkfatddphillaqiaqqtaqkvYiqnsgkierctvancgdpqVIY-HGDNPKErreisndekkaspALHA 1515
Cdd:cd06528 216 EEDE----------------------------Y-------------------VIYtEGSNLKA-------------VLKV 235
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1516 SGVDFpalwefqdkldvRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRM 1595
Cdd:cd06528 236 EGVDP------------TRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRH 303
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1596 GGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDL-MQR 1654
Cdd:cd06528 304 GIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELtMDP 363
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1095-1654 |
8.66e-46 |
|
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: 169.85 E-value: 8.66e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1095 LPISLKKGaekfVEAMPMNERIASKFvRQEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMN 1174
Cdd:TIGR02389 2 LPEKLLKE----LEETVKKREISDKE-ELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELN 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1175 VTLGIPRLQEILmTAAANIKTPIMTCPLLK--GKTKEDANDITDRLRKITVADIIKSMELSVVPYTVyenevcsihklki 1252
Cdd:TIGR02389 77 VTLGLPRLIEIV-DARKTPSTPSMTIYLEDeyEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTV------------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1253 nlykpehypkhtditeedweetmravflrkledAIETHMKMLHRiRGIhndvtgpiagnetdnddsvsgkqneddgdddg 1332
Cdd:TIGR02389 143 ---------------------------------IIELDEEQLKE-RGI-------------------------------- 156
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1333 egtEVDDLGSDAQKQKKQEtdemdyeensedetnepssisgvedpEMDSENEDTEVskedTPEPQEESMepqkevkgvkn 1412
Cdd:TIGR02389 157 ---TVDDVEKAIKKAKLGK--------------------------VIEIDMDNNTI----TIKPGNPSL----------- 192
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1413 vkeqskKKRRKfvRAKSDRHIFVKGegekfevhfkfatddphillaqiaqqtaqkvyIQNsgkIERCTVANCGDPQVIY- 1491
Cdd:TIGR02389 193 ------KELRK--LKEKIKNLHIKG--------------------------------IKG---IKRVVIRKEGDEYVIYt 229
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1492 HGDNPKErreisndekkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISV 1571
Cdd:TIGR02389 230 EGSNLKE-------------VLKLEGV------------DKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDV 284
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1572 SIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDL 1651
Cdd:TIGR02389 285 DIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDL 364
|
...
gi 1063717413 1652 MQR 1654
Cdd:TIGR02389 365 VMD 367
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
387-1248 |
1.45e-43 |
|
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: 174.08 E-value: 1.45e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 387 RNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 462
Cdd:TIGR02386 279 RMLQEAVDALFDNgrrgKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALEL 358
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 463 TYPervtpwnveklreAIINGPDIHPGAthysdksstmklPSTEKARRAIARkllssrgattELGKTCDInFEgKTVHRH 542
Cdd:TIGR02386 359 FKP-------------FIIKRLIDRELA------------ANIKSAKKMIEQ----------EDPEVWDV-LE-DVIKEH 401
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 543 MrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 622
Cdd:TIGR02386 402 P-----VLLNRAPTLHRLGIQAFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNP 475
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 623 SNGEPLRALIQDHIVSSVLLTkrdtfldKDHFNQL----LFSSgVTDMVLSTFSGRSGKKVMVS-ASDAELLTVTPailk 697
Cdd:TIGR02386 476 KDGKPIVTPSQDMVLGLYYLT-------TEKPGAKgegkIFSN-VDEAIRAYDNGKVHLHALIGvRTSGEILETTV---- 543
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 698 pvplwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrsrevkP--NSGDLTKKKEIDEswkqnlnedklhirknef 775
Cdd:TIGR02386 544 ------GR----VIFNEI--------------LPEGF---------PyiNDNEPLSKKEISS------------------ 572
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 776 vcgvidkaqfadygLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECEnvgervl 855
Cdd:TIGR02386 573 --------------LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVA------- 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 856 rktfgidvdvQIDPQdmrsrierilYEDGesALASLDRsivnYLNQCSSKGVMNDLLSDGLLK-----TPGRNCISLMTI 930
Cdd:TIGR02386 632 ----------KIQKF----------YNKG--LITDEER----YRKVVSIWSETKDKVTDAMMKllkkdTYKFNPIFMMAD 685
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 931 SGAKGSKVNFQQISshlGQQDLEGKrvprmVSGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTA 1010
