|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1-1499 |
0e+00 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 1029.89 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1 MKFR-TPIFFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGV 79
Cdd:CHL00117 1 MAERaNLVFHNKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 80 EAAQALETGNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRATNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAI 159
Cdd:CHL00117 81 ILEKHYHYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 160 LEFPIQSNFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITFKGLH-------I 232
Cdd:CHL00117 161 IDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNgmmieriL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 233 EQNLLGRVLLKDVILNTTTVIPKDTLVSSSLAKKLAAIN-QKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGI 311
Cdd:CHL00117 241 IQTLIGRVLADDIYIGSRCIATRNQDIGIGLANRFITFRaQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGI 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 312 IAAQSIGEPGTQLTMRTFHTGGVgvFSEQAMKSFPAPFDGKIEFQEALPGRfVRTPYGKIVYLLKhtgtnpKQVLLRVVS 391
Cdd:CHL00117 321 IAGQSIGEPGTQLTLRTFHTGGV--FTGGTAEQVRAPFNGKIKFNEDLVHP-TRTRHGHPAFLCK------IDLYVTIES 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 392 ssltmrplvYEILHQ-DVPAGSLLWVKQGEDVRTGQLLVQ---GSRLQKSKQKMpesTHIVRTPFSGELFFEHMPIVSLE 467
Cdd:CHL00117 392 ---------EDIIHNvNIPPKSLLLVQNDQYVESEQVIAEiraGTSTLNFKEKV---RKHIYSDSEGEMHWSTDVYHAPE 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 468 KIitrgprtnpkeefSPIKVFLKDLGRFWVFSSFIQKQTFSFLDQKKGKANSFFfkgDLVSAETPLSQYNLQIPVRGHLK 547
Cdd:CHL00117 460 FT-------------YGNVHLLPKTSHLWILSGGVYRSSLVSFSLHKDQDQINI---HLSVERRYISRLSVINTNNGQVR 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 548 KLGSS------------VVLAQTVFKFcFSKIYYFSKFYflvENQNLIASTTTLNFT--------------------SLT 595
Cdd:CHL00117 524 HKLFSsdgkkekrildySELNRIISNG-HCNFIYPAILH---ENSDLLAKRRRNRFLipfqsiqerekelmpcgisiEIP 599
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 596 WYPFFNQFETSGYYVDLSF-SSDSEVLK--------------TTELTKVKSETYDFTKNGG--FFTSHQSFVGSTTRVFL 658
Cdd:CHL00117 600 INGILRRNSIFAYFDDPRYrTKSSGITKygtievdsivkkedLIEYRGVKEFKPKYQMKVDrfFFIPEEVHILPESSSIL 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 659 LKTFEFFSAASKQTQKTALERLPFVdsmsfslekiQLKKqNQKRKENPLFSLEVGKVKRNTQqrLPQFGFMVTceENSLS 738
Cdd:CHL00117 680 VRNNSIIGVDTQITLNIRSKVGGLV----------RIEK-KKKRIELKIFSGDIHFPGETDK--ISRHSGILI--PPGTG 744
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 739 RKGIFQIKKAqeKNWSHKKTFQLSfllnpkkrkkplkkhfmcsslflekavkraqttfgiqtetklieKKcswfsvsKNF 818
Cdd:CHL00117 745 KKNSKESKKI--KNWIYVQRITPT--------------------------------------------KK-------KYF 771
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 819 tdfssqltgIVLEPGKHMESfsfqHSYVSVNLISRENVFLVKSKTKRSQFSYVlkdLLSSSRFCHKVfeKNFSEQK---- 894
Cdd:CHL00117 772 ---------VLVRPVVTYEI----ADGINLATLFPQDLLQEKDNLQLRVVNYI---LYGNGKPIRGI--SSIQLVRtclv 833
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 895 ---MESVeKISQIFSSQTESFFSRNNQLLSFFSQKKRIKNKLFFhsqlnfpskMPRRSDvLNSSKLLFFTREFLSDFSFY 971
Cdd:CHL00117 834 lnwDQDK-KSSSIEEARASFVEVRTNGLIRDFLRINLVKSPISY---------IRKRND-PSSSGLLVQSNNFLDSTNIY 902
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 972 KRKELIQKRERKPH-TLQNIKVKNKkflqviqpcfqlkkkrCLSNLFFLQKLSYqiFPERKFFYETWLNQSSFDFSLPSP 1050
