|
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 ... |
31-1048 |
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: 1134.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 31 RFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHPLLFNL 110
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 111 LFNFLQRACFFCHHFMAKPEDVERAVSQLKLIIKGDIVSAKQLESNtptkskssdescesvvttdsseecedsdvedqrw 190
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKLKLLDKGLLVEAAELDFG---------------------------------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 191 tslqfaevtavlknfmrlsskscsrckginpklekpmfgwvrmramkdsdvganvirglklkkstssvenpdgfddsgid 270
Cdd:cd01435 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 271 alsevedgdketrekstevaaefeehnskrdllpsevrnilkhlwqnehefcsfigdlwqsgsekidYSMFFLESVLVPP 350
Cdd:cd01435 127 -------------------------------------------------------------------YDMFFLDVLLVPP 139
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 351 TKFRPPTTGGDSVMEHPQTVGLNKVIESNNILGNACT---------------NKLDQSKVIFRWRNLQESVNVLFDSKTA 415
Cdd:cd01435 140 NRFRPPSFLGDKVFENPQNVLLSKILKDNQQIRDLLAsmrqaesqskldlisGKTNSEKLINAWLQLQSAVNELFDSTKA 219
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 416 TVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIIN 495
Cdd:cd01435 220 PKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVIN 299
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 496 GPDIHPGATHYSDKSSTM-KLPSTEKARRAIARKLLSSRGATTELgktcdiNFEGKTVHRHMRDGDIVLVNRQPTLHKPS 574
Cdd:cd01435 300 GPDVYPGANAIEDEDGRLiLLSALSEERRKALAKLLLLLSSAKLL------LNGPKKVYRHLLDGDVVLLNRQPTLHKPS 373
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 575 LMAHKVRVLKGEKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVL 654
Cdd:cd01435 374 IMAHKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVL 453
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 655 LTKRDTFLDKDHFNQLLFsSGVTDMVLSTFSGRsgkkvmvsasdaeLLTVTPAILKPVPLWTGKQVITAVLNQITKGHPP 734
Cdd:cd01435 454 LTSRDTFFTREEYQQLVY-AALRPLFTSDKDGR-------------IKLLPPAILKPKPLWTGKQVISTILKNLIPGNAP 519
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 735 FTVEkatklpvdffkcrsrevkpNSGDLTKKKEIDESWKQNLNEDKLHIRKNEFVCGVIDKAQFAD--YGLVHTVHELYG 812
Cdd:cd01435 520 LLNL-------------------SGKKKTKKKVGGGKWGGGSEESQVIIRNGELLTGVLDKSQFGAsaYGLVHAVYELYG 580
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 813 SNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENVGERVLRKTFGIdvdvqidpqdmrsrieri 892
Cdd:cd01435 581 GETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEFLGL------------------ 642
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 893 lyedgesalasldrsivnYLNQCSSKgVMNDLLSDGLLKTPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPR 972
Cdd:cd01435 643 ------------------KLNKVTSS-IIKACLPKGLLKPFPENNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPL 703
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15230368 973 MVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1048
Cdd:cd01435 704 MVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
23-1668 |
3.97e-167 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 542.69 E-value: 3.97e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 23 ASQVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPI 102
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 103 YHPLLFNLLFNFLQRACFFCHHFMAKPEDVeravSQLKLIikgdivsakqlesntptkskssdESCESVVTTDSSEECED 182
Cdd:PRK14977 85 IHIAFIDNIKDLLNSTCHKCAKLKLPQEDL----NVFKLI-----------------------EEAHAAARDIPEKRIDD 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 183 SDVEDQRWTSLQFAEvtavlknfmrlSSKSCSRCkginpklekpmfgwvrmramkdsdvGANVIRgLKLKKSTSSVENpd 262
Cdd:PRK14977 138 EIIEEVRDQVKVYAK-----------KAKECPHC-------------------------GAPQHE-LEFEEPTIFIEK-- 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 263 gfddsgidalsevedgdketrekstevaAEFEEHNskrdLLPSEVRNILKHLWQNEHEFCSFigdlwqsGSEKIDYSMFF 342
Cdd:PRK14977 179 ----------------------------TEIEEHR----LLPIEIRDIFEKIIDDDLELIGF-------DPKKARPEWAV 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 343 LESVLVPPTKFRPPT---TGGDSvmEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDSKTATV-- 417
Cdd:PRK14977 220 LQAFLVPPLTARPSIileTGERS--EDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIpq 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 418 ----QSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAI 493
Cdd:PRK14977 298 ahhkGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELV 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 494 INGPDIHPGAtHYSDKSSTMKlpstekarraIARKLLSSRG--ATTELGKTCDInfeGKTVHRHMRDGDIVLVNRQPTLH 571
Cdd:PRK14977 378 INGPDEFPGA-NAIRKGDGTK----------IRLDFLEDKGkdALREAAEQLEI---GDIVERHLADGDIVIFNRQPSLH 443
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 572 KPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVS 651
Cdd:PRK14977 444 KLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITA 522
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 652 SVLLTKRDTFLDKDHFNQLLFSSGVTDMVLStfsgrsgkkvmvsasdaelltvtPAI-LKPVPLWTGKQVITAVlnqitk 730
Cdd:PRK14977 523 AYLITKDDALFDKNEASNIAMLAGITDPLPE-----------------------PAIkTKDGPAWTGKQLFSLF------ 573
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 731 ghppftvekatkLPVDFfkcrSREVKPNSGDLTKKKEIDESWkqnLNEDKLHIRKNEFVCGVIDKAQFADY-----GLVH 805
Cdd:PRK14977 574 ------------LPKDF----NFEGIAKWSAGKAGEAKDPSC---LGDGYVLIKEGELISGVIDDNIIGALveepeSLID 634
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 806 TVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIIlkdMDEERTKQLQECENVGERVLRKTFGIDVDVQIDPQDM 885
Cdd:PRK14977 635 RIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLII---PDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKG 711
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 886 RSRIERILYEDgesalASLDRSIVNYLNQCSSK--GVMNDLLsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGQQ 963
Cdd:PRK14977 712 KEELLRGMKEE-----EALEADIVNELDKARDKagSSANDCI-------DADNAGKIMAKTGARGSMANLAQIAGALGQQ 779
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 964 D--------LEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRC 1035
Cdd:PRK14977 780 KrktrigfvLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRR 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1036 LMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHR---------SSFIEKFKELTINQDMVLQKCSEDMLSGASSYIS 1106
Cdd:PRK14977 860 LANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKldhgeafnlERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNA 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1107 DLPISLkkgAEKFVEAMPMNERIaskfvrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEM 1186
Cdd:PRK14977 940 NLPKLL---ADAIHGAELKEDEL-------EAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAM 1009
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1187 NVTLGIPRLQEiLMTAAANIKTPIMTCpLLKGKTKED---ANDITDRLRKITVADIIKSMElsvvpyTVYENEVCSIhkl 1263
Cdd:PRK14977 1010 DVTHGLERFIE-LVDARAKPSTPTMDI-YLDDECKEDiekAIEIARNLKELKVRALIADSA------IDNANEIKLI--- 1078
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1264 kinlyKPEHypkhtditeedweetmravflRKLEDAIETHMKMLHRIRGIHNDVTGPIagnETDNDdsvsgkqneddgdd 1343
Cdd:PRK14977 1079 -----KPDK---------------------RALENGCIPMERFAEIEAALAKGKKFEM---ELEDD-------------- 1115
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1344 dgegTEVDDLGSDAQKQKKQETdemdyeensedetnepssISGVEDPEMDsenedtevskedtpepqeesmepqKEVKGV 1423
Cdd:PRK14977 1116 ----LIILDLVEAADRDKPLAT------------------LIAIRNKILD------------------------KPVKGV 1149
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1424 KNVKeqskkkrRKFVraksdrhifvkgegekfevhfkfatddphillaQIAQQTAQKVY-IQNSGkierctvancgdpqv 1502
Cdd:PRK14977 1150 PDIE-------RAWV---------------------------------ELVEKDGRDEWiIQTSG--------------- 1174
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1503 iyhgdnpkerreiSNDEKkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGI 1582
Cdd:PRK14977 1175 -------------SNLAA----VLEMKCI------------DIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGL 1225
|
1610 1620 1630 1640 1650 1660 1670 1680
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1583 SVSIRHLNLIADYMTFSG-----GYRPMSRMGGIA-ESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPAL 1656
Cdd:PRK14977 1226 EVDNRYIMLVADIMCSRGtieaiGLQAAGVRHGFAgEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIP 1305
|
1690
....*....|..
gi 15230368 1657 SGTGCFDLMQRV 1668
Cdd:PRK14977 1306 IGSGKVDLLMDF 1317
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
21-1075 |
3.35e-166 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 526.73 E-value: 3.35e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 21 MGASQVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVF 100
Cdd:PRK08566 3 MMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELAR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 101 PIYHPLLFNLLFNFLQRACFFCHHFMAKPEDVERAVSQLKliikgdivsakqlesntptkskssdescesvvttdsseec 180
Cdd:PRK08566 83 PVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLE---------------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 181 edsdvEDQRWTSLqfaeVTAVLKNFMRLSSK--SCSRC--KGINPKLEKPmfgwvrmramkdsdvganvirglklkksTS 256
Cdd:PRK08566 123 -----RLKEWGSL----ADDLIKEVKKEAAKrmVCPHCgeKQYKIKFEKP----------------------------TT 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 257 SVENpdgfddsgidalsevedgDKETREKstevaaefeehnskrdLLPSEVRNILkhlwqnehefcsfigdlwqsgsEKI 336
Cdd:PRK08566 166 FYEE------------------RKEGLVK----------------LTPSDIRERL----------------------EKI 189
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 337 ---DYSMFFLE-----------SVL-VPPTKFRPPTT---GGDSvmEHPQTVGLNKVIESN-----NILGNACTNKLDQs 393
Cdd:PRK08566 190 pdeDLELLGINpevarpewmvlTVLpVPPVTVRPSITletGQRS--EDDLTHKLVDIIRINqrlkeNIEAGAPQLIIED- 266
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 394 kvifRWRNLQESVNVLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIP 468
Cdd:PRK08566 267 ----LWELLQYHVTTYFDNEIPGIPPARHRSGrplktLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVP 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 469 PCFALKLTYPERVTPWNVEKLREAIINGPDIHPGAThYSDKSSTMKLPSTEKARRAIARKLLssrgattelgktcdinfE 548
Cdd:PRK08566 343 EAIAKELTVPERVTEWNIEELREYVLNGPEKHPGAN-YVIRPDGRRIKLTDKNKEELAEKLE-----------------P 404
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 549 GKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNA 628
Cdd:PRK08566 405 GWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLV 483
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 629 NNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLFSSGVTdmvlstfsgrsgkkvmvsasdaELLTVTPAI 708
Cdd:PRK08566 484 QEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGID----------------------ELPEPEPAI 541
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 709 LKPVPLWTGKQVITAVlnqitkghppftvekatkLPVDF-FKCRSrevKPNSGDLTKKKEIDEswkqnlNEDKLHIRKNE 787
Cdd:PRK08566 542 ENGKPYWTGKQIFSLF------------------LPKDLnLEFKA---KICSGCDECKKEDCE------HDAYVVIKNGK 594
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 788 FVCGVIDKAQFADYG--LVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLiilkDMDEERTKQLQECENVGE 865
Cdd:PRK08566 595 LLEGVIDKKAIGAEQgsILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDE----DIPEEAKEEIDEIIEEAE 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 866 RvlrktfgiDVDvqidpqdmrSRIERilYEDGESALA---SLDRSIVNYLNQCSSKG--VMNDLLSDGLLKTpgrNCISL 940
Cdd:PRK08566 671 K--------RVE---------ELIEA--YENGELEPLpgrTLEETLEMKIMQVLGKArdEAGEIAEKYLGLD---NPAVI 728
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 941 MTISGAKGSKVNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLV 1020
Cdd:PRK08566 729 MARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLV 808
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*
gi 15230368 1021 DTAVKTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHRSSF 1075
Cdd:PRK08566 809 DTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDH 863
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1146-1665 |
8.90e-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: 8.90e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1146 KFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTAAANIKTPIMTCPLLKGKTKEDAN 1225
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1226 DITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinlykpehypkhtditeEDWEETMRAVFLRKLedaiethmk 1305
Cdd:cd02735 81 TLKKRLSRVTLSDVVEKVEV------------------------------------TEILKTIERVFKKLL--------- 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1306 mlhrirgihndvtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssis 1385
Cdd:cd02735 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1386 gvedpemdsenedtevskedtpepqeesmepqkevkgvknvkeqskkkrrkfvraksdrhifvkgeGEKFEVHFKFATDD 1465
Cdd:cd02735 116 ------------------------------------------------------------------GKWCEVTIKLPLSS 129
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1466 PHILLAQIAQQTAQKVYIQNSGKIERCTVANCgdpqviyhgdnpkerreisNDEKKASPALHASGVDFPALWEFQDKLDV 1545
Cdd:cd02735 130 PKLLLLSIVEKLARKAVIREIPGITRCFVVEE-------------------DKGGKTKYLVITEGVNLAALWKFSDILDV 190
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1546 RYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIAESTSPFCRMTFET 1625
Cdd:cd02735 191 NRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRI-GMESSTSPLQKMSFET 269
|
490 500 510 520
....*....|....*....|....*....|....*....|
gi 15230368 1626 ATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1665
Cdd:cd02735 270 TLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
339-653 |
4.02e-115 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 365.69 E-value: 4.02e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 339 SMFFLESVLVPPTKFRPPTTGGDS-VMEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDS---KT 414
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGrFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNeglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 415 ATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAII 494
Cdd:smart00663 81 ANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 495 NGPdihPGATHYSDKSSTMKlpsTEKARRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPS 574
Cdd:smart00663 161 NGP---NGAKYIIRGKKTNL---KLAKKSKIANHLK-----------------IGDIVERHVIDGDVVLFNRQPTLHRMS 217
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15230368 575 LMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSV 653
Cdd:smart00663 218 IQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
1002-1618 |
4.10e-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: 4.10e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1002 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDV----------- 1070
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPlkiekqgrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1071 -HRSSFIEKFKELTINQDMVLQKCSEDMLSGASSYISDLPISLKKGAEKFVEAMPMNE-----RIASKFVRQ-------- 1136
Cdd:pfam04998 81 eFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSKEAQERATLLFElllksGLESKRVRSeltcnska 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1137 -EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTaAANIKTPIMTCPL 1215
Cdd:pfam04998 161 fVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINV-SKNIKSPSLTVYL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1216 L--KGKTKEDANDITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinLYKPehYPKHTDITEEdweetmravfl 1293
Cdd:pfam04998 240 FdeVGRELEKAKKVYGAIEKVTLGSVVESGEI---------------------LYDP--DPFNTPIISD----------- 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1294 rklEDAIETHMKMlhrirgiHNDVTgpiagnETDNDDSVSGKQNEddgdddgegtevddlgsdaqkqkkqetdemdyeeN 1373
Cdd:pfam04998 286 ---VKGVVKFFDI-------IDEVT------NEEEIDPETGLLIL----------------------------------V 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1374 SEDETNEPSSISGVedpemdsenedteVSKEDTPEPQEES-MEPQKEVKGVKNVKEQSKKKRRKfvraksdrhifvKGEG 1452
Cdd:pfam04998 316 IRLLKILNKSIKKV-------------VKSEVIPRSIRNKvDEGRDIAIGEITAFIIKISKKIR------------QDTG 370
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1453 EKFEVHFKFATDDPhiLLAQIAQQTAQKVYIQNSGKIERCTVancgdpqviyhgdnpkerREISNDEKKASPALHASGVD 1532
Cdd:pfam04998 371 GLRRVDELFMEEDP--KLAILVASLLGNITLRGIPGIKRILV------------------NEDDKGKVEPDWVLETEGVN 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1533 FPALWEFQDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIA 1612
Cdd:pfam04998 431 LLRVLLVPGFVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH-GIN 509
|
....*.