Cdd:TIGR02386 686 SGARGNISQFRQLA---GMRGLMAK-----PSGDIIE-------LP-----IKSSFREGLTVLEYFISTHGARKGLADTA 745
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1011 VKTSRSGYLQRCLMKNLESLKVNY-DC---------TVRDADGSIIQFQYgeDGVdVHRSSfIEKFKElTINQDMVLQkc 1080
Cdd:TIGR02386 746 LKTADSGYLTRRLVDVAQDVVVREeDCgteegieveAIVEGKDEIIESLK--DRI-VGRYS-AEDVYD-PDTGKLIAE-- 818
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1081 SEDMLSGASsyisdlpislkkgAEKFVEAmpmneRIASKFVRQE---ELLKLVKSKFF------ASLAQPGEPVGVLAAQ 1151
Cdd:TIGR02386 819 ANTLITEEI-------------AEKIENS-----GIEKVKVRSVltcESEHGVCQKCYgrdlatGKLVEIGEAVGVIAAQ 880
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1152 SVGEPSTQMTLNTFHL---AGRGEmNVTLGIPRLQEILMTAAANIKTPIMTcplLKGKTKEDANDITDRlRKItvadIIK 1228
Cdd:TIGR02386 881 SIGEPGTQLTMRTFHTggvAGASG-DITQGLPRVKELFEARTPKDKAVIAE---VDGTVEIIEDIVKNK-RVV----VIK 951
|
890 900
....*....|....*....|
gi 1063717413 1229 SMELSVVPYTVYENEVCSIH 1248
Cdd:TIGR02386 952 DENDEEKKYTIPFGAQLRVK 971
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1075-1652 |
2.40e-43 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 163.09 E-value: 2.40e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1075 MVLQKCSEDMLSGASSyisDLPISLKKGAEKFVEAMPMNERIAskfvrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVG 1154
Cdd:PRK04309 1 MMSEETLEEKLEDASL---ELPQKLKEELREKLEERKLTEEEV------EEIIEEVVREYLRSLVEPGEAVGVVAAQSIG 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1155 EPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIlMTAAANIKTPIMTCPLLK--GKTKEDANDITDRLRKITVADIIKSMEl 1232
Cdd:PRK04309 72 EPGTQMTMRTFHYAGVAEINVTLGLPRLIEI-VDARKEPSTPMMTIYLKDeyAYDREKAEEVARKIEATTLENLAKDIS- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1233 svvpytvyenevcsihklkinlykpehypkhTDITEedweetMRAVflrkledaIETHMKMLHRiRGIhndvtgpiagne 1312
Cdd:PRK04309 150 -------------------------------VDLAN------MTII--------IELDEEMLED-RGL------------ 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1313 tdnddsvsgkqneddgdddgegtEVDDLGSDAQKQKKQETDEmdyeensedetnEPSSIsgvedpemdsenedtevsked 1392
Cdd:PRK04309 172 -----------------------TVDDVKEAIEKKKGGEVEI------------EGNTL--------------------- 195
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1393 tpepqeesmepqkevkgVKNVKEQSKKKRRKfvRAKSDRHIFVKGegekfevhfkfatddphillaqiaqqtaqkvyIQN 1472
Cdd:PRK04309 196 -----------------IISPKEPSYRELRK--LAEKIRNIKIKG--------------------------------IKG 224
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1473 sgkIERCTVANCGDPQVIY-HGDNPKErreisndekkaspALHASGVDFpalwefqdkldvRYLYSNSIHDMLNIFGVEA 1551
Cdd:PRK04309 225 ---IKRVIIRKEGDEYVIYtEGSNLKE-------------VLKVEGVDA------------TRTTTNNIHEIEEVLGIEA 276
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1552 ARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLET 1631
Cdd:PRK04309 277 ARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKG 356
|
570 580
....*....|....*....|.
gi 1063717413 1632 PSARICLGLPALSGTGCFDLM 1652
Cdd:PRK04309 357 VTENIIVGQPIPLGTGDVELT 377
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1133-1649 |
9.44e-41 |
|
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: 153.14 E-value: 9.44e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1133 KFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIlMTAAANIKTPIMTCPLLKGKTKEDAN 1212
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEI-INASKNISTPIITAKLENDRDEKSAR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1213 DITDRLRKITVADIIKSMElsvvpyTVYENEVCSIhKLKINLykpehypkhtditeedweETMRAVFLRKLEdaiethmk 1292
Cdd:cd02736 80 IVKGRIEKTYLGEVASYIE------EVYSPDDCYI-LIKLDK------------------KIIEKLQLSKSN-------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1293 MLHRIRGIHNDVtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssis 1372
Cdd:cd02736 127 LYFLLQSLKRKL-------------------------------------------------------------------- 138
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1373 gvedpemdsenedtevskedtpepqeesmePQKEVKGVKNVKeqskkkrrkfvRAksdrHIFVKGEGEKFEVhfkfatdd 1452
Cdd:cd02736 139 ------------------------------PDVVVSGIPEVK-----------RA----VINKDKKKGKYKL-------- 165
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1453 phillaqiaqqtaqkvyiqnsgKIErctvancgdpqviyhGDNPKErreisndekkaspALHASGVDFpalwefqdkldv 1532
Cdd:cd02736 166 ----------------------LVE---------------GYGLRA-------------VMNTPGVIG------------ 183
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1533 RYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIAE-STSPFCRMTFE 1611
Cdd:cd02736 184 TRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRF-GIAKmKESVLMLASFE 262
|
490 500 510
....*....|....*....|....*....|....*...