Cdd:CHL00117 903 SKAEIQSQSLSQNQgTIRTLLNRNK----------------ESQSLLILSSSDC--FRIGPFNGKKSKYHNIKESNPLIP 964
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1051 FstkqFKTTGFFSKNeLQKASFdfqpsFLSQKISSSSQLtLRGSWVSMTNSFKIhFEVKTPKFFgkieefqqkkffdkkl 1130
Cdd:CHL00117 965 I----RNSLGPLGTV-LQIANF-----SSSYHLLTHNQI-LVTKYLQLDNLKQT-FQVKVLKYY---------------- 1016
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1131 kfgiqspskslskalsfgipipefslavsrkiifekahtyifqsfqcrqvlpkvpitqvflksktvgefqriqlkNQKGS 1210
Cdd:CHL00117 1017 ---------------------------------------------------------------------------LIDEN 1021
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1211 SSFLRAEDTVTFLLPSLVPKKqSFLKKEEKVLVScgQRIRWGQEIFPGFASSL-----SGRILDITATQITVRKALPFLG 1285
Cdd:CHL00117 1022 GKIYNPDPCSNIILNPFNLNW-YFLHHNYCEETS--TIISLGQFICENVCISKngphkSGQIIIVQVDSLVIRSAKPYLA 1098
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1286 SRRGLVHVAQNDLLQKNHILMTLRSKQLQTEDIVQGIPKIEQLFEAREtkdGEIIRYNMHFRLNSFF----SLAKRVKPF 1361
Cdd:CHL00117 1099 TPGATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARS---IDSISMNLEKRLEGWNeritRILGIPWGF 1175
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1362 LEAFDLSLLYIQRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVRITF-GKDTSLLPGEFIQLRLLEEINRSLveakK 1440
Cdd:CHL00117 1176 LIGAELSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEdGMSNVFLPGELIGLLRAERINRAL----E 1251
|
1530 1540 1550 1560 1570
....*....|....*....|....*....|....*....|....*....|....*....
gi 196128985 1441 EPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLRGLMKPLYVASL 1499
Cdd:CHL00117 1252 EAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGL 1310
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
6-499 |
7.43e-156 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 508.77 E-value: 7.43e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 6 PIFFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAA--SVSGVEAAQ 83
Cdd:PRK02597 1 PIFRNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAeeEITATEERY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 84 ALetGNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRATNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFP 163
Cdd:PRK02597 81 RR--GEITEVERFQKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLP 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 164 IQSNFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITFKGL--------HIEQN 235
Cdd:PRK02597 159 IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMddgdrvliPLGDR 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 236 LLGRVLLKDVILNTTTVI-PKDTLVSSSLAKKLAAIN-QKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGIIA 313
Cdd:PRK02597 239 LLGRVLAEDVVDPEGEVIaERNTAIDPDLAKKIEKAGvEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIA 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 314 AQSIGEPGTQLTMRTFHTGgvGVFSEQAMKSFPAPFDGKIEFQEALPGRFVRTPYGKIVYL--------LKHTGTNPKQV 385
Cdd:PRK02597 319 AQSIGEPGTQLTMRTFHTG--GVFTGEVARQVRSPFAGTVEFGKKLRTRPYRTRHGVEALQaevdfdlvLKPSGKGKPQK 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 386 LlrvvsssltmrplvyeilhqDVPAGSLLWVKQGEDVRTGQLLVQ--GSRLQKSKQKmpeSTHIVRTPFSGELFFEhmPI 463
Cdd:PRK02597 397 I--------------------EITQGSLLFVDDGQTVEADQLLAEvaAGAVKKSTEK---ATKDVICDLAGEVRFA--DL 451
|
490 500 510 520
....*....|....*....|....*....|....*....|..