gi 15230368 1613 ESTSPF 1618
Cdd:pfam04998 510 KAELSA 515
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
443-628 |
4.03e-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: 4.03e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 443 GKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGATHYSDKS-STMKLpstEKA 521
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINgARRDL---RYQ 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 522 RRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNA 601
Cdd:pfam00623 78 KRRLDKELE-----------------IGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG-KTFRLNLSVTTPYNA 139
|
170 180
....*....|....*....|....*..
gi 15230368 602 DFDGDEMNVHFPQDEISRAEAYNIVNA 628
Cdd:pfam00623 140 DFDGDEMNLHVPQSEEARAEAEELMLV 166
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1108-1667 |
5.64e-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: 170.62 E-value: 5.64e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1108 LPISLKKGaekfVEAMPMNERIASKFvRQEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMN 1187
Cdd:TIGR02389 2 LPEKLLKE----LEETVKKREISDKE-ELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELN 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1188 VTLGIPRLQEILmTAAANIKTPIMTCPLLK--GKTKEDANDITDRLRKITVADIIKSMELSVVPYTVyenevcsihklki 1265
Cdd:TIGR02389 77 VTLGLPRLIEIV-DARKTPSTPSMTIYLEDeyEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTV------------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1266 nlykpehypkhtditeedweetmravflrkledAIETHMKMLHRiRGIhndvtgpiagnetdnddsvsgkqneddgdddg 1345
Cdd:TIGR02389 143 ---------------------------------IIELDEEQLKE-RGI-------------------------------- 156
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1346 egtEVDDLGSDAQKQKKQEtdemdyeensedetnepssisgvedpEMDSENEDTEVskedTPEPQEESMepqkevkgvkn 1425
Cdd:TIGR02389 157 ---TVDDVEKAIKKAKLGK--------------------------VIEIDMDNNTI----TIKPGNPSL----------- 192
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1426 vkeqskKKRRKfvRAKSDRHIFVKGegekfevhfkfatddphillaqiaqqtaqkvyIQNsgkIERCTVANCGDPQVIY- 1504
Cdd:TIGR02389 193 ------KELRK--LKEKIKNLHIKG--------------------------------IKG---IKRVVIRKEGDEYVIYt 229
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1505 HGDNPKErreisndekkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISV 1584
Cdd:TIGR02389 230 EGSNLKE-------------VLKLEGV------------DKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDV 284
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1585 SIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDL 1664
Cdd:TIGR02389 285 DIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDL 364
|
...
gi 15230368 1665 MQR 1667
Cdd:TIGR02389 365 VMD 367
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
400-1261 |
1.31e-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: 1.31e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 400 RNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 475
Cdd:TIGR02386 279 RMLQEAVDALFDNgrrgKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALEL 358
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 476 TYPervtpwnveklreAIINGPDIHPGAthysdksstmklPSTEKARRAIARkllssrgattELGKTCDInFEgKTVHRH 555
Cdd:TIGR02386 359 FKP-------------FIIKRLIDRELA------------ANIKSAKKMIEQ----------EDPEVWDV-LE-DVIKEH 401
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 556 MrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 635
Cdd:TIGR02386 402 P-----VLLNRAPTLHRLGIQAFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNP 475
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 636 SNGEPLRALIQDHIVSSVLLTkrdtfldKDHFNQL----LFSSgVTDMVLSTFSGRSGKKVMVS-ASDAELLTVTPailk 710
Cdd:TIGR02386 476 KDGKPIVTPSQDMVLGLYYLT-------TEKPGAKgegkIFSN-VDEAIRAYDNGKVHLHALIGvRTSGEILETTV---- 543
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 711 pvplwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrsrevkP--NSGDLTKKKEIDEswkqnlnedklhirknef 788
Cdd:TIGR02386 544 ------GR----VIFNEI--------------LPEGF---------PyiNDNEPLSKKEISS------------------ 572
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 789 vcgvidkaqfadygLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECEnvgervl 868
Cdd:TIGR02386 573 --------------LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVA------- 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 869 rktfgidvdvQIDPQdmrsrierilYEDGesALASLDRsivnYLNQCSSKGVMNDLLSDGLLK-----TPGRNCISLMTI 943
Cdd:TIGR02386 632 ----------KIQKF----------YNKG--LITDEER----YRKVVSIWSETKDKVTDAMMKllkkdTYKFNPIFMMAD 685
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 944 SGAKGSKVNFQQISshlGQQDLEGKrvprmVSGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTA 1023
Cdd:TIGR02386 686 SGARGNISQFRQLA---GMRGLMAK-----PSGDIIE-------LP-----IKSSFREGLTVLEYFISTHGARKGLADTA 745
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1024 VKTSRSGYLQRCLMKNLESLKVNY-DC---------TVRDADGSIIQFQYgeDGVdVHRSSfIEKFKElTINQDMVLQkc 1093
Cdd:TIGR02386 746 LKTADSGYLTRRLVDVAQDVVVREeDCgteegieveAIVEGKDEIIESLK--DRI-VGRYS-AEDVYD-PDTGKLIAE-- 818
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1094 SEDMLSGASsyisdlpislkkgAEKFVEAmpmneRIASKFVRQE---ELLKLVKSKFF------ASLAQPGEPVGVLAAQ 1164
Cdd:TIGR02386 819 ANTLITEEI-------------AEKIENS-----GIEKVKVRSVltcESEHGVCQKCYgrdlatGKLVEIGEAVGVIAAQ 880
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1165 SVGEPSTQMTLNTFHL---AGRGEmNVTLGIPRLQEILMTAAANIKTPIMTcplLKGKTKEDANDITDRlRKItvadIIK 1241
Cdd:TIGR02386 881 SIGEPGTQLTMRTFHTggvAGASG-DITQGLPRVKELFEARTPKDKAVIAE---VDGTVEIIEDIVKNK-RVV----VIK 951
|
890 900
....*....|....*....|
gi 15230368 1242 SMELSVVPYTVYENEVCSIH 1261
Cdd:TIGR02386 952 DENDEEKKYTIPFGAQLRVK 971
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
371-1459 |
5.69e-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: 129.89 E-value: 5.69e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 371 GLNKVIESNNILgnACTNKLDQSKVIFR--WRNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGK 444
Cdd:COG0086 258 LYRRVINRNNRL--KRLLELKAPDIIVRneKRMLQEAVDALFDngrrGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGK 335
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 445 RVNHACRSVISPDPYIAVNDIGIPPCFALKLtyperVTPWNVEKLREAIIngpdihpgathysdkSSTMKlpsteKARRA 524
Cdd:COG0086 336 RVDYSGRSVIVVGPELKLHQCGLPKKMALEL-----FKPFIYRKLEERGL---------------ATTIK-----SAKKM 390
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 525 IARKllssrgaTTELGktcDINFEGKTVHRhmrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFD 604
Cdd:COG0086 391 VERE-------EPEVW---DILEEVIKEHP-------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFD 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 605 GDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKrdtfLDKDHFNQLLFSSGVTDMVLSTF 684
Cdd:COG0086 453 GDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTR----EREGAKGEGMIFADPEEVLRAYE 528
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 685 SGRsgkkvmvsasdAELLTVTPAILKPVPLWTGKQVITAV----LNQItkghppftvekatkLPVDFFKCRSrevkpnsg 760
Cdd:COG0086 529 NGA-----------VDLHARIKVRITEDGEQVGKIVETTVgrylVNEI--------------LPQEVPFYNQ-------- 575
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 761 dLTKKKEIdeswkQNLnedklhIRKNEFVCGVIDKAQFADyglvhtvhelygsnaagNLLSVFSRLFTVflqtHGFTCGV 840
Cdd:COG0086 576 -VINKKHI-----EVI------IRQMYRRCGLKETVIFLD-----------------RLKKLGFKYATR----AGISIGL 622
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 841 DDLIIlkdmDEERTKQLQECEnvgERVlrktfgidvdVQIDPQDMRSRIerilyEDGESALASLDrsIVNYLNQCSSKGV 920
Cdd:COG0086 623 DDMVV----PKEKQEIFEEAN---KEV----------KEIEKQYAEGLI-----TEPERYNKVID--GWTKASLETESFL 678
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 921 MNDLlsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGqqdLEGKRvprmvSGKT--LPCFHpwdwspraggfisdR 998
Cdd:COG0086 679 MAAF--------SSQNTTYMMADSGARGSADQLRQLAGMRG---LMAKP-----SGNIieTPIGS--------------N 728
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 999 FLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD---GSIIQFQYGEDGVDVhrssf 1075
Cdd:COG0086 729 FREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVTEEDcgtDRGITVTAIKEGGEV----- 797
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1076 IEKFKE----LTINQDmVLQKCSEDMLSGASSYISDLPISL--KKGAEKFVEAMPMNERIASKFVRQEELLKLVKskffA 1149
Cdd:COG0086 798 IEPLKErilgRVAAED-VVDPGTGEVLVPAGTLIDEEVAEIieEAGIDSVKVRSVLTCETRGGVCAKCYGRDLAR----G 872
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1150 SLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEmnvtlgipRLQEILMTAAANIKTPIMTCPLLKGKTKEDANDITD 1229
Cdd:COG0086 873 HLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS--------RAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSR 944
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1230 RLRKITVADIIKSMELSVVPYTVYENEVCSIHKLKINLYKpEHYPKHTDITEEDWEETMR------AVFLRKLEDAIETH 1303
Cdd:COG0086 945 NSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVA-EWDPHTPPIIEEVGGGVVFddivegGVIVEKTDEETGGL 1023
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1304 MKMLHRIRGIHNDVTGPIAGNETDNDDSVSGKQNEDDGDDDGEGTEVDDLGSDAQKQKKQETDEMDyeensedetnepss 1383
Cdd:COG0086 1024 SIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIAR-------------- 1089
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15230368 1384 ISGVEDPEMDSENEDTEVSKEDTPEPQEESMEPQKEVKGVKNVKEQSKKKRRKFVRAKSDRHIFVKGEGEKFEVHF 1459
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 ... |
31-1048 |
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: 1134.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 31 RFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHPLLFNL 110
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 111 LFNFLQRACFFCHHFMAKPEDVERAVSQLKLIIKGDIVSAKQLESNtptkskssdescesvvttdsseecedsdvedqrw 190
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKLKLLDKGLLVEAAELDFG---------------------------------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 191 tslqfaevtavlknfmrlsskscsrckginpklekpmfgwvrmramkdsdvganvirglklkkstssvenpdgfddsgid 270
Cdd:cd01435 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 271 alsevedgdketrekstevaaefeehnskrdllpsevrnilkhlwqnehefcsfigdlwqsgsekidYSMFFLESVLVPP 350
Cdd:cd01435 127 -------------------------------------------------------------------YDMFFLDVLLVPP 139
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 351 TKFRPPTTGGDSVMEHPQTVGLNKVIESNNILGNACT---------------NKLDQSKVIFRWRNLQESVNVLFDSKTA 415
Cdd:cd01435 140 NRFRPPSFLGDKVFENPQNVLLSKILKDNQQIRDLLAsmrqaesqskldlisGKTNSEKLINAWLQLQSAVNELFDSTKA 219
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 416 TVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIIN 495
Cdd:cd01435 220 PKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVIN 299
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 496 GPDIHPGATHYSDKSSTM-KLPSTEKARRAIARKLLSSRGATTELgktcdiNFEGKTVHRHMRDGDIVLVNRQPTLHKPS 574
Cdd:cd01435 300 GPDVYPGANAIEDEDGRLiLLSALSEERRKALAKLLLLLSSAKLL------LNGPKKVYRHLLDGDVVLLNRQPTLHKPS 373
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 575 LMAHKVRVLKGEKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVL 654
Cdd:cd01435 374 IMAHKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVL 453
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 655 LTKRDTFLDKDHFNQLLFsSGVTDMVLSTFSGRsgkkvmvsasdaeLLTVTPAILKPVPLWTGKQVITAVLNQITKGHPP 734
Cdd:cd01435 454 LTSRDTFFTREEYQQLVY-AALRPLFTSDKDGR-------------IKLLPPAILKPKPLWTGKQVISTILKNLIPGNAP 519
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 735 FTVEkatklpvdffkcrsrevkpNSGDLTKKKEIDESWKQNLNEDKLHIRKNEFVCGVIDKAQFAD--YGLVHTVHELYG 812
Cdd:cd01435 520 LLNL-------------------SGKKKTKKKVGGGKWGGGSEESQVIIRNGELLTGVLDKSQFGAsaYGLVHAVYELYG 580