gi 1063717413 1612 TATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCF 1649
Cdd:cd02736 263 KTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
387-1185 |
1.36e-40 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 165.04 E-value: 1.36e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 387 RNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 462
Cdd:PRK14906 375 RMLQEAVDSLFDNgrrgRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALEL 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 463 typerVTPWNVEKLREAiingpdihpgathysDKSSTMKlpsteKARRAIarkllsSRGATTelgkTCDINFEGKTVHrh 542
Cdd:PRK14906 455 -----FKPFVMKRLVEL---------------EYAANIK-----AAKRAV------DRGASY----VWDVLEEVIQDH-- 497
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 543 mrdgdIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 622
Cdd:PRK14906 498 -----PVLLNRAPTLHRLGIQAFEPVLVEG-KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSP 571
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 623 SNGEPLRALIQDHIVSSVLLT-KRD-------TFLDKDhfNQLLFSSGVTDMVLSTFSGRSGKKVMVSASDAELLTVTPA 694
Cdd:PRK14906 572 AHGRPLTVPTQDMIIGVYYLTtERDgfegegrTFADFD--DALNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEETKA 649
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 695 ilkpvplwtGKQVITAV----LNQItkghppftvekatkLPVDFfkcrsrevkpnsgdltkkkeideswkqnlnedklhi 770
Cdd:PRK14906 650 ---------GERIETTVgriiFNQV--------------LPEDY------------------------------------ 670
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 771 rknEFVCGVIDKAQFAdyGLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEertkQLQECEnv 850
Cdd:PRK14906 671 ---PYLNYKMVKKDIG--RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPE----ILAEAD-- 739
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 851 gervlRKTFGIDVDvqidpqdmrsrierilYEDGESALASLDRSIVNYLNQCsskgvmNDLLSDGLLKT-PGRNCISLMT 929
Cdd:PRK14906 740 -----EKVAAIDED----------------YEDGFLSERERHKQVVDIWTEA------TEEVGEAMLAGfDEDNPIYMMA 792
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 930 ISGAKGSKVNFQQISSHLG-QQDLEGKRVPRmvsgktlPcfhpwdwspraggfISDRFLSGLRPQEYYFHCMAGREGLVD 1008
Cdd:PRK14906 793 DSGARGNIKQIRQLAGMRGlMADMKGEIIDL-------P--------------IKANFREGLSVLEYFISTHGARKGLVD 851
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1009 TAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-GSiiqfqygEDGV--DVHRSsfiekfkELTINQDMVLQKCSEDml 1085
Cdd:PRK14906 852 TALRTADSGYLTRRL------VDVAQDVIVREEDcGT-------DEGVtyPLVKP-------KGDVDTNLIGRCLLED-- 909
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1086 sgassyISDLPISLKKGAEKFVEAMPMNERIASKFVRQEELLKLV--KSKFFA---------SLAQP---GEPVGVLAAQ 1151
Cdd:PRK14906 910 ------VCDPNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMtcHAEYGVcqkcygwdlATRRPvniGTAVGIIAAQ 983
|
810 820 830
....*....|....*....|....*....|....
gi 1063717413 1152 SVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEI 1185
Cdd:PRK14906 984 SIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAEL 1017
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
376-1169 |
4.18e-40 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 163.94 E-value: 4.18e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 376 KLDQSKVIFR--WRNLQESVNVLFDS--KTATVQ--SQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAV 449
Cdd:PRK09603 1673 ELGAPEIIVRneKRMLQEAVDVLFDNgrSTNAVKgaNKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKM 1752
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 450 NDIGIPPCFALKLTYPERVTpwnveKLREaiingpdihpgathySDKSSTMKlpsteKARRAIARKllssrgaTTELGKT 529
Cdd:PRK09603 1753 DECGLPKNMALELFKPHLLS-----KLEE---------------RGYATTLK-----QAKRMIEQK-------SNEVWEC 1800
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 530 CdinfegktvhRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEA 609
Cdd:PRK09603 1801 L----------QEITEGYPVLLNRAPTLHKQSIQAFHPKLIDG-KAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAEC 1869
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 610 YNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHfnqLLFSSgVTDMVLStfsgrsgkkvmVSASDAELL 689
Cdd:PRK09603 1870 KVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEH---KLFSS-VNEIITA-----------IDTKELDIH 1934
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 690 TVTPAILKPVPLWT--GKQVITAVLnqitkghPPFtvekatkLPVDFFKcrsrevKPnsgdlTKKKEIdeswkqnlnedk 767
Cdd:PRK09603 1935 AKIRVLDQGNIIATsaGRMIIKSIL-------PDF-------IPTDLWN------RP-----MKKKDI------------ 1977
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 768 lhirknefvcgvidkAQFADYglvhtVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDmdeeRTKQLQEC 847
Cdd:PRK09603 1978 ---------------GVLVDY-----VHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKD----KQKMVEKA 2033
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 848 envgervlrktfgidvdvqidpqdmRSRIERILYEDGESALASLDR-----SIVNYLNQCSSKGVMNDLLSDgllkTPGR 922
Cdd:PRK09603 2034 -------------------------KVEVKKIQQQYDQGLLTDQERynkiiDTWTEVNDKMSKEMMTAIAKD----KEGF 2084
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 923 NCISLMTISGAKGSKVNFQQISSHLGqqdLEGKRVPRMVSgktlpcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAG 1002
Cdd:PRK09603 2085 NSIYMMADSGARGSAAQIRQLSAMRG---LMTKPDGSIIE------------TP-----IISNFKEGLNVLEYFNSTHGA 2144
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1003 REGLVDTAVKTSRSGYLQRCLMKNLESLKVNY-DCTVrdadgsiiqfqygEDGVDVHR----SSFIEKFKELTINQDM-- 1075
Cdd:PRK09603 2145 RKGLADTALKTANAGYLTRKLIDVSQNVKVVSdDCGT-------------HEGIEITDiavgSELIEPLEERIFGRVLle 2211
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1076 -VLQKCSEDMLSGASSYISDlpislkKGAEKFVEAmpmneRIASKFVRQEELLKLVK---SKFF------ASLAQPGEPV 1145
Cdd:PRK09603 2212 dVIDPITNEILLYADTLIDE------EGAKKVVEA-----GIKSITIRTPVTCKAPKgvcAKCYglnlgeGKMSYPGEAV 2280
|
810 820
....*....|....*....|....