gi 196128985 464 VSLEKI-----ITR-GPRtnpkeefspikvflkdLGRFWVFS 499
Cdd:PRK02597 452 IPEEKTdrqgnTTRkAQR----------------GGLLWVLS 477
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
7-499 |
2.63e-147 |
|
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: 482.81 E-value: 2.63e-147
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 7 IFFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALE 86
Cdd:TIGR02388 1 IFKNRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 87 TGNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRATNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFPIQS 166
Cdd:TIGR02388 81 RGEITEVERFQKVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 167 NFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITF-------KGLHIEQNLLGR 239
Cdd:TIGR02388 161 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVramtegdKKISLGDRLLGR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 240 VLLKDVILNTTTVI-PKDTLVSSSLAKKLAAIN-QKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGIIAAQSI 317
Cdd:TIGR02388 241 LVAEDVLHPEGEVIvPKNTAIDPDLAKTIETAGiSEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSI 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 318 GEPGTQLTMRTFHTGgvGVFSEQAMKSFPAPFDGKIEFQEALPGRFVRTPYGKIVYLLKHTGtnpkqVLLRVVSSSLTMR 397
Cdd:TIGR02388 321 GEPGTQLTMRTFHTG--GVFTGEVARQVRSKIDGTVEFGKKLRTRGYRTRHGEDAKQVEVAG-----LLIIKPTGSITNK 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 398 PLVYeilhqDVPAGSLLWVKQGEDVRTGQLLVQGSrLQKSKQKMPESTHIVRTPFSGELFFEHmpIVSLEKIITRGPRTN 477
Cdd:TIGR02388 394 AQEI-----EVTQGSLLFVEDGQTVDAGQLLAEIA-LGAVRKSTEKATKDVASDLAGEVKFDK--VVPEEKTDRQGNTTR 465
|
490 500
....*....|....*....|..
gi 196128985 478 PKEEfspikvflkdLGRFWVFS 499
Cdd:TIGR02388 466 IAQR----------GGLIWVLS 477
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
7-432 |
9.18e-135 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 446.44 E-value: 9.18e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 7 IFFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAAS--VSGVEaaQA 84
Cdd:PRK00566 568 INVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEkeVAEIE--KQ 645
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 85 LETGNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRAT-NPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFP 163
Cdd:PRK00566 646 YRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDqESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETP 725
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 164 IQSNFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITFKGL--------HIEQN 235
Cdd:PRK00566 726 IKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIieggeviePLEER 805
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 236 LLGRVLLKDVILNTT--TVIPKDTLVSSSLAKKLAAIN-QKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGII 312
Cdd:PRK00566 806 ILGRVLAEDVVDPETgeVIVPAGTLIDEEIADKIEEAGiEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVI 885
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 313 AAQSIGEPGTQLTMRTFHTGGV---------------------GVFSEqamksfpapFDGKIEFQEALPGR---FVRTPY 368
Cdd:PRK00566 886 AAQSIGEPGTQLTMRTFHTGGVditgglprvaelfearkpkgpAIIAE---------IDGTVSFGKETKGKrriVITPDD 956
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 196128985 369 G-KIVYLlkhtgtnpkqvllrvvsssltmrplvyeilhqdVPAGSLLWVKQGEDVRTGQLLVQGS 432
Cdd:PRK00566 957 GeEREYL---------------------------------IPKGKHLLVQEGDHVEAGDKLTDGS 988
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
10-432 |
1.32e-116 |
|
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: 395.57 E-value: 1.32e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 10 NVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALETGN 89
Cdd:TIGR02386 562 NEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGL 641
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 90 LTSVEKSQRLIDTWNKTSESLRQAAVHNFRA-TNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFPIQSNF 168
Cdd:TIGR02386 642 ITDEERYRKVVSIWSETKDKVTDAMMKLLKKdTYKFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSF 721
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 169 REGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGI----TFKGLH-----IEQNLLGR 239
Cdd:TIGR02386 722 REGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIeveaIVEGKDeiiesLKDRIVGR 801
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 240 VLLKDVILNTT--TVIPKDTLVSSSLAKKLAAIN-QKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGIIAAQS 316
Cdd:TIGR02386 802 YSAEDVYDPDTgkLIAEANTLITEEIAEKIENSGiEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQS 881
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 317 IGEPGTQLTMRTFHTGGVGVFSEQAMKSFPapfdgkiEFQEALPgrfVRTPYGKIVyLLKHTGT--------NPKQVLlr 388
Cdd:TIGR02386 882 IGEPGTQLTMRTFHTGGVAGASGDITQGLP-------RVKELFE---ARTPKDKAV-IAEVDGTveiiedivKNKRVV-- 948
|
410 420 430 440
....*....|....*....|....*....|....*....|....