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 813 SNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENVGERVLRKTFGIdvdvqidpqdmrsrieri 892
Cdd:cd01435 581 GETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEFLGL------------------ 642
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 893 lyedgesalasldrsivnYLNQCSSKgVMNDLLSDGLLKTPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPR 972
Cdd:cd01435 643 ------------------KLNKVTSS-IIKACLPKGLLKPFPENNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPL 703
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15230368 973 MVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1048
Cdd:cd01435 704 MVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
334-1048 |
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 15230368 334 EKIDYSMFFLESVLVPPTKFRPPTtggdsvmehpqtvglnkviesnnilgnactnkldqsKVIFRWRNLQESVNVLFDSK 413
Cdd:cd00399 80 SFLGPEWMILTCLPVPPPCLRPSV------------------------------------IIEERWRLLQEHVDTYLDNG 123
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 414 TATVQ----SQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLtypervtpwnvekl 489
Cdd:cd00399 124 IAGQPqtqkSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL-------------- 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 490 reaiingpdihpgathysdksstmklpstekarraiarkllssrgattelgktcdinfegktvhrhmrDGDIVLVNRQPT 569
Cdd:cd00399 190 --------------------------------------------------------------------DGDPVLFNRQPS 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 570 LHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHI 649
Cdd:cd00399 202 LHKLSIMAHRVRVLPG-STFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTL 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 650 VSSVLLTKrdtfldkdhfnqllfssgvtdmvlstfsgrsgkkvmvsasdaelltvtpailkpvplwtGKQVITAVLNqit 729
Cdd:cd00399 281 LGAYLLTL-----------------------------------------------------------GKQIVSAALP--- 298
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 730 kghppftvekatklpvdffkcrsrevkpnsgdltkkkeideswkqnlnedklhirknefvcgvidkaqfadYGLVHTVHE 809
Cdd:cd00399 299 -----------------------------------------------------------------------GGLLHTVTR 307
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 810 LYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENVGERVLRKTFGIDVDVQIDPQDMrsri 889
Cdd:cd00399 308 ELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLE---- 383
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 890 erilyedgesalASLDRSIVNYLNQCSSKGVMNDLLSDGLlkTPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKR 969
Cdd:cd00399 384 ------------ESLEDNILDFLNEARDKAGSAASVNLDL--VSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKR 449
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15230368 970 VPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1048
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 ... |
26-1074 |
7.91e-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: 551.85 E-value: 7.91e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 26 VVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHP 105
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 106 LLFNLLFNFLQRACFFCHHFMAKPEDVERAVSQLKLIIKgdivsakqlesntptkskssdescesvvttdsseecedsdv 185
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKE----------------------------------------- 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 186 edqRWTSLQFAEVTAVLKNFMRlsSKSCSRCKGINPKLekpmfgwvrmramkdsdvganvirglKLKKSTSSVEnpdgfd 265
Cdd:cd02582 122 ---KWPELVKRVIEKVKKKAKK--RKVCPHCGAPQYKI--------------------------KLEKPTTFYE------ 164
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 266 dsgidalsevedgdketrekstevaaEFEEHNSKrdLLPSEVRNILkhlwqnehefcsfigdlwqsgsEKI---DYSMF- 341
Cdd:cd02582 165 --------------------------EKEEGEVK--LTPSEIRERL----------------------EKIpdeDLELLg 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 342 ----------FLESVL-VPPTKFRPPT---TGGDSvmEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVN 407
Cdd:cd02582 195 idpktarpewMVLTVLpVPPVTVRPSItleTGERS--EDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVT 272
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 408 VLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVT 482
Cdd:cd02582 273 TYFDNEIPGIPPARHRSGrplktLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVT 352
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 483 PWNVEKLREAIINGPDIHPGAThYSDKSSTMKLPSTEKARRAIARKLlssrgattelgktcdinfE-GKTVHRHMRDGDI 561
Cdd:cd02582 353 EWNIEKMRKLVLNGPDKWPGAN-YVIRPDGRRIRLRYVNREELAERL------------------EpGWIVERHLIDGDI 413
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 562 VLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPL 641
Cdd:cd02582 414 VLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPI 492
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 642 RALIQDHIVSSVLLTKRDTFLDKDHFNQLLfssgvtdmvlstfsgrsgkkvmvSASDAELLTVTPAILKPVPLWTGKQVI 721
Cdd:cd02582 493 IGGIQDYISGAYLLTRKTTLFTKEEALQLL-----------------------SAAGYDGLLPEPAILEPKPLWTGKQLF 549
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 722 TAVlnqitkghppftvekatkLPVDF-FKCRSrevKPNSGDLTKKKEIDEswkqnlNEDKLHIRKNEFVCGVIDKAQFAD 800
Cdd:cd02582 550 SLF------------------LPKDLnFEGKA---KVCSGCSECKDEDCP------NDGYVVIKNGKLLEGVIDKKAIGA 602
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 801 YG---LVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENvgervlrktfgiDVD 877
Cdd:cd02582 603 EQpgsLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEK------------KVY 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 878 vqidpqdmrSRIERilYEDGE-------SALASLDRSIVNYLNQCSSKGVmnDLLSDGLLKTpgrNCISLMTISGAKGSK 950
Cdd:cd02582 671 ---------ELIEQ--YKNGEleplpgrTLEETLEMKIMQVLGKARDEAG--KVASKYLDPF---NNAVIMARTGARGSM 734
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 951 VNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSG 1030
Cdd:cd02582 735 LNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSG 814
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|....
gi 15230368 1031 YLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHRSS 1074
Cdd:cd02582 815 YMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSD 858
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
23-1668 |
3.97e-167 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 542.69 E-value: 3.97e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 23 ASQVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPI 102
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 103 YHPLLFNLLFNFLQRACFFCHHFMAKPEDVeravSQLKLIikgdivsakqlesntptkskssdESCESVVTTDSSEECED 182
Cdd:PRK14977 85 IHIAFIDNIKDLLNSTCHKCAKLKLPQEDL----NVFKLI-----------------------EEAHAAARDIPEKRIDD 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 183 SDVEDQRWTSLQFAEvtavlknfmrlSSKSCSRCkginpklekpmfgwvrmramkdsdvGANVIRgLKLKKSTSSVENpd 262
Cdd:PRK14977 138 EIIEEVRDQVKVYAK-----------KAKECPHC-------------------------GAPQHE-LEFEEPTIFIEK-- 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 263 gfddsgidalsevedgdketrekstevaAEFEEHNskrdLLPSEVRNILKHLWQNEHEFCSFigdlwqsGSEKIDYSMFF 342
Cdd:PRK14977 179 ----------------------------TEIEEHR----LLPIEIRDIFEKIIDDDLELIGF-------DPKKARPEWAV 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 343 LESVLVPPTKFRPPT---TGGDSvmEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDSKTATV-- 417
Cdd:PRK14977 220 LQAFLVPPLTARPSIileTGERS--EDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIpq 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 418 ----QSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAI 493
Cdd:PRK14977 298 ahhkGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELV 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 494 INGPDIHPGAtHYSDKSSTMKlpstekarraIARKLLSSRG--ATTELGKTCDInfeGKTVHRHMRDGDIVLVNRQPTLH 571
Cdd:PRK14977 378 INGPDEFPGA-NAIRKGDGTK----------IRLDFLEDKGkdALREAAEQLEI---GDIVERHLADGDIVIFNRQPSLH 443
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 572 KPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVS 651
Cdd:PRK14977 444 KLSILAHRVKVLPG-ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITA 522
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 652 SVLLTKRDTFLDKDHFNQLLFSSGVTDMVLStfsgrsgkkvmvsasdaelltvtPAI-LKPVPLWTGKQVITAVlnqitk 730
Cdd:PRK14977 523 AYLITKDDALFDKNEASNIAMLAGITDPLPE-----------------------PAIkTKDGPAWTGKQLFSLF------ 573
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 731 ghppftvekatkLPVDFfkcrSREVKPNSGDLTKKKEIDESWkqnLNEDKLHIRKNEFVCGVIDKAQFADY-----GLVH 805
Cdd:PRK14977 574 ------------LPKDF----NFEGIAKWSAGKAGEAKDPSC---LGDGYVLIKEGELISGVIDDNIIGALveepeSLID 634
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 806 TVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIIlkdMDEERTKQLQECENVGERVLRKTFGIDVDVQIDPQDM 885
Cdd:PRK14977 635 RIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLII---PDEAKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKG 711
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 886 RSRIERILYEDgesalASLDRSIVNYLNQCSSK--GVMNDLLsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGQQ 963
Cdd:PRK14977 712 KEELLRGMKEE-----EALEADIVNELDKARDKagSSANDCI-------DADNAGKIMAKTGARGSMANLAQIAGALGQQ 779
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 964 D--------LEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRC 1035
Cdd:PRK14977 780 KrktrigfvLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRR 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1036 LMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHR---------SSFIEKFKELTINQDMVLQKCSEDMLSGASSYIS 1106
Cdd:PRK14977 860 LANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKldhgeafnlERIIEKQKIEDRGKGASKDEIEELAKEYTKTFNA 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1107 DLPISLkkgAEKFVEAMPMNERIaskfvrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEM 1186
Cdd:PRK14977 940 NLPKLL---ADAIHGAELKEDEL-------EAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAM 1009
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1187 NVTLGIPRLQEiLMTAAANIKTPIMTCpLLKGKTKED---ANDITDRLRKITVADIIKSMElsvvpyTVYENEVCSIhkl 1263
Cdd:PRK14977 1010 DVTHGLERFIE-LVDARAKPSTPTMDI-YLDDECKEDiekAIEIARNLKELKVRALIADSA------IDNANEIKLI--- 1078
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1264 kinlyKPEHypkhtditeedweetmravflRKLEDAIETHMKMLHRIRGIHNDVTGPIagnETDNDdsvsgkqneddgdd 1343
Cdd:PRK14977 1079 -----KPDK---------------------RALENGCIPMERFAEIEAALAKGKKFEM---ELEDD-------------- 1115
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1344 dgegTEVDDLGSDAQKQKKQETdemdyeensedetnepssISGVEDPEMDsenedtevskedtpepqeesmepqKEVKGV 1423
Cdd:PRK14977 1116 ----LIILDLVEAADRDKPLAT------------------LIAIRNKILD------------------------KPVKGV 1149
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1424 KNVKeqskkkrRKFVraksdrhifvkgegekfevhfkfatddphillaQIAQQTAQKVY-IQNSGkierctvancgdpqv 1502
Cdd:PRK14977 1150 PDIE-------RAWV---------------------------------ELVEKDGRDEWiIQTSG--------------- 1174
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1503 iyhgdnpkerreiSNDEKkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGI 1582
Cdd:PRK14977 1175 -------------SNLAA----VLEMKCI------------DIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGL 1225
|
1610 1620 1630 1640 1650 1660 1670 1680
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1583 SVSIRHLNLIADYMTFSG-----GYRPMSRMGGIA-ESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPAL 1656
Cdd:PRK14977 1226 EVDNRYIMLVADIMCSRGtieaiGLQAAGVRHGFAgEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIP 1305
|
1690
....*....|..