gi 1063717413 1146 GVLAAQSVGEPSTQMTLNTFHLAG 1169
Cdd:PRK09603 2281 GVVAAQSIGEPGTQLTLRTFHVGG 2304
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1063-1654 |
1.87e-34 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 139.94 E-value: 1.87e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1063 IEKFKELTINQDmvlqkcSEDMLSGASSYISDLPISLkkgAEKFVEAMPMNERIASKFvrqEELLKLVKSKFFASLAQPG 1142
Cdd:PRK14897 115 EKEYYEENSNED------VLKVIDDVKKLGFRLPPSV---IEEIAKAMKKKELSDDEY---EEILRRIREEYERARVDPY 182
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1143 EPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIlMTAAANIKTPIMTCpLLKGKTKEDANDITDRLRKI- 1221
Cdd:PRK14897 183 EAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEI-VDARKKPSTPTMTI-YLKKDYREDEEKVREVAKKIe 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1222 -----TVADIIKSM-ELSVvpyTVYENEvcsihklkinlykpehypkhtditeedweetmravflRKLEDaiethmkmlh 1295
Cdd:PRK14897 261 nttliDVADIITDIaEMSV---VVELDE-------------------------------------EKMKE---------- 290
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1296 riRGIhndvtgpiagnetdnddsvsgkqneddgdddgegtEVDDLGSDAQKQKKqETDEMDyeensedetnepssisgve 1375
Cdd:PRK14897 291 --RLI-----------------------------------EYDDILAAISKLTF-KTVEID------------------- 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1376 dpemdsenedtevSKEDTPEPQEESMEP---------QKEVKGVKNVKeqskkkrRKFVRAKSDRHIFVkgegekfevhf 1446
Cdd:PRK14897 314 -------------DGIIRLKPQQPSFKKlyllaekvkSLTIKGIKGIK-------RAIARKENDERRWV----------- 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1447 kfatddphillaqiaqqtaqkVYIQnsgkierctvancgdpqviyhGDNPKERREIsndekkaspalhasgvdfpalwef 1526
Cdd:PRK14897 363 ---------------------IYTQ---------------------GSNLKDVLEI------------------------ 376
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1527 qDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFC 1606
Cdd:PRK14897 377 -DEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLA 455
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 1063717413 1607 RMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLMQR 1654
Cdd:PRK14897 456 RAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYK 503
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
611-830 |
1.95e-34 |
|
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: 129.67 E-value: 1.95e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 611 NIVNannqyarPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLFSSGVTdmvlstfsgrsgkkvmvsasdaellt 690
Cdd:pfam04983 1 NILS-------PQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGIVL-------------------------- 47
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 691 VTPAILKPV-PLWTGKQVITAVLNQitkghppftvekatklpvdffkcrsrEVKPNSGDLTKKKEIdeswkqNLNEDKLH 769
Cdd:pfam04983 48 PHPAILKPIkPLWTGKQTFSRLLPN--------------------------EINPKGKPKTNEEDL------CENDSYVL 95
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063717413 770 IRKNEFVCGVIDKAQFAD--YGLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDL 830
Cdd:pfam04983 96 INNGELISGVIDKKTVGKslGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
358-1446 |
7.58e-30 |
|
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: 129.51 E-value: 7.58e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 358 GLNKVIESNNILgnACTNKLDQSKVIFR--WRNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGK 431
Cdd:COG0086 258 LYRRVINRNNRL--KRLLELKAPDIIVRneKRMLQEAVDALFDngrrGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGK 335
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 432 RVNHACRSVISPDPYIAVNDIGIPPCFALKLtyperVTPWNVEKLREAIIngpdihpgathysdkSSTMKlpsteKARRA 511
Cdd:COG0086 336 RVDYSGRSVIVVGPELKLHQCGLPKKMALEL-----FKPFIYRKLEERGL---------------ATTIK-----SAKKM 390
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 512 IARKllssrgaTTELGktcDINFEGKTVHRhmrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFD 591
Cdd:COG0086 391 VERE-------EPEVW---DILEEVIKEHP-------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFD 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 592 GDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKrdtfLDKDHFNQLLFSSGVTDMVLSTF 671
Cdd:COG0086 453 GDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTR----EREGAKGEGMIFADPEEVLRAYE 528
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 672 SGRsgkkvmvsasdAELLTVTPAILKPVPLWTGKQVITAV----LNQItkghppftvekatkLPVDFFKCRSrevkpnsg 747
Cdd:COG0086 529 NGA-----------VDLHARIKVRITEDGEQVGKIVETTVgrylVNEI--------------LPQEVPFYNQ-------- 575
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 748 dLTKKKEIdeswkQNLnedklhIRKNEFVCGVIDKAQFADyglvhtvhelygsnaagNLLSVFSRLFTVflqtHGFTCGV 827
Cdd:COG0086 576 -VINKKHI-----EVI------IRQMYRRCGLKETVIFLD-----------------RLKKLGFKYATR----AGISIGL 622
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 828 DDLIIlkdmDEERTKQLQECEnvgERVlrktfgidvdVQIDPQDMRSRIerilyEDGESALASLDrsIVNYLNQCSSKGV 907
Cdd:COG0086 623 DDMVV----PKEKQEIFEEAN---KEV----------KEIEKQYAEGLI-----TEPERYNKVID--GWTKASLETESFL 678
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 908 MNDLlsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGqqdLEGKRvprmvSGKT--LPCFHpwdwspraggfisdR 985