gi 196128985 389 VVSSSLTMRPLVYeilhqdVPAGSLLWVKQGEDVRTGQLLVQGS 432
Cdd:TIGR02386 949 VIKDENDEEKKYT------IPFGAQLRVKDGDSVSAGDKLTEGS 986
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
8-355 |
8.42e-103 |
|
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: 356.78 E-value: 8.42e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 8 FFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALET 87
Cdd:COG0086 572 FYNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQYAE 651
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 88 GNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRatnPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFPIQSN 167
Cdd:COG0086 652 GLITEPERYNKVIDGWTKASLETESFLMAAFS---SQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPIGSN 728
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 168 FREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITFKGL--------HIEQNLLGR 239
Cdd:COG0086 729 FREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDRGITVTAIkeggeviePLKERILGR 808
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 240 VLLKDVI--LNTTTVIPKDTLVSSSLAKKLA-AINQKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGIIAAQS 316
Cdd:COG0086 809 VAAEDVVdpGTGEVLVPAGTLIDEEVAEIIEeAGIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVIAAQS 888
|
330 340 350
....*....|....*....|....*....|....*....
gi 196128985 317 IGEPGTQLTMRTFHTGGVGVFSEQAmKSFPAPFDGKIEF 355
Cdd:COG0086 889 IGEPGTQLTMRTFHIGGAASRAAEE-SSIEAKAGGIVRL 926
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
8-432 |
4.21e-92 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 329.14 E-value: 4.21e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 8 FFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALET 87
Cdd:PRK14906 672 YLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYED 751
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 88 GNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRATNPVnpvYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFPIQSN 167
Cdd:PRK14906 752 GFLSERERHKQVVDIWTEATEEVGEAMLAGFDEDNPI---YMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKAN 828
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 168 FREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITF-----KGlHIEQNLLGRVLL 242
Cdd:PRK14906 829 FREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYplvkpKG-DVDTNLIGRCLL 907
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 243 KDVI-LNTTTVIPKDTLVSS--SLAKKLAAINQKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGIIAAQSIGE 319
Cdd:PRK14906 908 EDVCdPNGEVLLSAGDYIESmdDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGE 987
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 320 PGTQLTMRTFHTGGV-GVFSEQAMKSFPAPFDgkiefqealpgrfVRTPYGKIVyLLKHTGT-----NPKQVLLRVVSSS 393
Cdd:PRK14906 988 PGTQLTMRTFHSGGVaGDDITQGLPRVAELFE-------------ARKPKGEAV-LAEISGTlqitgDKTEKTLTIHDQD 1053
|
410 420 430
....*....|....*....|....*....|....*....