gi 15230368 1657 SGTGCFDLMQRV 1668
Cdd:PRK14977 1306 IGSGKVDLLMDF 1317
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
35-1052 |
1.91e-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: 525.19 E-value: 1.91e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 35 MTEQDVRKHSFLKVTSPILHDNV-GNPFPGGLYDLKLGPKDDKQACNSCGqLKLA-CPGHCGHIELVFPIYHPLLFNLLF 112
Cdd:cd02583 1 LSPEDIIRLSEVEVTNRNLYDIEtRKPLPYGVLDPRLGTSDKDGICETCG-LNLAdCVGHFGYIKLELPVFHIGYFKAII 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 113 NFLQRACFFCHHFMAKPEdvERAVSQLKLIIKGDIVSAKQLesntptKSKSSDESCESVvttdsseecedsdvedqrwts 192
Cdd:cd02583 80 NILQCICKTCSRVLLPEE--EKRKFLKRLRRPNLDNLQKKA------LKKKILEKCKKV--------------------- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 193 lqfaevtavlknfmrlssKSCSRCkginpklekpmfgwvrmramkdsdvganvirglklkkstssvenpdgfddsgiDAL 272
Cdd:cd02583 131 ------------------RKCPHC-----------------------------------------------------GLL 139
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 273 SEVEDgdketrekstevaaefeehnskrDLLPSEVRNILKhlwQNEHEFCSFIGDLwqsgSEKIDYSMFFLESVLVPPTK 352
Cdd:cd02583 140 KKAQE-----------------------DLNPLKVLNLFK---NIPPEDVELLLMN----PLAGRPENLILTRIPVPPLC 189
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 353 FRPPTTGGDSVM--EHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDSKT----ATVQSQRDSSGI 426
Cdd:cd02583 190 IRPSVVMDEKSGtnEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELpglpLSMQPKKPIRGF 269
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 427 CQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGATHY 506
Cdd:cd02583 270 CQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFV 349
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 507 SDKSSTMKlpsteKARRAIARKLLSSRGAttelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGe 586
Cdd:cd02583 350 IKRDGGKK-----KFLKYGNRRKIARELK------------IGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPW- 411
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 587 KTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDH 666
Cdd:cd02583 412 RTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQ 491
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 667 FNQLL--FSSGVTDMVLstfsgrsgkkvmvsasdaelltVTPAILKPVPLWTGKQVITAVLnqitkghppftvEKATKLP 744
Cdd:cd02583 492 FCQLCsyMLDGEIKIDL----------------------PPPAILKPVELWTGKQIFSLLL------------RPNKKSP 537
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 745 VDF-FKCRSREVKPNSGDLTkkkeIDESWkqnlnedkLHIRKNEFVCGVIDKAQFAD---YGLVHTVHELYGSNAAGNLL 820
Cdd:cd02583 538 VLVnLEAKEKSYTKKSPDMC----PNDGY--------VVIRNSELLCGRLDKSTLGSgskNSLFYVLLRDYGPEAAAAAM 605
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 821 SVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECENV--------GERVLRKTFGIDVDvqidpQDMRSRIERI 892
Cdd:cd02583 606 NRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKcdeyikqyKKGKLELQPGCTAE-----QTLEAKISGE 680
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 893 LyedgeSALasldRsivnylNQCSSkgVMNDLLSDgllktpgRNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPR 972
Cdd:cd02583 681 L-----SKI----R------EDAGK--ACLKELHK-------SNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPN 736
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 973 MVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYDCTVR 1052
Cdd:cd02583 737 GFEDRTLPHFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
21-1075 |
3.35e-166 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 526.73 E-value: 3.35e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 21 MGASQVVESVRFSFMTEQDVRKHSFLKVTSPILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVF 100
Cdd:PRK08566 3 MMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELAR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 101 PIYHPLLFNLLFNFLQRACFFCHHFMAKPEDVERAVSQLKliikgdivsakqlesntptkskssdescesvvttdsseec 180
Cdd:PRK08566 83 PVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLE---------------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 181 edsdvEDQRWTSLqfaeVTAVLKNFMRLSSK--SCSRC--KGINPKLEKPmfgwvrmramkdsdvganvirglklkksTS 256
Cdd:PRK08566 123 -----RLKEWGSL----ADDLIKEVKKEAAKrmVCPHCgeKQYKIKFEKP----------------------------TT 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 257 SVENpdgfddsgidalsevedgDKETREKstevaaefeehnskrdLLPSEVRNILkhlwqnehefcsfigdlwqsgsEKI 336
Cdd:PRK08566 166 FYEE------------------RKEGLVK----------------LTPSDIRERL----------------------EKI 189
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 337 ---DYSMFFLE-----------SVL-VPPTKFRPPTT---GGDSvmEHPQTVGLNKVIESN-----NILGNACTNKLDQs 393
Cdd:PRK08566 190 pdeDLELLGINpevarpewmvlTVLpVPPVTVRPSITletGQRS--EDDLTHKLVDIIRINqrlkeNIEAGAPQLIIED- 266
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 394 kvifRWRNLQESVNVLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIP 468
Cdd:PRK08566 267 ----LWELLQYHVTTYFDNEIPGIPPARHRSGrplktLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVP 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 469 PCFALKLTYPERVTPWNVEKLREAIINGPDIHPGAThYSDKSSTMKLPSTEKARRAIARKLLssrgattelgktcdinfE 548
Cdd:PRK08566 343 EAIAKELTVPERVTEWNIEELREYVLNGPEKHPGAN-YVIRPDGRRIKLTDKNKEELAEKLE-----------------P 404
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 549 GKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNA 628
Cdd:PRK08566 405 GWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPG-KTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLV 483
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 629 NNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLFSSGVTdmvlstfsgrsgkkvmvsasdaELLTVTPAI 708
Cdd:PRK08566 484 QEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGID----------------------ELPEPEPAI 541
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 709 LKPVPLWTGKQVITAVlnqitkghppftvekatkLPVDF-FKCRSrevKPNSGDLTKKKEIDEswkqnlNEDKLHIRKNE 787
Cdd:PRK08566 542 ENGKPYWTGKQIFSLF------------------LPKDLnLEFKA---KICSGCDECKKEDCE------HDAYVVIKNGK 594
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 788 FVCGVIDKAQFADYG--LVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLiilkDMDEERTKQLQECENVGE 865
Cdd:PRK08566 595 LLEGVIDKKAIGAEQgsILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDE----DIPEEAKEEIDEIIEEAE 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 866 RvlrktfgiDVDvqidpqdmrSRIERilYEDGESALA---SLDRSIVNYLNQCSSKG--VMNDLLSDGLLKTpgrNCISL 940
Cdd:PRK08566 671 K--------RVE---------ELIEA--YENGELEPLpgrTLEETLEMKIMQVLGKArdEAGEIAEKYLGLD---NPAVI 728
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 941 MTISGAKGSKVNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFISDRFLSGLRPQEYYFHCMAGREGLV 1020
Cdd:PRK08566 729 MARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLV 808
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*
gi 15230368 1021 DTAVKTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDVHRSSF 1075
Cdd:PRK08566 809 DTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDH 863
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
299-1048 |
6.36e-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: 6.36e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 299 KRDLLPSEVRNILKHLwqnEHEFCSFIG-DLwqsgsekiDYS---MFFLESVLVPPTKFRPP-TTGGDSVMEHPQTVGLN 373
Cdd:cd02733 93 KRELSAERVLEIFKRI---SDEDCRILGfDP--------KFSrpdWMILTVLPVPPPAVRPSvVMDGSARSEDDLTHKLA 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 374 KVIESNNILgNACTNKLDQSKVIFRWRN-LQESVNVLFDSKTATVQSQRDSSG-----ICQLLEKKEGLFRQKMMGKRVN 447
Cdd:cd02733 162 DIIKANNQL-KRQEQNGAPAHIIEEDEQlLQFHVATYMDNEIPGLPQATQKSGrplksIRQRLKGKEGRIRGNLMGKRVD 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 448 HACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGAThYSDKSSTMKlpstekarraIAR 527
Cdd:cd02733 241 FSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK-YIIRDDGER----------IDL 309
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 528 KLLSSRGattelgktcDINFE-GKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGD 606
Cdd:cd02733 310 RYLKKAS---------DLHLQyGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPY-STFRLNLSVTTPYNADFDGD 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 607 EMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLfssgvtdMVLSTFSG 686
Cdd:cd02733 380 EMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLL-------MWLPDWDG 452
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 687 RSGKkvmvsasdaelltvtPAILKPVPLWTGKQVITAVLNQITKghppftvekatklpvdffkcrsrEVKPNSGDLTKKK 766
Cdd:cd02733 453 KIPQ---------------PAILKPKPLWTGKQIFSLIIPKINN-----------------------LIRSSSHHDGDKK 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 767 EIdeswkqNLNEDKLHIRKNEFVCGVIDKAQFADY--GLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLI 844
Cdd:cd02733 495 WI------SPGDTKVIIENGELLSGILCKKTVGASsgGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTI 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 845 ILKDMDEERTKQLQECENVGERVLRKtfGIDVDVQIDP-QDMR----SRIERIL----YEDGESALASLDRSivnylnqc 915
Cdd:cd02733 569 ADKETMKKIQETIKKAKRDVIKLIEK--AQNGELEPQPgKTLResfeNKVNRILnkarDKAGKSAQKSLSED-------- 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 916 sskgvmndllsdgllktpgrNCISLMTISGAKGSKVNFQQISSHLGQQDLEGKRVPRMVSGKTLPCFHPWDWSPRAGGFI 995
Cdd:cd02733 639 --------------------NNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFV 698
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|...
gi 15230368 996 SDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYD 1048
Cdd:cd02733 699 ENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1146-1665 |
8.90e-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: 8.90e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1146 KFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTAAANIKTPIMTCPLLKGKTKEDAN 1225
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIKTPSMTLPLKNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1226 DITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinlykpehypkhtditeEDWEETMRAVFLRKLedaiethmk 1305
Cdd:cd02735 81 TLKKRLSRVTLSDVVEKVEV------------------------------------TEILKTIERVFKKLL--------- 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1306 mlhrirgihndvtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssis 1385
Cdd:cd02735 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1386 gvedpemdsenedtevskedtpepqeesmepqkevkgvknvkeqskkkrrkfvraksdrhifvkgeGEKFEVHFKFATDD 1465
Cdd:cd02735 116 ------------------------------------------------------------------GKWCEVTIKLPLSS 129
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1466 PHILLAQIAQQTAQKVYIQNSGKIERCTVANCgdpqviyhgdnpkerreisNDEKKASPALHASGVDFPALWEFQDKLDV 1545
Cdd:cd02735 130 PKLLLLSIVEKLARKAVIREIPGITRCFVVEE-------------------DKGGKTKYLVITEGVNLAALWKFSDILDV 190
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1546 RYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIAESTSPFCRMTFET 1625
Cdd:cd02735 191 NRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRI-GMESSTSPLQKMSFET 269
|
490 500 510 520
....*....|....*....|....*....|....*....|
gi 15230368 1626 ATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1665
Cdd:cd02735 270 TLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
339-653 |
4.02e-115 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 365.69 E-value: 4.02e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 339 SMFFLESVLVPPTKFRPPTTGGDS-VMEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDS---KT 414
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGrFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNeglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 415 ATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAII 494
Cdd:smart00663 81 ANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 495 NGPdihPGATHYSDKSSTMKlpsTEKARRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPS 574
Cdd:smart00663 161 NGP---NGAKYIIRGKKTNL---KLAKKSKIANHLK-----------------IGDIVERHVIDGDVVLFNRQPTLHRMS 217
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15230368 575 LMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSV 653
Cdd:smart00663 218 IQAHRVRVLEG-KTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
1002-1618 |
4.10e-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: 4.10e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1002 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLMKNLESLKVNYDCTVRDADGSIIQFQYGEDGVDV----------- 1070
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPlkiekqgrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1071 -HRSSFIEKFKELTINQDMVLQKCSEDMLSGASSYISDLPISLKKGAEKFVEAMPMNE-----RIASKFVRQ-------- 1136
Cdd:pfam04998 81 eFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSKEAQERATLLFElllksGLESKRVRSeltcnska 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1137 -EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTaAANIKTPIMTCPL 1215
Cdd:pfam04998 161 fVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINV-SKNIKSPSLTVYL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1216 L--KGKTKEDANDITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinLYKPehYPKHTDITEEdweetmravfl 1293
Cdd:pfam04998 240 FdeVGRELEKAKKVYGAIEKVTLGSVVESGEI---------------------LYDP--DPFNTPIISD----------- 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1294 rklEDAIETHMKMlhrirgiHNDVTgpiagnETDNDDSVSGKQNEddgdddgegtevddlgsdaqkqkkqetdemdyeeN 1373
Cdd:pfam04998 286 ---VKGVVKFFDI-------IDEVT------NEEEIDPETGLLIL----------------------------------V 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1374 SEDETNEPSSISGVedpemdsenedteVSKEDTPEPQEES-MEPQKEVKGVKNVKEQSKKKRRKfvraksdrhifvKGEG 1452
Cdd:pfam04998 316 IRLLKILNKSIKKV-------------VKSEVIPRSIRNKvDEGRDIAIGEITAFIIKISKKIR------------QDTG 370
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1453 EKFEVHFKFATDDPhiLLAQIAQQTAQKVYIQNSGKIERCTVancgdpqviyhgdnpkerREISNDEKKASPALHASGVD 1532
Cdd:pfam04998 371 GLRRVDELFMEEDP--KLAILVASLLGNITLRGIPGIKRILV------------------NEDDKGKVEPDWVLETEGVN 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1533 FPALWEFQDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIA 1612
Cdd:pfam04998 431 LLRVLLVPGFVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH-GIN 509
|
....*.