Cdd:COG0086 679 MAAF--------SSQNTTYMMADSGARGSADQLRQLAGMRG---LMAKP-----SGNIieTPIGS--------------N 728
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 986 FLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD---GSIIQFQYGEDGVDVhrssf 1062
Cdd:COG0086 729 FREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVTEEDcgtDRGITVTAIKEGGEV----- 797
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1063 IEKFKE----LTINQDmVLQKCSEDMLSGASSYISDLPISL--KKGAEKFVEAMPMNERIASKFVRQEELLKLVKskffA 1136
Cdd:COG0086 798 IEPLKErilgRVAAED-VVDPGTGEVLVPAGTLIDEEVAEIieEAGIDSVKVRSVLTCETRGGVCAKCYGRDLAR----G 872
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1137 SLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEmnvtlgipRLQEILMTAAANIKTPIMTCPLLKGKTKEDANDITD 1216
Cdd:COG0086 873 HLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS--------RAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSR 944
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1217 RLRKITVADIIKSMELSVVPYTVYENEVCSIHKLKINLYKpEHYPKHTDITEEDWEETMR------AVFLRKLEDAIETH 1290
Cdd:COG0086 945 NSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVA-EWDPHTPPIIEEVGGGVVFddivegGVIVEKTDEETGGL 1023
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1291 MKMLHRIRGIHNDVTGPIAGNETDNDDSVSGKQNEDDGDDDGEGTEVDDLGSDAQKQKKQETDEMDyeensedetnepss 1370
Cdd:COG0086 1024 SIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIAR-------------- 1089
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063717413 1371 ISGVEDPEMDSENEDTEVSKEDTPEPQEESMEPQKEVKGVKNVKEQSKKKRRKFVRAKSDRHIFVKGEGEKFEVHF 1446
Cdd:COG0086 1090 IPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
252-1169 |
1.78e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 125.89 E-value: 1.78e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 252 DDSGIDALSEVEdGDKETREKSTEVaaefEEHNSKRDL------LPSEVR--NILKHLwqnehefcSFIGDLWQSGSEKi 323
Cdd:PRK14844 1601 DSYGIDSFVAMQ-GVEAIRELLTRL----DLHEIRKDLrlelesVASEIRrkKIIKRL--------RIVENFIKSGNRP- 1666
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 324 dySMFFLESVLVPPTKFRPPTTggdsvME--HPQTVGLN----KVIESNNILGNACTnkLDQSKVIFR--WRNLQESVNV 395
Cdd:PRK14844 1667 --EWMILTTIPILPPDLRPLVS-----LEsgRPAVSDLNhhyrTIINRNNRLRKLLS--LNPPEIMIRneKRMLQEAVDS 1737
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 396 LFD-SKTATVQSQRDSSG----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLtyperVTP 470
Cdd:PRK14844 1738 LFDnSRRNALVNKAGAVGykksISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALEL-----FKP 1812
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 471 WNVEKLReaiINGpdihpgathysdKSSTMKLpstekarraiARKLLssRGATTELGKTCDinfegKTVHRHMrdgdiVL 550
Cdd:PRK14844 1813 FVYSKLK---MYG------------MAPTIKF----------ASKLI--RAEKPEVWDMLE-----EVIKEHP-----VL 1855
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 551 VNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRA 630
Cdd:PRK14844 1856 LNRAPTLHRLGIQAFEPILIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIV 1934
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 631 LIQDHIVSSVLLT----KRDTFLDKDHFNQLLFSsgVTDMVLSTFSGRSGKKVMVSaSDAEL----LTVTPAILkpvplw 702
Cdd:PRK14844 1935 PSKDIVLGIYYLTlqepKEDDLPSFGAFCEVEHS--LSDGTLHIHSSIKYRMEYIN-SSGEThyktICTTPGRL------ 2005
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 703 tgkqvitaVLNQITKGHppftvekatklpvdffkcrsrevkpnsgdltkkkeideswkQNLNEDKLHirknefvcgvidk 782
Cdd:PRK14844 2006 --------ILWQIFPKH-----------------------------------------ENLGFDLIN------------- 2023
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 783 aQFADYGLVHTVHELYGSNAAGNLLSVFS-RLFTVFLQTHGFTcGVddliilkdmdeertkQLQECenvgERVLRKTFGI 861
Cdd:PRK14844 2024 -QVLTVKEITSIVDLVYRNCGQSATVAFSdKLMVLGFEYATFS-GV---------------SFSRC----DMVIPETKAT 2082
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 862 DVDvqidpqDMRSRIER--ILYEDGESALASLDRSIVNYLNQCSSKgVMNDLLSDGLL--KTPGRNCISLMTISGAKGSK 937
Cdd:PRK14844 2083 HVD------HARGEIKKfsMQYQDGLITRSERYNKVIDEWSKCTDM-IANDMLKAISIydGNSKYNSVYMMVNSGARGST 2155
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 938 VNFQQISshlGQQDLEGKRvprmvSGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSG 1017
Cdd:PRK14844 2156 SQMKQLA---GMRGLMTKP-----SGEIIE-------TP-----IISNFREGLNVFEYFNSTHGARKGLADTALKTANSG 2215
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1018 YLQRCLMKNLESLKV-NYDCTVRdaDGSIIQfqygedgVDVHRSSFIEKFKELTINQ---DMVLQKCSEDMLSGASSYIS 1093
Cdd:PRK14844 2216 YLTRRLVDVSQNCIVtKHDCKTK--NGLVVR-------ATVEGSTIVASLESVVLGRtaaNDIYNPVTKELLVKAGELID 2286
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063717413 1094 DLPIslKKGAEKFVEAMPMNERIASKFvrQEELLKLVKSKFFAS--LAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAG 1169
Cdd:PRK14844 2287 EDKV--KQINIAGLDVVKIRSPLTCEI--SPGVCSLCYGRDLATgkIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGG 2360
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
387-1042 |
1.65e-27 |
|
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: 120.32 E-value: 1.65e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 387 RNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 462