gi 196128985 394 LTMRPLVYEILHQDVPAgsllwVKQGEDVRTGQLLVQGS 432
Cdd:PRK14906 1054 GNSREYVVSARVQFMPG-----VEDGVEVRVGQQITRGS 1087
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
8-340 |
1.09e-85 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 311.47 E-value: 1.09e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 8 FFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALET 87
Cdd:PRK09603 1967 LWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQ 2046
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 88 GNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRATNP-VNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFPIQS 166
Cdd:PRK09603 2047 GLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKDKEgFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIIS 2126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 167 NFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITFKGLHI--------EQNLLG 238
Cdd:PRK09603 2127 NFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVgselieplEERIFG 2206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 239 RVLLKDVI--LNTTTVIPKDTLVSSSLAKKLAAINQK-IFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGIIAAQ 315
Cdd:PRK09603 2207 RVLLEDVIdpITNEILLYADTLIDEEGAKKVVEAGIKsITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQ 2286
|
330 340
....*....|....*....|....*
gi 196128985 316 SIGEPGTQLTMRTFHTGGVGVFSEQ 340
Cdd:PRK09603 2287 SIGEPGTQLTLRTFHVGGTASRSQD 2311
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
8-214 |
9.87e-85 |
|
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: 292.12 E-value: 9.87e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 8 FFNVSFDKNTLKTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALET 87
Cdd:cd01609 450 FINKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQYEK 529
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 88 GNLTSVEKSQRLIDTWNKTSESLRQAAVHNFRaTNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFPIQSN 167
Cdd:cd01609 530 GLLTEEERYNKVIEIWTEVTEKVADAMMKNLD-KDPFNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPIKSN 608
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 196128985 168 FREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVI 214
Cdd:cd01609 609 FREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIV 655
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
30-425 |
5.54e-74 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 274.19 E-value: 5.54e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 30 GGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQALETGNLTSVEKSQRLIDTWNKTSES 109
Cdd:PRK14844 2043 GQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDM 2122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 110 LRQ---AAVHNFRATNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAILEFPIQSNFREGLTITEYLLSCYGARK 186
Cdd:PRK14844 2123 IANdmlKAISIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARK 2202
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 187 GLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITFKGL--------HIEQNLLGRVLLKDvILNTTTvipKDTL 258
Cdd:PRK14844 2203 GLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATvegstivaSLESVVLGRTAAND-IYNPVT---KELL 2278
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 259 VSSSL---AKKLAAIN----QKIFVRSPLTCQTEKTVCQLCYGLDLAQGKLVCFGEAVGIIAAQSIGEPGTQLTMRTFHT 331
Cdd:PRK14844 2279 VKAGElidEDKVKQINiaglDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHI 2358
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 332 GGV---GVFSEQAMKSFPApfdgKIEFQEAlpgrfvrtpygKIVyllkhTGTNPKQVLLRVVSSSLTMRPLVYEILHQDV 408
Cdd:PRK14844 2359 GGVmtrGVESSNIIASINA----KIKLNNS-----------NII-----IDKNGNKIVISRSCEVVLIDSLGSEKLKHSV 2418
|
410
....*....|....*..
gi 196128985 409 PAGSLLWVKQGEDVRTG 425
Cdd:PRK14844 2419 PYGAKLYVDEGGSVKIG 2435
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1155-1490 |
1.19e-57 |
|
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: 219.34 E-value: 1.19e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1155 SLAVSRKIIFEKAHTYIFQSFQCR---QVLPKVPITQVFLKSKTVGEFQRIQlknqKGSSSF-----LRAEDTVTFLLPS 1226
Cdd:TIGR02388 823 SLVLRRDIASDSTQGSTHTSLLVKdgdLIKPGAVIARTQILCKEAGVVQGID----SGGESIrrllvERNSDRLKVNIKA 898
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1227 lvpkkqsflkkeeKVLVSCGQRIRWGQEIFPGFASSLSGRILDITATQITVRKALPFLGSRRGLVHVAQNDLLQKNHILM 1306
Cdd:TIGR02388 899 -------------KPVVKTGDLVVAGDELAKGVKAEESGEIEEVASDYVILRIGRPYRVSPGAVLHIEDGDLVQRGDNLA 965
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1307 TLRSKQLQTEDIVQGIPKIEQLFEARETK------------------------------DGEIIRY-------------- 1342
Cdd:TIGR02388 966 LLVFERAKTGDIVQGLPRIEELLEARKPKeacilakrpgvvqvkygtddesvsikvierDGTISEYpllpgqnimvsdgq 1045
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1343 -------------NMHFRLNSFFSLAKRVKPFLEAFDLSLLYIQRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVRI 1409
Cdd:TIGR02388 1046 qvtggepltdgpiNPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRI 1125
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1410 TFGKDTSLLPGEFIQLRLLEEINRSLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLRG 1489
Cdd:TIGR02388 1126 DDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRG 1205
|
.