gi 15230368 1613 ESTSPF 1618
Cdd:pfam04998 510 KAELSA 515
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
443-628 |
4.03e-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: 4.03e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 443 GKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIINGPDIHPGATHYSDKS-STMKLpstEKA 521
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINgARRDL---RYQ 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 522 RRAIARKLLssrgattelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNA 601
Cdd:pfam00623 78 KRRLDKELE-----------------IGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPG-KTFRLNLSVTTPYNA 139
|
170 180
....*....|....*....|....*..
gi 15230368 602 DFDGDEMNVHFPQDEISRAEAYNIVNA 628
Cdd:pfam00623 140 DFDGDEMNLHVPQSEEARAEAEELMLV 166
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1137-1665 |
2.71e-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: 2.71e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1137 EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILmTAAANIKTPIMTCPLL 1216
Cdd:cd02584 9 DWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEII-NVAKNIKTPSLTVYLE 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1217 KG--KTKEDANDITDRLRKITVADIIKSMELsvvpytvyenevcsihklkinLYKPEhyPKHTDItEEDwEETMRAVF-L 1293
Cdd:cd02584 88 PGfaKDEEKAKKIQSRLEHTTLKDVTAATEI---------------------YYDPD--PQNTVI-EED-KEFVESYFeF 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1294 RKLEDAIETHMKMLHRIrgihndvtgpiagnETDNDDSVSGKQneddgdddgegtevdDLGSDAQKQKkqetdemdyeEN 1373
Cdd:cd02584 143 PDEDVEQDRLSPWLLRI--------------ELDRKKMTDKKL---------------SMEQIAKKIK----------EE 183
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1374 SEDETNEPSSISGVEDPEM-----DSENEDTEVSKEDTPEPQEES-MEPQKEVKGVKNVkeqskkkRRKFVRaKSDRHIF 1447
Cdd:cd02584 184 FKDDLNVIFSDDNAEKLVIririiNDDEEKEEDSEDDVFLKKIESnMLSDMTLKGIEGI-------RKVFIR-EENKKKV 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1448 VKGEGEkfevhfkFATDDPHILlaqiaqQTaqkvyiqnsgkierctvancgdpqviyhgdnpkerrEISNDEKkaspALH 1527
Cdd:cd02584 256 DIETGE-------FKKREEWVL------ET------------------------------------DGVNLRE----VLS 282
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1528 ASGVDFpalwefqdkldVRyLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSR 1607
Cdd:cd02584 283 HPGVDP-----------TR-TTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITR 350
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 15230368 1608 MGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1665
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 ... |
341-1052 |
4.11e-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: 209.95 E-value: 4.11e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 341 FFLESVLVPPTKFRPPTtggdsvMEHPQTVGlnkvieSNNILGNacTNKLDQSKVIFRWRnlqesvnvlfdsktatvqSQ 420
Cdd:cd10506 146 LFLKCLPVPPNCHRVTE------FTHGFSTG------SRLIFDE--RTRAYKKLVDFIGT------------------AN 193
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 421 RDSSGICQLLEKkeglFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLTYPERVTPWNVEKLREAIingpDIH 500
Cdd:cd10506 194 ESAASKKSGLKW----MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERLQEYC----DLT 265
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 501 PGathysdksstmklpstEKARRAIARK--LLSSRGaTTELGKtcdinfeGKTVHRHMRDGDIVLVNRQPTLHKPSLMAH 578
Cdd:cd10506 266 LL----------------LKGVIGVRRNgrLVGVRS-HNTLQI-------GDVIHRPLVDGDVVLVNRPPSIHQHSLIAL 321
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 579 KVRVLKGEKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKR 658
Cdd:cd10506 322 SVKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTER 401
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 659 DTFLDKDHFNQLlfssgvtdMVLSTFSgrsgkkvmvsasdaellTVTPAILK----PVPLWTGKQvitavLNQITkghpp 734
Cdd:cd10506 402 GVFLDKAQMQQL--------QMLCPSQ-----------------LPPPAIIKsppsNGPLWTGKQ-----LFQML----- 446
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 735 ftvekatkLPVDF-FKCRSREVKPNSGDLTKKKEIDeSWKQNLNedklhirknefvcgvidkaqfadyGLVHTVHELYGS 813
Cdd:cd10506 447 --------LPTDLdYSFPSNLVFISDGELISSSGGS-SWLRDSE------------------------GNLFSILVKHGP 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 814 NAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIIL------KDMDEERTKQLQECENVG--ERVLRKTFGIDVDVQIDPQDM 885
Cdd:cd10506 494 GKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSsdsysrQKMIEEISLGLREAEIACniKQLLVDSRKDFLSGSGEENDV 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 886 RSRIERILYEdgESALASLDRSIVnylnqCSSKGVMNDLLSDGLLKTPGRNCISLMTISGAKGSKVNFQQISSHLG-QQD 964
Cdd:cd10506 574 SSDVERVIYE--RQKSAALSQASV-----SAFKQVFRDIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGlQLS 646
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 965 LEGK----------------RVPRMVSGKTLPCFHPWDwsprAGGFISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTsr 1028
Cdd:cd10506 647 LVKLsyriprqlscaawnsqKSPRVIEKDGSECTESYI----PYGVVESSFLDGLNPLECFVHSITSRDSSFSSNADL-- 720
|
730 740
....*....|....*....|....
gi 15230368 1029 SGYLQRCLMKNLESLKVNYDCTVR 1052
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 ... |
1552-1661 |
4.37e-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: 4.37e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1552 SIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIV 1631
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 15230368 1632 QAATYGEKDTLETPSARICLGLPALSGTGC 1661
Cdd:cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1137-1667 |
8.52e-50 |
|
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: 181.29 E-value: 8.52e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1137 EELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILmTAAANIKTPIMTCPlL 1216
Cdd:cd06528 22 EEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV-DARKEPSTPTMTIY-L 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1217 KGKTKED---ANDITDRLRKITVADIIKSMELSVVPYTVyenevcsihklKINLYKpehypkhtditeedweetmravfl 1293
Cdd:cd06528 100 EEEYKYDrekAEEVARKIEETTLENLAEDISIDLFNMRI-----------TIELDE------------------------ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1294 RKLEDaiethmkmlhriRGIhndvtgpiagnetdnddsvsgkqneddgdddgegtEVDDLGSDAQKQKKQEtdemdyeen 1373
Cdd:cd06528 145 EMLED------------RGI-----------------------------------TVDDVLKAIEKLKKGK--------- 168
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1374 sedetnepssisgvedpEMDSENEDTEVSKEDTPEPQE-ESMEPQ---KEVKGVKNVKeqskkkrrkfvraksdRHIFVK 1449
Cdd:cd06528 169 -----------------VGEEGDVTLIVLKAEEPSIKElRKLAEKilnTKIKGIKGIK----------------RVIVRK 215
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1450 GEGEkfevhfkfatddphillaqiaqqtaqkvYiqnsgkierctvancgdpqVIY-HGDNPKErreisndekkaspALHA 1528
Cdd:cd06528 216 EEDE----------------------------Y-------------------VIYtEGSNLKA-------------VLKV 235
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1529 SGVDFpalwefqdkldvRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRM 1608
Cdd:cd06528 236 EGVDP------------TRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRH 303
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1609 GGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDL-MQR 1667
Cdd:cd06528 304 GIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELtMDP 363
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1108-1667 |
5.64e-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: 170.62 E-value: 5.64e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1108 LPISLKKGaekfVEAMPMNERIASKFvRQEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMN 1187
Cdd:TIGR02389 2 LPEKLLKE----LEETVKKREISDKE-ELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELN 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1188 VTLGIPRLQEILmTAAANIKTPIMTCPLLK--GKTKEDANDITDRLRKITVADIIKSMELSVVPYTVyenevcsihklki 1265
Cdd:TIGR02389 77 VTLGLPRLIEIV-DARKTPSTPSMTIYLEDeyEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTV------------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1266 nlykpehypkhtditeedweetmravflrkledAIETHMKMLHRiRGIhndvtgpiagnetdnddsvsgkqneddgdddg 1345
Cdd:TIGR02389 143 ---------------------------------IIELDEEQLKE-RGI-------------------------------- 156
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1346 egtEVDDLGSDAQKQKKQEtdemdyeensedetnepssisgvedpEMDSENEDTEVskedTPEPQEESMepqkevkgvkn 1425
Cdd:TIGR02389 157 ---TVDDVEKAIKKAKLGK--------------------------VIEIDMDNNTI----TIKPGNPSL----------- 192
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1426 vkeqskKKRRKfvRAKSDRHIFVKGegekfevhfkfatddphillaqiaqqtaqkvyIQNsgkIERCTVANCGDPQVIY- 1504
Cdd:TIGR02389 193 ------KELRK--LKEKIKNLHIKG--------------------------------IKG---IKRVVIRKEGDEYVIYt 229
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1505 HGDNPKErreisndekkaspALHASGVdfpalwefqdklDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISV 1584
Cdd:TIGR02389 230 EGSNLKE-------------VLKLEGV------------DKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDV 284
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1585 SIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDL 1664
Cdd:TIGR02389 285 DIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDL 364
|
...