Cdd:cd01609 202 RMLQEAVDALIDngrrGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALEL 281
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 463 typerVTPWNVEKLreaiingpdIHPGATHysdkssTMKlpsteKARRAIARKllssrgaTTELgktCDInFEGKTVHRH 542
Cdd:cd01609 282 -----FKPFVIREL---------IERGLAP------NIK-----SAKKMIERK-------DPEV---WDI-LEEVIKGHP 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 543 mrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 622
Cdd:cd01609 326 ------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSP 398
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 623 SNGEPLRALIQdhivssvlltkrdtfldkdhfnqllfssgvtDMVLSTF---SGRSGKKvmvsasDAELLTVTPailkpv 699
Cdd:cd01609 399 ASGKPIVTPSQ-------------------------------DMVLGLYyltKERKGDK------GEGIIETTV------ 435
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 700 plwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrsrevkPNSGDLTKKKEIdeswkqnlnedKLHIRKNEFVCGV 779
Cdd:cd01609 436 ----GR----VIFNEI--------------LPEGL---------PFINKTLKKKVL-----------KKLINECYDRYGL 473
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 780 IDKAQFADyglvhTVHELygsnaaGNLLSVFSrlftvflqthGFTCGVDDLIIlkdmDEERTKQLQECEnvgERVlrktf 859
Cdd:cd01609 474 EETAELLD-----DIKEL------GFKYATRS----------GISISIDDIVV----PPEKKEIIKEAE---EKV----- 520
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 860 gidvdvqidpqdmrSRIERiLYEDGESALASLDRSIVNYLNQCSSKgvMNDLLSDGLLKTPgRNCISLMTISGAKGSKVN 939
Cdd:cd01609 521 --------------KEIEK-QYEKGLLTEEERYNKVIEIWTEVTEK--VADAMMKNLDKDP-FNPIYMMADSGARGSKSQ 582
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 940 FQQISshlGQQDLegkrvprMV--SGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSG 1017
Cdd:cd01609 583 IRQLA---GMRGL-------MAkpSGKIIE-------LP-----IKSNFREGLTVLEYFISTHGARKGLADTALKTADSG 640
|
650 660
....*....|....*....|....*
gi 1063717413 1018 YLQRCLmknlesLKVNYDCTVRDAD 1042
Cdd:cd01609 641 YLTRRL------VDVAQDVIVTEED 659
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
22-162 |
9.69e-27 |
|
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: 116.76 E-value: 9.69e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 22 MTEQDVRKHSFLKVTSPILHDNVGNPFP-GGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHPLLFNLLFN 100
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAErGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 101 FLQRACFF---------CHHFMAKPEDVERAVS-QLKLIIKGDIVSAKQLESNT-PTKS------------------KSS 151
Cdd:cd00399 81 FLGPEWMIltclpvpppCLRPSVIIEERWRLLQeHVDTYLDNGIAGQPQTQKSGrPLRSlaqrlkgkegrfrgnlmgKRV 160
|
170
....*....|.
gi 1063717413 152 DESCESVVTTD 162
Cdd:cd00399 161 DFSGRSVISPD 171
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
387-1185 |
7.68e-26 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 116.32 E-value: 7.68e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 387 RNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 462
Cdd:PRK00566 287 RMLQEAVDALFDngrrGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALEL 366
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 463 TYP----------------------ERVTP--WNVekLREAIINgpdiHPgathysdksstmklpstekarraiarklls 518
Cdd:PRK00566 367 FKPfimkklverglattiksakkmvEREDPevWDV--LEEVIKE----HP------------------------------ 410
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 519 srgattelgktcdinfegktvhrhmrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVH 598
Cdd:PRK00566 411 ------------------------------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVH 459
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 599 FPQDEISRAEA-------YNIVNannqyarPSNGEPLraliqdhIVSS---VL----LTKRDTFLDKDHfnqLLFSSgvT 664
Cdd:PRK00566 460 VPLSLEAQAEArvlmlssNNILS-------PANGKPI-------IVPSqdmVLglyyLTREREGAKGEG---MVFSS--P 520
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 665 DMVLSTFsgRSGK-----KVMVSASDAELLTVTPailkpvplwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrs 739
Cdd:PRK00566 521 EEALRAY--ENGEvdlhaRIKVRITSKKLVETTV----------GR----VIFNEI--------------LPEGL----- 565
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 740 revkP--NSGDLTKKKE----IDESWKQnlnedklhirknefvCGVIDKAQFADyglvhtvhelygsnaagNLLSVFSRL 813
Cdd:PRK00566 566 ----PfiNVNKPLKKKEiskiINEVYRR---------------YGLKETVIFLD-----------------KIKDLGFKY 609
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 814 FTVFlqthGFTCGVDDLIILkdmdEERTKQLQECEnvgERVlrktfgidvdvqidpqdmrSRIERiLYEDGesALASLDR 893
Cdd:PRK00566 610 ATRS----GISIGIDDIVIP----PEKKEIIEEAE---KEV-------------------AEIEK-QYRRG--LITDGER 656
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 894 --SIVNYLNQCSSK--GVMNDLLSDgllKTPGRNCISLMTISGAKGSKVNFQQISshlGQQDLEGKrvPrmvSGKT--LP 967
Cdd:PRK00566 657 ynKVIDIWSKATDEvaKAMMKNLSK---DQESFNPIYMMADSGARGSASQIRQLA---GMRGLMAK--P---SGEIieTP 725
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 968 cfhpwdwspraggfISDRFLSGLRPQEYYF--HcmaG-REGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-G 1043
Cdd:PRK00566 726 --------------IKSNFREGLTVLEYFIstH---GaRKGLADTALKTADSGYLTRRL------VDVAQDVIVREDDcG 782
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1044 SiiqfqygEDGVDVHR----SSFIEKFKEL----TINQDmVLQKCSEDMLSGASSYISDlpislkKGAEKFVEAmpmneR 1115