gi 196128985 1490 L 1490
Cdd:TIGR02388 1206 L 1206
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1214-1490 |
3.54e-56 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 214.86 E-value: 3.54e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1214 LRAEDTVTfllpslvpkkqsfLKKEEKVLVSCGQRIRWGQEIFPGFASSLSGRILDITATQITVRKALPFLGSRRGLVHV 1293
Cdd:PRK02597 888 ERDEDTIT-------------IPLSGKPTVKVGDLVVAGDELAPGVPAPESGEVEAVSGGSVTLRLGRPYRVSPGAVLHV 954
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1294 AQNDLLQKNHILMTL---RSKqlqTEDIVQGIPKIEQLFEARETK-----------------------------DGEIIR 1341
Cdd:PRK02597 955 RDGDLVQRGDNLALLvfeRAK---TGDIIQGLPRIEELLEARKPKescilakkpgtvqikygddesvdvkviesDGTITE 1031
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1342 Y---------------------------NMHFRLNSFFSLAKRVKPFLEAFDLSLLYIQRFLVKTLLEAYSNQGVNIAEK 1394
Cdd:PRK02597 1032 YpilpgqnvmvsdgqqvdagepltdgpiNPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDK 1111
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1395 HVEVVVRQMTARVRITFGKDTSLLPGEFIQLRLLEEINRSLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKV 1474
Cdd:PRK02597 1112 HIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRV 1191
|
330
....*....|....*.
gi 196128985 1475 LVRSALATKTDFLRGL 1490
Cdd:PRK02597 1192 LTEAAIEGKSDWLRGL 1207
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1317-1490 |
8.75e-55 |
|
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: 189.66 E-value: 8.75e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1317 DIVQGIPKIEQLFEARETKDGEIIRYnmhfrlnsffslakrvkpfleaFDLSLLYIQRFLVKTLLEAYSNQGVNIAEKHV 1396
Cdd:cd02655 37 DITQGLPRVEELFEARKINPHDLLRI----------------------KFLGPEAVQKYLVEEIQKVYRSQGVNINDKHI 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1397 EVVVRQMTARVRITFGKDTSLLPGEFIQLRLLEEINRSLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLV 1476
Cdd:cd02655 95 EIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLT 174
|
170
....*....|....
gi 196128985 1477 RSALATKTDFLRGL 1490
Cdd:cd02655 175 EAAIEGKIDWLRGL 188
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
171-335 |
4.32e-44 |
|
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: 168.69 E-value: 4.32e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 171 GLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVIYTKNCKTEKGITF----------KGLHIEqnLLGRV 240
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIvqflygedglDPLKIE--KQGRF 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 241 LLKDV-------ILNTTTVIPKDTLVSSSLAKKLAAINQK-----------------------------IFVRSPLTCQT 284
Cdd:pfam04998 79 TIEFSdlkledkFKNDLLDDLLLLSEFSLSYKKEILVRDSklgrdrlskeaqeratllfelllksglesKRVRSELTCNS 158
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 196128985 285 EKTVCQLCYGLDLAQGKLVCFGEAVGIIAAQSIGEPGTQLTMRTFHTGGVG 335
Cdd:pfam04998 159 KAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVA 209
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
24-214 |
2.71e-40 |
|
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: 157.59 E-value: 2.71e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 24 WFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDL----QIPPQKASFLSAASVSGVEAAQALETGNLTSVEKSQ-- 97
Cdd:cd00399 304 TVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDViddgVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTle 383
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 98 -----RLIDTWNKTSESLRQAAVHNFRATNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGAI------------- 159
Cdd:cd00399 384 esledNILDFLNEARDKAGSAASVNLDLVSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIprgfsdrtlphfs 463
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 196128985 160 -------LEFPIQSNFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQHVVI 214
Cdd:cd00399 464 kddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVV 525
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1317-1490 |
2.33e-39 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 160.23 E-value: 2.33e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1317 DIVQGIPKIEQLFEAR-----------------------------ETKDGEIIRYNMHFRlnsffslaKRVK----PFLE 1363
Cdd:PRK00566 908 DITGGLPRVAELFEARkpkgpaiiaeidgtvsfgketkgkrriviTPDDGEEREYLIPKG--------KHLLvqegDHVE 979
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1364 AFD-LS--------LLYI------QRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVRITFGKDTSLLPGEFIQLRLL 1428
Cdd:PRK00566 980 AGDkLTdgsidphdILRVlgveavQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEF 1059
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 196128985 1429 EEINRSLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLRGL 1490
Cdd:PRK00566 1060 EEENRKLIAEGKEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGL 1121
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
1315-1490 |
4.15e-37 |
|
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: 152.90 E-value: 4.15e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1315 TEDIVQGIPKIEQLFEARETK--------DGEI--------------IRYNMHFRLNSFFSLAK--RVKPFLE------- 1363