gi 15230368 1665 MQR 1667
Cdd:TIGR02389 365 VMD 367
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
400-1261 |
1.31e-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: 1.31e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 400 RNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 475
Cdd:TIGR02386 279 RMLQEAVDALFDNgrrgKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALEL 358
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 476 TYPervtpwnveklreAIINGPDIHPGAthysdksstmklPSTEKARRAIARkllssrgattELGKTCDInFEgKTVHRH 555
Cdd:TIGR02386 359 FKP-------------FIIKRLIDRELA------------ANIKSAKKMIEQ----------EDPEVWDV-LE-DVIKEH 401
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 556 MrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 635
Cdd:TIGR02386 402 P-----VLLNRAPTLHRLGIQAFEPVLVEG-KAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNP 475
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 636 SNGEPLRALIQDHIVSSVLLTkrdtfldKDHFNQL----LFSSgVTDMVLSTFSGRSGKKVMVS-ASDAELLTVTPailk 710
Cdd:TIGR02386 476 KDGKPIVTPSQDMVLGLYYLT-------TEKPGAKgegkIFSN-VDEAIRAYDNGKVHLHALIGvRTSGEILETTV---- 543
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 711 pvplwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrsrevkP--NSGDLTKKKEIDEswkqnlnedklhirknef 788
Cdd:TIGR02386 544 ------GR----VIFNEI--------------LPEGF---------PyiNDNEPLSKKEISS------------------ 572
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 789 vcgvidkaqfadygLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEERTKQLQECEnvgervl 868
Cdd:TIGR02386 573 --------------LIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVA------- 631
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 869 rktfgidvdvQIDPQdmrsrierilYEDGesALASLDRsivnYLNQCSSKGVMNDLLSDGLLK-----TPGRNCISLMTI 943
Cdd:TIGR02386 632 ----------KIQKF----------YNKG--LITDEER----YRKVVSIWSETKDKVTDAMMKllkkdTYKFNPIFMMAD 685
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 944 SGAKGSKVNFQQISshlGQQDLEGKrvprmVSGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTA 1023
Cdd:TIGR02386 686 SGARGNISQFRQLA---GMRGLMAK-----PSGDIIE-------LP-----IKSSFREGLTVLEYFISTHGARKGLADTA 745
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1024 VKTSRSGYLQRCLMKNLESLKVNY-DC---------TVRDADGSIIQFQYgeDGVdVHRSSfIEKFKElTINQDMVLQkc 1093
Cdd:TIGR02386 746 LKTADSGYLTRRLVDVAQDVVVREeDCgteegieveAIVEGKDEIIESLK--DRI-VGRYS-AEDVYD-PDTGKLIAE-- 818
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1094 SEDMLSGASsyisdlpislkkgAEKFVEAmpmneRIASKFVRQE---ELLKLVKSKFF------ASLAQPGEPVGVLAAQ 1164
Cdd:TIGR02386 819 ANTLITEEI-------------AEKIENS-----GIEKVKVRSVltcESEHGVCQKCYgrdlatGKLVEIGEAVGVIAAQ 880
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1165 SVGEPSTQMTLNTFHL---AGRGEmNVTLGIPRLQEILMTAAANIKTPIMTcplLKGKTKEDANDITDRlRKItvadIIK 1241
Cdd:TIGR02386 881 SIGEPGTQLTMRTFHTggvAGASG-DITQGLPRVKELFEARTPKDKAVIAE---VDGTVEIIEDIVKNK-RVV----VIK 951
|
890 900
....*....|....*....|
gi 15230368 1242 SMELSVVPYTVYENEVCSIH 1261
Cdd:TIGR02386 952 DENDEEKKYTIPFGAQLRVK 971
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1088-1665 |
1.58e-43 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 163.86 E-value: 1.58e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1088 MVLQKCSEDMLSGASSyisDLPISLKKGAEKFVEAMPMNERIAskfvrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVG 1167
Cdd:PRK04309 1 MMSEETLEEKLEDASL---ELPQKLKEELREKLEERKLTEEEV------EEIIEEVVREYLRSLVEPGEAVGVVAAQSIG 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1168 EPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIlMTAAANIKTPIMTCPLLK--GKTKEDANDITDRLRKITVADIIKSMEl 1245
Cdd:PRK04309 72 EPGTQMTMRTFHYAGVAEINVTLGLPRLIEI-VDARKEPSTPMMTIYLKDeyAYDREKAEEVARKIEATTLENLAKDIS- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1246 svvpytvyenevcsihklkinlykpehypkhTDITEedweetMRAVflrkledaIETHMKMLHRiRGIhndvtgpiagne 1325
Cdd:PRK04309 150 -------------------------------VDLAN------MTII--------IELDEEMLED-RGL------------ 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1326 tdnddsvsgkqneddgdddgegtEVDDLGSDAQKQKKQETDEmdyeensedetnEPSSIsgvedpemdsenedtevsked 1405
Cdd:PRK04309 172 -----------------------TVDDVKEAIEKKKGGEVEI------------EGNTL--------------------- 195
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1406 tpepqeesmepqkevkgVKNVKEQSKKKRRKfvRAKSDRHIFVKGegekfevhfkfatddphillaqiaqqtaqkvyIQN 1485
Cdd:PRK04309 196 -----------------IISPKEPSYRELRK--LAEKIRNIKIKG--------------------------------IKG 224
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1486 sgkIERCTVANCGDPQVIY-HGDNPKErreisndekkaspALHASGVDFpalwefqdkldvRYLYSNSIHDMLNIFGVEA 1564
Cdd:PRK04309 225 ---IKRVIIRKEGDEYVIYtEGSNLKE-------------VLKVEGVDA------------TRTTTNNIHEIEEVLGIEA 276
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1565 ARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLET 1644
Cdd:PRK04309 277 ARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKG 356
|
570 580
....*....|....*....|.
gi 15230368 1645 PSARICLGLPALSGTGCFDLM 1665
Cdd:PRK04309 357 VTENIIVGQPIPLGTGDVELT 377
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1146-1662 |
8.74e-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: 8.74e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1146 KFFASLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIlMTAAANIKTPIMTCPLLKGKTKEDAN 1225
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEI-INASKNISTPIITAKLENDRDEKSAR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1226 DITDRLRKITVADIIKSMElsvvpyTVYENEVCSIhKLKINLykpehypkhtditeedweETMRAVFLRKLEdaiethmk 1305
Cdd:cd02736 80 IVKGRIEKTYLGEVASYIE------EVYSPDDCYI-LIKLDK------------------KIIEKLQLSKSN-------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1306 MLHRIRGIHNDVtgpiagnetdnddsvsgkqneddgdddgegtevddlgsdaqkqkkqetdemdyeensedetnepssis 1385
Cdd:cd02736 127 LYFLLQSLKRKL-------------------------------------------------------------------- 138
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1386 gvedpemdsenedtevskedtpepqeesmePQKEVKGVKNVKeqskkkrrkfvRAksdrHIFVKGEGEKFEVhfkfatdd 1465
Cdd:cd02736 139 ------------------------------PDVVVSGIPEVK-----------RA----VINKDKKKGKYKL-------- 165
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1466 phillaqiaqqtaqkvyiqnsgKIErctvancgdpqviyhGDNPKErreisndekkaspALHASGVDFpalwefqdkldv 1545
Cdd:cd02736 166 ----------------------LVE---------------GYGLRA-------------VMNTPGVIG------------ 183
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1546 RYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMgGIAE-STSPFCRMTFE 1624
Cdd:cd02736 184 TRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRF-GIAKmKESVLMLASFE 262
|
490 500 510
....*....|....*....|....*....|....*...
gi 15230368 1625 TATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCF 1662
Cdd:cd02736 263 KTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
400-1198 |
9.96e-41 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 165.43 E-value: 9.96e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 400 RNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 475
Cdd:PRK14906 375 RMLQEAVDSLFDNgrrgRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALEL 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 476 typerVTPWNVEKLREAiingpdihpgathysDKSSTMKlpsteKARRAIarkllsSRGATTelgkTCDINFEGKTVHrh 555
Cdd:PRK14906 455 -----FKPFVMKRLVEL---------------EYAANIK-----AAKRAV------DRGASY----VWDVLEEVIQDH-- 497
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 556 mrdgdIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 635
Cdd:PRK14906 498 -----PVLLNRAPTLHRLGIQAFEPVLVEG-KAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSP 571
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 636 SNGEPLRALIQDHIVSSVLLT-KRD-------TFLDKDhfNQLLFSSGVTDMVLSTFSGRSGKKVMVSASDAELLTVTPA 707
Cdd:PRK14906 572 AHGRPLTVPTQDMIIGVYYLTtERDgfegegrTFADFD--DALNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEETKA 649
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 708 ilkpvplwtGKQVITAV----LNQItkghppftvekatkLPVDFfkcrsrevkpnsgdltkkkeideswkqnlnedklhi 783
Cdd:PRK14906 650 ---------GERIETTVgriiFNQV--------------LPEDY------------------------------------ 670
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 784 rknEFVCGVIDKAQFAdyGLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDMDEertkQLQECEnv 863
Cdd:PRK14906 671 ---PYLNYKMVKKDIG--RLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPE----ILAEAD-- 739
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 864 gervlRKTFGIDVDvqidpqdmrsrierilYEDGESALASLDRSIVNYLNQCsskgvmNDLLSDGLLKT-PGRNCISLMT 942
Cdd:PRK14906 740 -----EKVAAIDED----------------YEDGFLSERERHKQVVDIWTEA------TEEVGEAMLAGfDEDNPIYMMA 792
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 943 ISGAKGSKVNFQQISSHLG-QQDLEGKRVPRmvsgktlPcfhpwdwspraggfISDRFLSGLRPQEYYFHCMAGREGLVD 1021
Cdd:PRK14906 793 DSGARGNIKQIRQLAGMRGlMADMKGEIIDL-------P--------------IKANFREGLSVLEYFISTHGARKGLVD 851
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1022 TAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-GSiiqfqygEDGV--DVHRSsfiekfkELTINQDMVLQKCSEDml 1098
Cdd:PRK14906 852 TALRTADSGYLTRRL------VDVAQDVIVREEDcGT-------DEGVtyPLVKP-------KGDVDTNLIGRCLLED-- 909
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1099 sgassyISDLPISLKKGAEKFVEAMPMNERIASKFVRQEELLKLV--KSKFFA---------SLAQP---GEPVGVLAAQ 1164
Cdd:PRK14906 910 ------VCDPNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMtcHAEYGVcqkcygwdlATRRPvniGTAVGIIAAQ 983
|
810 820 830
....*....|....*....|....*....|....
gi 15230368 1165 SVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEI 1198
Cdd:PRK14906 984 SIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAEL 1017
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
389-1182 |
2.49e-40 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 164.71 E-value: 2.49e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 389 KLDQSKVIFR--WRNLQESVNVLFDS--KTATVQ--SQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAV 462
Cdd:PRK09603 1673 ELGAPEIIVRneKRMLQEAVDVLFDNgrSTNAVKgaNKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKM 1752
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 463 NDIGIPPCFALKLTYPERVTpwnveKLREaiingpdihpgathySDKSSTMKlpsteKARRAIARKllssrgaTTELGKT 542
Cdd:PRK09603 1753 DECGLPKNMALELFKPHLLS-----KLEE---------------RGYATTLK-----QAKRMIEQK-------SNEVWEC 1800
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 543 CdinfegktvhRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEA 622
Cdd:PRK09603 1801 L----------QEITEGYPVLLNRAPTLHKQSIQAFHPKLIDG-KAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAEC 1869
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 623 YNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHfnqLLFSSgVTDMVLStfsgrsgkkvmVSASDAELL 702
Cdd:PRK09603 1870 KVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEH---KLFSS-VNEIITA-----------IDTKELDIH 1934
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 703 TVTPAILKPVPLWT--GKQVITAVLnqitkghPPFtvekatkLPVDFFKcrsrevKPnsgdlTKKKEIdeswkqnlnedk 780
Cdd:PRK09603 1935 AKIRVLDQGNIIATsaGRMIIKSIL-------PDF-------IPTDLWN------RP-----MKKKDI------------ 1977
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 781 lhirknefvcgvidkAQFADYglvhtVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLIILKDmdeeRTKQLQEC 860
Cdd:PRK09603 1978 ---------------GVLVDY-----VHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKD----KQKMVEKA 2033
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 861 envgervlrktfgidvdvqidpqdmRSRIERILYEDGESALASLDR-----SIVNYLNQCSSKGVMNDLLSDgllkTPGR 935
Cdd:PRK09603 2034 -------------------------KVEVKKIQQQYDQGLLTDQERynkiiDTWTEVNDKMSKEMMTAIAKD----KEGF 2084
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 936 NCISLMTISGAKGSKVNFQQISSHLGqqdLEGKRVPRMVSgktlpcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAG 1015
Cdd:PRK09603 2085 NSIYMMADSGARGSAAQIRQLSAMRG---LMTKPDGSIIE------------TP-----IISNFKEGLNVLEYFNSTHGA 2144
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1016 REGLVDTAVKTSRSGYLQRCLMKNLESLKVNY-DCTVrdadgsiiqfqygEDGVDVHR----SSFIEKFKELTINQDM-- 1088
Cdd:PRK09603 2145 RKGLADTALKTANAGYLTRKLIDVSQNVKVVSdDCGT-------------HEGIEITDiavgSELIEPLEERIFGRVLle 2211
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1089 -VLQKCSEDMLSGASSYISDlpislkKGAEKFVEAmpmneRIASKFVRQEELLKLVK---SKFF------ASLAQPGEPV 1158
Cdd:PRK09603 2212 dVIDPITNEILLYADTLIDE------EGAKKVVEA-----GIKSITIRTPVTCKAPKgvcAKCYglnlgeGKMSYPGEAV 2280
|
810 820
....*....|....*....|....