Cdd:PRK00566 783 T-------DRGIEVTAiiegGEVIEPLEERilgrVLAED-VVDPETGEVIVPAGTLIDE------EIADKIEEA-----G 843
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1116 IASKFVRQeellklV---KSKF----------FAS--LAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGrgeMNVTLGIP 1180
Cdd:PRK00566 844 IEEVKIRS------VltcETRHgvcakcygrdLATgkLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGG---VDITGGLP 914
|
....*
gi 1063717413 1181 RLQEI 1185
Cdd:PRK00566 915 RVAEL 919
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
875-982 |
9.92e-25 |
|
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: 100.13 E-value: 9.92e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 875 RIERILyedGESALASLDRSIVNYLNQCSSKgvMNDLLSDGLlktPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEG 954
Cdd:pfam05000 9 KLEDIW---GMTLEESFEALINNILNKARDP--AGNIASKSL---DPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 1063717413 955 KRVPRMVSGKTLPCFHPWDWSPRAGGFI 982
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1142-1189 |
8.32e-24 |
|
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: 99.41 E-value: 8.32e-24
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1063717413 1142 GEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTA 1189
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
361-634 |
5.28e-22 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 103.06 E-value: 5.28e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 361 KVIESNNILGNACT--NKLDQSKVIFRWRNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVN 434
Cdd:CHL00018 298 RVIYRNNTLTDLLTtsRSTPGELVMCQKKLLQEAVDALLDNgirgQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVD 377
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 435 HACRSVISPDPYIAVNDIGIPPCFALKLTYPervtpwnveklreAIIngpdihpgathysdksstmklpstekaRRAIAR 514
Cdd:CHL00018 378 YSGRSVIVVGPSLSLHQCGLPREIAIELFQP-------------FVI---------------------------RGLIRQ 417
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 515 KLLSS-RGATTELGKTCDINFEgktVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGD 593
Cdd:CHL00018 418 HLASNiRAAKSKIREKEPIVWE---ILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEG-RAICLHPLVCKGFNADFDGD 493
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 1063717413 594 EMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQD 634
Cdd:CHL00018 494 QMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQD 534
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
361-643 |
1.39e-21 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 101.36 E-value: 1.39e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 361 KVIESNNILgnACTNKLDQSKVIFR--WRNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVN 434
Cdd:PRK02625 279 RVINRNNRL--ARLQEILAPEIIVRneKRMLQEAVDALIDNgrrgRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVD 356
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 435 HACRSVISPDPYIAVNDIGIPPCFALKLtyperVTPWNVEKL-REAIINgpDIhpgathysdksstmklpsteKArraiA 513
Cdd:PRK02625 357 YSGRSVIVVGPKLKMHQCGLPKEMAIEL-----FQPFVIHRLiRQGIVN--NI--------------------KA----A 405
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 514 RKLLSSRGAttelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGD 593
Cdd:PRK02625 406 KKLIQRADP------------EVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEG-RAIQLHPLVCPAFNADFDGD 472
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 1063717413 594 EMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLT 643
Cdd:PRK02625 473 QMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLT 522
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-426 |
4.31e-21 |
|
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: 96.20 E-value: 4.31e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 14 VESVRFSFMTEQDVRKHSFLKVTSP-ILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHp 92
Cdd:pfam04997 4 IKEIQFGIASPEEIRKWSVGEVTKPeTYNYGSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFH- 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 93 llfnllfnflqracffchhfmakpedveraVSQLKLIIKgdIVsakqlesntptkskssdescesvvttdsseECedsdv 172
Cdd:pfam04997 83 ------------------------------IGFFKKTLK--IL------------------------------EC----- 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 173 edqrwtslqfaevtaVLKNfmrlssksCSRCKgINPKLEKPMFGWVRMRAMKDSDVGANVIRGLKLKKSTSSVENPDGFD 252
Cdd:pfam04997 96 ---------------VCKY--------CSKLL-LDPGKPKLFNKDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKNGV 151
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 253 DSGIDALSEVEDGDKETREKSTevaaefEEHNSKRDLLPSEVRNILKHLwqnEHEFCSFIGdLWQSGSeKIDYsmFFLES 332
Cdd:pfam04997 152 CGSQQPVSRKEGLKLKAAIKKS------KEEEEKEILNPEKVLKIFKRI---SDEDVEILG-FNPSGS-RPEW--MILTV 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 333 VLVPPTKFRPP-TTGGDSVMEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDS-----KTATVQS 406
Cdd:pfam04997 219 LPVPPPCIRPSvQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNeipglPPALQKS 298
|
410 420
....*....|....*....|
gi 1063717413 407 QRDSSGICQLLEKKEGLFRQ 426
Cdd:pfam04997 299 KRPLKSISQRLKGKEGRFRG 318
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1513-1652 |