Cdd:TIGR02386 903 SGDITQGLPRVKELFEARTPKdkaviaevDGTVeiiedivknkrvvvIKDENDEEKKYTIPFGAqlRVKDGDSvsagdkl 982
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1364 ---AFDL-SLLYI------QRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVRITFGKDTSLLPGEFIQLRLLEEINR 1433
Cdd:TIGR02386 983 tegSIDPhDLLRIkgiqavQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENR 1062
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 196128985 1434 SLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLRGL 1490
Cdd:TIGR02386 1063 KLLEQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGL 1119
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1291-1490 |
1.06e-24 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 113.09 E-value: 1.06e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1291 VHVAQNDLLQKNHILMTLRSKQLQTEDIVQGIPKIEQLFEARETK----------DGEI-----IRYNMHFRLNS----- 1350
Cdd:PRK09603 2616 IAISDGSSVEQAEVLAKIPKATVKSRDITGGLPRVSELFEARKPKpkdvailsevDGIVsfgkpIRNKEHIIVTSkdgrs 2695
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1351 ---FFSLAKRV----KPFLEAFDL---------SLLYI------QRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVR 1408
Cdd:PRK09603 2696 mdyFVDKGKQIlvhaDEFVHAGEAmtdgvvsshDILRIsgekelYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVR 2775
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1409 ITFGKDTSLLPGEFIQLRLLEEINRSLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLR 1488
Cdd:PRK09603 2776 ILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLE 2855
|
..
gi 196128985 1489 GL 1490
Cdd:PRK09603 2856 DL 2857
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
1307-1490 |
5.46e-24 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 110.35 E-value: 5.46e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1307 TLRSKQLQTEDIVQGIPKIEQLFEARETKDGEII------------------------------RYNMHFRLNSFFSLAK 1356
Cdd:PRK14906 996 TFHSGGVAGDDITQGLPRVAELFEARKPKGEAVLaeisgtlqitgdktektltihdqdgnsreyVVSARVQFMPGVEDGV 1075
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1357 RVKP-------FLEAFDLSLLY----IQRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVRITFGKDTSLLPGEFIQL 1425
Cdd:PRK14906 1076 EVRVgqqitrgSVNPHDLLRLTdpntTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNR 1155
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 196128985 1426 RLLEEINRSLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLRGL 1490
Cdd:PRK14906 1156 YEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGL 1220
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
1311-1499 |
1.56e-20 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 99.31 E-value: 1.56e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1311 KQLQTEDIVQGIPKIEQLFEARETKDGEII-RYNMHFRLNSFFSLAKR---VKP------------------------FL 1362
Cdd:PRK14844 2546 ESVKTRDITGGLPRVIELFEARRPKEHAIVsEIDGYVAFSEKDRRGKRsilIKPvdeqispveylvsrskhvivnegdFV 2625
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 1363 EAFDL---------------SLLYIQRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVRITFGKDTSLLPGEFIQLRL 1427
Cdd:PRK14844 2626 RKGDLlmdgdpdlhdilrvlGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLE 2705
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 196128985 1428 LEEINRSLVEAKKEPALYEPVILGLTKSVLQSESFLLAASFQQVSKVLVRSALATKTDFLRGLMKPLYVASL 1499
Cdd:PRK14844 2706 VDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRL 2777
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
20-334 |
5.02e-20 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 97.40 E-value: 5.02e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 20 TVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPpQKASFLSAASVSGVEAaqalETGNLTSVEKSQRL 99
Cdd:PRK14977 631 SLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIP-DEAKQEIEDDIQGMKD----EVSDLIDQRKITRK 705
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 100 IDTWNKTSESLR---------------------QAAVHNFRATNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQGA 158
Cdd:PRK14977 706 ITIYKGKEELLRgmkeeealeadivneldkardKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRI 785
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 159 ILEFP----------------------------IQSNFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQ 210
Cdd:PRK14977 786 GFVLTggrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALE 865
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 211 HV-VIYTKNCKTEKG--ITF----------KGLHIEQNLLGRVLLKDVILNTTTVIPKDTLvsSSLAKKLAAINQKIFVR 277
Cdd:PRK14977 866 DIrLEYDETVRDPHGhiIQFkfgedgidpqKLDHGEAFNLERIIEKQKIEDRGKGASKDEI--EELAKEYTKTFNANLPK 943
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 196128985 278 S---------PLTCQTEKTVCQLCYGLDLAQgklVCFGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 334
Cdd:PRK14977 944 LladaihgaeLKEDELEAICAEGKEGFEKAK---VEPGQAIGIISAQSIAEPGTQMTLRTFHAAGI 1006
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
301-334 |
1.90e-19 |
|
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: 88.35 E-value: 1.90e-19
10 20 30
....*....|....*....|....*....|....