gi 15230368 1159 GVLAAQSVGEPSTQMTLNTFHLAG 1182
Cdd:PRK09603 2281 GVVAAQSIGEPGTQLTLRTFHVGG 2304
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1076-1667 |
9.20e-35 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 141.10 E-value: 9.20e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1076 IEKFKELTINQDmvlqkcSEDMLSGASSYISDLPISLkkgAEKFVEAMPMNERIASKFvrqEELLKLVKSKFFASLAQPG 1155
Cdd:PRK14897 115 EKEYYEENSNED------VLKVIDDVKKLGFRLPPSV---IEEIAKAMKKKELSDDEY---EEILRRIREEYERARVDPY 182
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1156 EPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEIlMTAAANIKTPIMTCpLLKGKTKEDANDITDRLRKI- 1234
Cdd:PRK14897 183 EAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEI-VDARKKPSTPTMTI-YLKKDYREDEEKVREVAKKIe 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1235 -----TVADIIKSM-ELSVvpyTVYENEvcsihklkinlykpehypkhtditeedweetmravflRKLEDaiethmkmlh 1308
Cdd:PRK14897 261 nttliDVADIITDIaEMSV---VVELDE-------------------------------------EKMKE---------- 290
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1309 riRGIhndvtgpiagnetdnddsvsgkqneddgdddgegtEVDDLGSDAQKQKKqETDEMDyeensedetnepssisgve 1388
Cdd:PRK14897 291 --RLI-----------------------------------EYDDILAAISKLTF-KTVEID------------------- 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1389 dpemdsenedtevSKEDTPEPQEESMEP---------QKEVKGVKNVKeqskkkrRKFVRAKSDRHIFVkgegekfevhf 1459
Cdd:PRK14897 314 -------------DGIIRLKPQQPSFKKlyllaekvkSLTIKGIKGIK-------RAIARKENDERRWV----------- 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1460 kfatddphillaqiaqqtaqkVYIQnsgkierctvancgdpqviyhGDNPKERREIsndekkaspalhasgvdfpalwef 1539
Cdd:PRK14897 363 ---------------------IYTQ---------------------GSNLKDVLEI------------------------ 376
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1540 qDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPMSRMGGIAESTSPFC 1619
Cdd:PRK14897 377 -DEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLA 455
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 15230368 1620 RMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLMQR 1667
Cdd:PRK14897 456 RAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYK 503
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
624-843 |
1.99e-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: 1.99e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 624 NIVNannqyarPSNGEPLRALIQDHIVSSVLLTKRDTFLDKDHFNQLLFSSGVTdmvlstfsgrsgkkvmvsasdaellt 703
Cdd:pfam04983 1 NILS-------PQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGIVL-------------------------- 47
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 704 VTPAILKPV-PLWTGKQVITAVLNQitkghppftvekatklpvdffkcrsrEVKPNSGDLTKKKEIdeswkqNLNEDKLH 782
Cdd:pfam04983 48 PHPAILKPIkPLWTGKQTFSRLLPN--------------------------EINPKGKPKTNEEDL------CENDSYVL 95
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15230368 783 IRKNEFVCGVIDKAQFAD--YGLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDL 843
Cdd:pfam04983 96 INNGELISGVIDKKTVGKslGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
371-1459 |
5.69e-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: 129.89 E-value: 5.69e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 371 GLNKVIESNNILgnACTNKLDQSKVIFR--WRNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGK 444
Cdd:COG0086 258 LYRRVINRNNRL--KRLLELKAPDIIVRneKRMLQEAVDALFDngrrGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGK 335
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 445 RVNHACRSVISPDPYIAVNDIGIPPCFALKLtyperVTPWNVEKLREAIIngpdihpgathysdkSSTMKlpsteKARRA 524
Cdd:COG0086 336 RVDYSGRSVIVVGPELKLHQCGLPKKMALEL-----FKPFIYRKLEERGL---------------ATTIK-----SAKKM 390
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 525 IARKllssrgaTTELGktcDINFEGKTVHRhmrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFD 604
Cdd:COG0086 391 VERE-------EPEVW---DILEEVIKEHP-------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFD 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 605 GDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLTKrdtfLDKDHFNQLLFSSGVTDMVLSTF 684
Cdd:COG0086 453 GDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTR----EREGAKGEGMIFADPEEVLRAYE 528
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 685 SGRsgkkvmvsasdAELLTVTPAILKPVPLWTGKQVITAV----LNQItkghppftvekatkLPVDFFKCRSrevkpnsg 760
Cdd:COG0086 529 NGA-----------VDLHARIKVRITEDGEQVGKIVETTVgrylVNEI--------------LPQEVPFYNQ-------- 575
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 761 dLTKKKEIdeswkQNLnedklhIRKNEFVCGVIDKAQFADyglvhtvhelygsnaagNLLSVFSRLFTVflqtHGFTCGV 840
Cdd:COG0086 576 -VINKKHI-----EVI------IRQMYRRCGLKETVIFLD-----------------RLKKLGFKYATR----AGISIGL 622
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 841 DDLIIlkdmDEERTKQLQECEnvgERVlrktfgidvdVQIDPQDMRSRIerilyEDGESALASLDrsIVNYLNQCSSKGV 920
Cdd:COG0086 623 DDMVV----PKEKQEIFEEAN---KEV----------KEIEKQYAEGLI-----TEPERYNKVID--GWTKASLETESFL 678
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 921 MNDLlsdgllktPGRNCISLMTISGAKGSKVNFQQISSHLGqqdLEGKRvprmvSGKT--LPCFHpwdwspraggfisdR 998
Cdd:COG0086 679 MAAF--------SSQNTTYMMADSGARGSADQLRQLAGMRG---LMAKP-----SGNIieTPIGS--------------N 728
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 999 FLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD---GSIIQFQYGEDGVDVhrssf 1075
Cdd:COG0086 729 FREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVTEEDcgtDRGITVTAIKEGGEV----- 797
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1076 IEKFKE----LTINQDmVLQKCSEDMLSGASSYISDLPISL--KKGAEKFVEAMPMNERIASKFVRQEELLKLVKskffA 1149
Cdd:COG0086 798 IEPLKErilgRVAAED-VVDPGTGEVLVPAGTLIDEEVAEIieEAGIDSVKVRSVLTCETRGGVCAKCYGRDLAR----G 872
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1150 SLAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEmnvtlgipRLQEILMTAAANIKTPIMTCPLLKGKTKEDANDITD 1229
Cdd:COG0086 873 HLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS--------RAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSR 944
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1230 RLRKITVADIIKSMELSVVPYTVYENEVCSIHKLKINLYKpEHYPKHTDITEEDWEETMR------AVFLRKLEDAIETH 1303
Cdd:COG0086 945 NSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVA-EWDPHTPPIIEEVGGGVVFddivegGVIVEKTDEETGGL 1023
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1304 MKMLHRIRGIHNDVTGPIAGNETDNDDSVSGKQNEDDGDDDGEGTEVDDLGSDAQKQKKQETDEMDyeensedetnepss 1383
Cdd:COG0086 1024 SIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIAR-------------- 1089
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15230368 1384 ISGVEDPEMDSENEDTEVSKEDTPEPQEESMEPQKEVKGVKNVKEQSKKKRRKFVRAKSDRHIFVKGEGEKFEVHF 1459
Cdd:COG0086 1090 IPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
265-1182 |
1.55e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 125.89 E-value: 1.55e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 265 DDSGIDALSEVEdGDKETREKSTEVaaefEEHNSKRDL------LPSEVR--NILKHLwqnehefcSFIGDLWQSGSEKi 336
Cdd:PRK14844 1601 DSYGIDSFVAMQ-GVEAIRELLTRL----DLHEIRKDLrlelesVASEIRrkKIIKRL--------RIVENFIKSGNRP- 1666
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 337 dySMFFLESVLVPPTKFRPPTTggdsvME--HPQTVGLN----KVIESNNILGNACTnkLDQSKVIFR--WRNLQESVNV 408
Cdd:PRK14844 1667 --EWMILTTIPILPPDLRPLVS-----LEsgRPAVSDLNhhyrTIINRNNRLRKLLS--LNPPEIMIRneKRMLQEAVDS 1737
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 409 LFD-SKTATVQSQRDSSG----ICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKLtyperVTP 483
Cdd:PRK14844 1738 LFDnSRRNALVNKAGAVGykksISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALEL-----FKP 1812
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 484 WNVEKLReaiINGpdihpgathysdKSSTMKLpstekarraiARKLLssRGATTELGKTCDinfegKTVHRHMrdgdiVL 563
Cdd:PRK14844 1813 FVYSKLK---MYG------------MAPTIKF----------ASKLI--RAEKPEVWDMLE-----EVIKEHP-----VL 1855
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 564 VNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRA 643
Cdd:PRK14844 1856 LNRAPTLHRLGIQAFEPILIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIV 1934
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 644 LIQDHIVSSVLLT----KRDTFLDKDHFNQLLFSsgVTDMVLSTFSGRSGKKVMVSaSDAEL----LTVTPAILkpvplw 715
Cdd:PRK14844 1935 PSKDIVLGIYYLTlqepKEDDLPSFGAFCEVEHS--LSDGTLHIHSSIKYRMEYIN-SSGEThyktICTTPGRL------ 2005
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 716 tgkqvitaVLNQITKGHppftvekatklpvdffkcrsrevkpnsgdltkkkeideswkQNLNEDKLHirknefvcgvidk 795
Cdd:PRK14844 2006 --------ILWQIFPKH-----------------------------------------ENLGFDLIN------------- 2023
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 796 aQFADYGLVHTVHELYGSNAAGNLLSVFS-RLFTVFLQTHGFTcGVddliilkdmdeertkQLQECenvgERVLRKTFGI 874
Cdd:PRK14844 2024 -QVLTVKEITSIVDLVYRNCGQSATVAFSdKLMVLGFEYATFS-GV---------------SFSRC----DMVIPETKAT 2082
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 875 DVDvqidpqDMRSRIER--ILYEDGESALASLDRSIVNYLNQCSSKgVMNDLLSDGLL--KTPGRNCISLMTISGAKGSK 950
Cdd:PRK14844 2083 HVD------HARGEIKKfsMQYQDGLITRSERYNKVIDEWSKCTDM-IANDMLKAISIydGNSKYNSVYMMVNSGARGST 2155
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 951 VNFQQISshlGQQDLEGKRvprmvSGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSG 1030
Cdd:PRK14844 2156 SQMKQLA---GMRGLMTKP-----SGEIIE-------TP-----IISNFREGLNVFEYFNSTHGARKGLADTALKTANSG 2215
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1031 YLQRCLMKNLESLKV-NYDCTVRdaDGSIIQfqygedgVDVHRSSFIEKFKELTINQ---DMVLQKCSEDMLSGASSYIS 1106
Cdd:PRK14844 2216 YLTRRLVDVSQNCIVtKHDCKTK--NGLVVR-------ATVEGSTIVASLESVVLGRtaaNDIYNPVTKELLVKAGELID 2286
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15230368 1107 DLPIslKKGAEKFVEAMPMNERIASKFvrQEELLKLVKSKFFAS--LAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAG 1182
Cdd:PRK14844 2287 EDKV--KQINIAGLDVVKIRSPLTCEI--SPGVCSLCYGRDLATgkIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGG 2360
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
400-1055 |
1.66e-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: 1.66e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 400 RNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 475
Cdd:cd01609 202 RMLQEAVDALIDngrrGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALEL 281
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 476 typerVTPWNVEKLreaiingpdIHPGATHysdkssTMKlpsteKARRAIARKllssrgaTTELgktCDInFEGKTVHRH 555
Cdd:cd01609 282 -----FKPFVIREL---------IERGLAP------NIK-----SAKKMIERK-------DPEV---WDI-LEEVIKGHP 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 556 mrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVHFPQDEISRAEAYNIVNANNQYARP 635
Cdd:cd01609 326 ------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSP 398
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 636 SNGEPLRALIQdhivssvlltkrdtfldkdhfnqllfssgvtDMVLSTF---SGRSGKKvmvsasDAELLTVTPailkpv 712
Cdd:cd01609 399 ASGKPIVTPSQ-------------------------------DMVLGLYyltKERKGDK------GEGIIETTV------ 435
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 713 plwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrsrevkPNSGDLTKKKEIdeswkqnlnedKLHIRKNEFVCGV 792
Cdd:cd01609 436 ----GR----VIFNEI--------------LPEGL---------PFINKTLKKKVL-----------KKLINECYDRYGL 473
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 793 IDKAQFADyglvhTVHELygsnaaGNLLSVFSrlftvflqthGFTCGVDDLIIlkdmDEERTKQLQECEnvgERVlrktf 872
Cdd:cd01609 474 EETAELLD-----DIKEL------GFKYATRS----------GISISIDDIVV----PPEKKEIIKEAE---EKV----- 520
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 873 gidvdvqidpqdmrSRIERiLYEDGESALASLDRSIVNYLNQCSSKgvMNDLLSDGLLKTPgRNCISLMTISGAKGSKVN 952
Cdd:cd01609 521 --------------KEIEK-QYEKGLLTEEERYNKVIEIWTEVTEK--VADAMMKNLDKDP-FNPIYMMADSGARGSKSQ 582
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 953 FQQISshlGQQDLegkrvprMV--SGKTLPcfhpwdwSPraggfISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSG 1030
Cdd:cd01609 583 IRQLA---GMRGL-------MAkpSGKIIE-------LP-----IKSNFREGLTVLEYFISTHGARKGLADTALKTADSG 640
|
650 660
....*....|....*....|....*
gi 15230368 1031 YLQRCLmknlesLKVNYDCTVRDAD 1055
Cdd:cd01609 641 YLTRRL------VDVAQDVIVTEED 659
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
35-175 |
9.53e-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: 9.53e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 35 MTEQDVRKHSFLKVTSPILHDNVGNPFP-GGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHPLLFNLLFN 113
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAErGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 114 FLQRACFF---------CHHFMAKPEDVERAVS-QLKLIIKGDIVSAKQLESNT-PTKS------------------KSS 164
Cdd:cd00399 81 FLGPEWMIltclpvpppCLRPSVIIEERWRLLQeHVDTYLDNGIAGQPQTQKSGrPLRSlaqrlkgkegrfrgnlmgKRV 160
|
170
....*....|.