3.71e-20 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 97.66 E-value: 3.71e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1513 LHASGVDFPALWEFqDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPM 1592
Cdd:PRK14898 709 LYTQGSNLREVFKI-EGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPI 787
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1593 SRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1652
Cdd:PRK14898 788 GRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLR 847
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
779-1169 |
2.53e-13 |
|
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: 75.66 E-value: 2.53e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 779 VIDKAQFADygLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLII------LKDMDEERTKQLQECENVGE 852
Cdd:TIGR02388 6 VVDKKALKN--LISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVppakqdLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 853 --RVLRKTFGIDVdvqidpqdMRSRIERilyedgesalasLDRSIVNYLNQcsskgvmNDLLsdgllktpgrNCISLMTI 930
Cdd:TIGR02388 84 itEVERFQKVIDT--------WNGTNEE------------LKDEVVNNFRQ-------TDPL----------NSVYMMAF 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 931 SGAKGskvNFQQISSHLGQQDLEGKRVPRMVSgktLPcfhpwdwspraggfISDRFLSGLRPQEYYFHCMAGREGLVDTA 1010
Cdd:TIGR02388 127 SGARG---NMSQVRQLVGMRGLMANPQGEIID---LP--------------IKTNFREGLTVTEYVISSYGARKGLVDTA 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1011 VKTSRSGYLQRCLmknlesLKVNYDCTVRDADGSIiqfqygEDGVDVhrSSFIEKFKELTINQDMVLQKCSEDMLSGASS 1090
Cdd:TIGR02388 187 LRTADSGYLTRRL------VDVSQDVIVREEDCGT------ERSIVV--RAMTEGDKKISLGDRLLGRLVAEDVLHPEGE 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1091 YISDLPISLKKGAEKFVEAMPMNERIASKFVRQEELLKLVKSKFFASLAQP-----GEPVGVLAAQSVGEPSTQMTLNTF 1165
Cdd:TIGR02388 253 VIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTF 332
|
....
gi 1063717413 1166 HLAG 1169
Cdd:TIGR02388 333 HTGG 336
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1142-1186 |
7.27e-12 |
|
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: 66.40 E-value: 7.27e-12
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 1063717413 1142 GEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEmNVTLGIPRLQEIL 1186
Cdd:cd02655 6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELF 49
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
982-1169 |
5.62e-11 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 67.71 E-value: 5.62e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 982 ISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-----GSIIQfqyGEDGVD 1056
Cdd:PRK02597 159 IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRL------VDVSQDVIVREEDcgttrGIVVE---AMDDGD 229
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1057 VHRSSFIEKFKELTINQDMVLQKcsEDMLSGASSYIS-DLpislkkgAEKFVEAmpmneRIASKFVRQE---ELLKLVKS 1132
Cdd:PRK02597 230 RVLIPLGDRLLGRVLAEDVVDPE--GEVIAERNTAIDpDL-------AKKIEKA-----GVEEVMVRSPltcEAARSVCR 295
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1063717413 1133 KFFA-SLAQP-----GEPVGVLAAQSVGEPSTQMTLNTFHLAG 1169
Cdd:PRK02597 296 KCYGwSLAHNhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGG 338
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1528-1652 |
9.70e-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: 65.52 E-value: 9.70e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1528 DKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSG--------GYRPMSRMGGIa 1599
Cdd:cd02737 250 DLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGefvglnakGYKAQRRSLKI- 328
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1063717413 1600 esTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGC-FDLM 1652
Cdd:cd02737 329 --SAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSkFEIL 380
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
989-1169 |
1.47e-08 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 59.95 E-value: 1.47e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 989 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-GSIiqfqygedgvdvhRSSFIEKFk 1067
Cdd:CHL00117 172 GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRL------VEVVQHIVVRETDcGTT-------------RGISVSPR- 231
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063717413 1068 eltinQDMVLQKCSEDMLSG---ASS-YIS---------DLPISLkkgAEKFVEAmpmneRIASKFVR------------ 1122
Cdd:CHL00117 232 -----NGMMIERILIQTLIGrvlADDiYIGsrciatrnqDIGIGL---ANRFITF-----RAQPISIRspltcrstswic 298
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 1063717413 1123 ---------QEELLKLvkskffaslaqpGEPVGVLAAQSVGEPSTQMTLNTFHLAG 1169
Cdd:CHL00117 299 qlcygwslaHGDLVEL------------GEAVGIIAGQSIGEPGTQLTLRTFHTGG 342
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1094-1162 |
6.63e-08 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 57.60 E-value: 6.63e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063717413 1094 DLPISLKkgaEKFVEAMPMNERIASKFVrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTL 1162
Cdd:PRK14898 14 DLPRSLK---DELFEKLSKRDGVTEEMV--EEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