gi 15230368 165 DESCESVVTTD 175
Cdd:cd00399 161 DFSGRSVISPD 171
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
400-1198 |
5.97e-26 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 116.71 E-value: 5.97e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 400 RNLQESVNVLFD----SKTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVNHACRSVISPDPYIAVNDIGIPPCFALKL 475
Cdd:PRK00566 287 RMLQEAVDALFDngrrGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALEL 366
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 476 TYP----------------------ERVTP--WNVekLREAIINgpdiHPgathysdksstmklpstekarraiarklls 531
Cdd:PRK00566 367 FKPfimkklverglattiksakkmvEREDPevWDV--LEEVIKE----HP------------------------------ 410
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 532 srgattelgktcdinfegktvhrhmrdgdiVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGDEMNVH 611
Cdd:PRK00566 411 ------------------------------VLLNRAPTLHRLGIQAFEPVLIEG-KAIQLHPLVCTAFNADFDGDQMAVH 459
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 612 FPQDEISRAEA-------YNIVNannqyarPSNGEPLraliqdhIVSS---VL----LTKRDTFLDKDHfnqLLFSSgvT 677
Cdd:PRK00566 460 VPLSLEAQAEArvlmlssNNILS-------PANGKPI-------IVPSqdmVLglyyLTREREGAKGEG---MVFSS--P 520
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 678 DMVLSTFsgRSGK-----KVMVSASDAELLTVTPailkpvplwtGKqvitAVLNQItkghppftvekatkLPVDFfkcrs 752
Cdd:PRK00566 521 EEALRAY--ENGEvdlhaRIKVRITSKKLVETTV----------GR----VIFNEI--------------LPEGL----- 565
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 753 revkP--NSGDLTKKKE----IDESWKQnlnedklhirknefvCGVIDKAQFADyglvhtvhelygsnaagNLLSVFSRL 826
Cdd:PRK00566 566 ----PfiNVNKPLKKKEiskiINEVYRR---------------YGLKETVIFLD-----------------KIKDLGFKY 609
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 827 FTVFlqthGFTCGVDDLIILkdmdEERTKQLQECEnvgERVlrktfgidvdvqidpqdmrSRIERiLYEDGesALASLDR 906
Cdd:PRK00566 610 ATRS----GISIGIDDIVIP----PEKKEIIEEAE---KEV-------------------AEIEK-QYRRG--LITDGER 656
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 907 --SIVNYLNQCSSK--GVMNDLLSDgllKTPGRNCISLMTISGAKGSKVNFQQISshlGQQDLEGKrvPrmvSGKT--LP 980
Cdd:PRK00566 657 ynKVIDIWSKATDEvaKAMMKNLSK---DQESFNPIYMMADSGARGSASQIRQLA---GMRGLMAK--P---SGEIieTP 725
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 981 cfhpwdwspraggfISDRFLSGLRPQEYYF--HcmaG-REGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-G 1056
Cdd:PRK00566 726 --------------IKSNFREGLTVLEYFIstH---GaRKGLADTALKTADSGYLTRRL------VDVAQDVIVREDDcG 782
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1057 SiiqfqygEDGVDVHR----SSFIEKFKEL----TINQDmVLQKCSEDMLSGASSYISDlpislkKGAEKFVEAmpmneR 1128
Cdd:PRK00566 783 T-------DRGIEVTAiiegGEVIEPLEERilgrVLAED-VVDPETGEVIVPAGTLIDE------EIADKIEEA-----G 843
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1129 IASKFVRQeellklV---KSKF----------FAS--LAQPGEPVGVLAAQSVGEPSTQMTLNTFHLAGrgeMNVTLGIP 1193
Cdd:PRK00566 844 IEEVKIRS------VltcETRHgvcakcygrdLATgkLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGG---VDITGGLP 914
|
....*
gi 15230368 1194 RLQEI 1198
Cdd:PRK00566 915 RVAEL 919
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
888-995 |
9.71e-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: 9.71e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 888 RIERILyedGESALASLDRSIVNYLNQCSSKgvMNDLLSDGLlktPGRNCISLMTISGAKGSKVNFQQISSHLGQQDLEG 967
Cdd:pfam05000 9 KLEDIW---GMTLEESFEALINNILNKARDP--AGNIASKSL---DPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 15230368 968 KRVPRMVSGKTLPCFHPWDWSPRAGGFI 995
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 ... |
1155-1202 |
8.39e-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: 8.39e-24
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 15230368 1155 GEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILMTA 1202
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
374-647 |
5.82e-22 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 103.06 E-value: 5.82e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 374 KVIESNNILGNACT--NKLDQSKVIFRWRNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVN 447
Cdd:CHL00018 298 RVIYRNNTLTDLLTtsRSTPGELVMCQKKLLQEAVDALLDNgirgQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVD 377
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 448 HACRSVISPDPYIAVNDIGIPPCFALKLTYPervtpwnveklreAIIngpdihpgathysdksstmklpstekaRRAIAR 527
Cdd:CHL00018 378 YSGRSVIVVGPSLSLHQCGLPREIAIELFQP-------------FVI---------------------------RGLIRQ 417
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 528 KLLSS-RGATTELGKTCDINFEgktVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGD 606
Cdd:CHL00018 418 HLASNiRAAKSKIREKEPIVWE---ILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEG-RAICLHPLVCKGFNADFDGD 493
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 15230368 607 EMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQD 647
Cdd:CHL00018 494 QMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQD 534
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
374-656 |
1.31e-21 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 101.75 E-value: 1.31e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 374 KVIESNNILgnACTNKLDQSKVIFR--WRNLQESVNVLFDS----KTATVQSQRDSSGICQLLEKKEGLFRQKMMGKRVN 447
Cdd:PRK02625 279 RVINRNNRL--ARLQEILAPEIIVRneKRMLQEAVDALIDNgrrgRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVD 356
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 448 HACRSVISPDPYIAVNDIGIPPCFALKLtyperVTPWNVEKL-REAIINgpDIhpgathysdksstmklpsteKArraiA 526
Cdd:PRK02625 357 YSGRSVIVVGPKLKMHQCGLPKEMAIEL-----FQPFVIHRLiRQGIVN--NI--------------------KA----A 405
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 527 RKLLSSRGAttelgktcdinfEGKTVHRHMRDGDIVLVNRQPTLHKPSLMAHKVRVLKGeKTLRLHYANCSTYNADFDGD 606
Cdd:PRK02625 406 KKLIQRADP------------EVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEG-RAIQLHPLVCPAFNADFDGD 472
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 15230368 607 EMNVHFPQDEISRAEAYNIVNANNQYARPSNGEPLRALIQDHIVSSVLLT 656
Cdd:PRK02625 473 QMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLT 522
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
27-439 |
4.47e-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: 4.47e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 27 VESVRFSFMTEQDVRKHSFLKVTSP-ILHDNVGNPFPGGLYDLKLGPKDDKQACNSCGQLKLACPGHCGHIELVFPIYHp 105
Cdd:pfam04997 4 IKEIQFGIASPEEIRKWSVGEVTKPeTYNYGSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFH- 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 106 llfnllfnflqracffchhfmakpedveraVSQLKLIIKgdIVsakqlesntptkskssdescesvvttdsseECedsdv 185
Cdd:pfam04997 83 ------------------------------IGFFKKTLK--IL------------------------------EC----- 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 186 edqrwtslqfaevtaVLKNfmrlssksCSRCKgINPKLEKPMFGWVRMRAMKDSDVGANVIRGLKLKKSTSSVENPDGFD 265
Cdd:pfam04997 96 ---------------VCKY--------CSKLL-LDPGKPKLFNKDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKNGV 151
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 266 DSGIDALSEVEDGDKETREKSTevaaefEEHNSKRDLLPSEVRNILKHLwqnEHEFCSFIGdLWQSGSeKIDYsmFFLES 345
Cdd:pfam04997 152 CGSQQPVSRKEGLKLKAAIKKS------KEEEEKEILNPEKVLKIFKRI---SDEDVEILG-FNPSGS-RPEW--MILTV 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 346 VLVPPTKFRPP-TTGGDSVMEHPQTVGLNKVIESNNILGNACTNKLDQSKVIFRWRNLQESVNVLFDS-----KTATVQS 419
Cdd:pfam04997 219 LPVPPPCIRPSvQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNeipglPPALQKS 298
|
410 420
....*....|....*....|
gi 15230368 420 QRDSSGICQLLEKKEGLFRQ 439
Cdd:pfam04997 299 KRPLKSISQRLKGKEGRFRG 318
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1526-1665 |
3.24e-20 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 97.66 E-value: 3.24e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1526 LHASGVDFPALWEFqDKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSGGYRPM 1605
Cdd:PRK14898 709 LYTQGSNLREVFKI-EGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPI 787
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1606 SRMGGIAESTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGCFDLM 1665
Cdd:PRK14898 788 GRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLR 847
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
792-1182 |
2.31e-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: 2.31e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 792 VIDKAQFADygLVHTVHELYGSNAAGNLLSVFSRLFTVFLQTHGFTCGVDDLII------LKDMDEERTKQLQECENVGE 865
Cdd:TIGR02388 6 VVDKKALKN--LISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVppakqdLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 866 --RVLRKTFGIDVdvqidpqdMRSRIERilyedgesalasLDRSIVNYLNQcsskgvmNDLLsdgllktpgrNCISLMTI 943
Cdd:TIGR02388 84 itEVERFQKVIDT--------WNGTNEE------------LKDEVVNNFRQ-------TDPL----------NSVYMMAF 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 944 SGAKGskvNFQQISSHLGQQDLEGKRVPRMVSgktLPcfhpwdwspraggfISDRFLSGLRPQEYYFHCMAGREGLVDTA 1023
Cdd:TIGR02388 127 SGARG---NMSQVRQLVGMRGLMANPQGEIID---LP--------------IKTNFREGLTVTEYVISSYGARKGLVDTA 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1024 VKTSRSGYLQRCLmknlesLKVNYDCTVRDADGSIiqfqygEDGVDVhrSSFIEKFKELTINQDMVLQKCSEDMLSGASS 1103
Cdd:TIGR02388 187 LRTADSGYLTRRL------VDVSQDVIVREEDCGT------ERSIVV--RAMTEGDKKISLGDRLLGRLVAEDVLHPEGE 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1104 YISDLPISLKKGAEKFVEAMPMNERIASKFVRQEELLKLVKSKFFASLAQP-----GEPVGVLAAQSVGEPSTQMTLNTF 1178
Cdd:TIGR02388 253 VIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTF 332
|
....
gi 15230368 1179 HLAG 1182
Cdd:TIGR02388 333 HTGG 336
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1155-1199 |
7.12e-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: 7.12e-12
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 15230368 1155 GEPVGVLAAQSVGEPSTQMTLNTFHLAGRGEmNVTLGIPRLQEIL 1199
Cdd:cd02655 6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELF 49
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
995-1182 |
4.79e-11 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 68.10 E-value: 4.79e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 995 ISDRFLSGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-----GSIIQfqyGEDGVD 1069
Cdd:PRK02597 159 IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRL------VDVSQDVIVREEDcgttrGIVVE---AMDDGD 229
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1070 VHRSSFIEKFKELTINQDMVLQKcsEDMLSGASSYIS-DLpislkkgAEKFVEAmpmneRIASKFVRQE---ELLKLVKS 1145
Cdd:PRK02597 230 RVLIPLGDRLLGRVLAEDVVDPE--GEVIAERNTAIDpDL-------AKKIEKA-----GVEEVMVRSPltcEAARSVCR 295
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 15230368 1146 KFFA-SLAQP-----GEPVGVLAAQSVGEPSTQMTLNTFHLAG 1182
Cdd:PRK02597 296 KCYGwSLAHNhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGG 338
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1541-1665 |
9.87e-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: 9.87e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1541 DKLDVRYLYSNSIHDMLNIFGVEAARETIIREINHVFKSYGISVSIRHLNLIADYMTFSG--------GYRPMSRMGGIa 1612
Cdd:cd02737 250 DLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGefvglnakGYKAQRRSLKI- 328
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 15230368 1613 esTSPFCRMTFETATKFIVQAATYGEKDTLETPSARICLGLPALSGTGC-FDLM 1665
Cdd:cd02737 329 --SAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSkFEIL 380
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1002-1182 |
1.43e-08 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 59.95 E-value: 1.43e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1002 GLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLmknlesLKVNYDCTVRDAD-GSIiqfqygedgvdvhRSSFIEKFk 1080
Cdd:CHL00117 172 GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRL------VEVVQHIVVRETDcGTT-------------RGISVSPR- 231
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15230368 1081 eltinQDMVLQKCSEDMLSG---ASS-YIS---------DLPISLkkgAEKFVEAmpmneRIASKFVR------------ 1135
Cdd:CHL00117 232 -----NGMMIERILIQTLIGrvlADDiYIGsrciatrnqDIGIGL---ANRFITF-----RAQPISIRspltcrstswic 298
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 15230368 1136 ---------QEELLKLvkskffaslaqpGEPVGVLAAQSVGEPSTQMTLNTFHLAG 1182
Cdd:CHL00117 299 qlcygwslaHGDLVEL------------GEAVGIIAGQSIGEPGTQLTLRTFHTGG 342
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1107-1175 |
6.25e-08 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 57.60 E-value: 6.25e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15230368 1107 DLPISLKkgaEKFVEAMPMNERIASKFVrqEELLKLVKSKFFASLAQPGEPVGVLAAQSVGEPSTQMTL 1175
Cdd:PRK14898 14 DLPRSLK---DELFEKLSKRDGVTEEMV--EEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