gi 196128985 301 KLVCFGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 334
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 34
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
13-214 |
1.38e-18 |
|
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: 92.31 E-value: 1.38e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 13 FDKNTL-----KTVIAWFLDQYGGKATVDLVETLKQVGFHQATRAGVSLGLEDLQIPPqkasflsaasvsgvEAAQALET 87
Cdd:cd02582 595 IDKKAIgaeqpGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPE--------------EARKEIEE 660
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 88 GNLTSVEKSQRLIDTWNK-------------TSESLRQAAVHNFRAT---------NPVNPVYMMAFSGARGNISQVRQL 145
Cdd:cd02582 661 IIKEAEKKVYELIEQYKNgeleplpgrtleeTLEMKIMQVLGKARDEagkvaskylDPFNNAVIMARTGARGSMLNLTQM 740
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 146 VAM------------RGLM-------------ADPQGaileFpIQSNFREGLTITEYLLSCYGARKGLVDTALRTASAGY 200
Cdd:cd02582 741 AAClgqqsvrgerinRGYRnrtlphfkpgdlgPEARG----F-VRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGY 815
|
250
....*....|....
gi 196128985 201 LTRRLVDAVQHVVI 214
Cdd:cd02582 816 MQRRLINALQDLYV 829
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
90-169 |
7.06e-17 |
|
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: 77.79 E-value: 7.06e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 90 LTSVEKSQRLIDTWNKTSESLRQAAVHNF-------------RATNPVNPVYMMAFSGARGNISQVRQLVAMRGLMADPQ 156
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNIlnkardpagniasKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 196128985 157 GAI---------------LEFPIQSNFR 169
Cdd:pfam05000 81 KRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
50-210 |
2.80e-16 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 84.91 E-value: 2.80e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 50 TRAGVSLGLEDLQIPPQKASFLSAASVSGVEAAQAL----ETGNLT-----SVEKS--QRLIDTWNKTSESLRQAAVHNF 118
Cdd:PRK08566 641 MLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELieayENGELEplpgrTLEETleMKIMQVLGKARDEAGEIAEKYL 720
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 119 ratNPVNPVYMMAFSGARG---NISQVRQLV---AMRG-------------------LMADPQGaileFpIQSNFREGLT 173
Cdd:PRK08566 721 ---GLDNPAVIMARTGARGsmlNLTQMAACVgqqSVRGerirrgyrdrtlphfkpgdLGAEARG----F-VRSSYKSGLT 792
|
170 180 190
....*....|....*....|....*....|....*..
gi 196128985 174 ITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDAVQ 210
Cdd:PRK08566 793 PTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQ 829
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
306-334 |
5.11e-13 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 72.57 E-value: 5.11e-13
10 20
....*....|....*....|....*....
gi 196128985 306 GEAVGIIAAQSIGEPGTQLTMRTFHTGGV 334
Cdd:PRK04309 59 GEAVGVVAAQSIGEPGTQMTMRTFHYAGV 87
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
306-334 |
1.85e-12 |
|
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: 70.74 E-value: 1.85e-12
10 20
....*....|....*....|....*....
gi 196128985 306 GEAVGIIAAQSIGEPGTQLTMRTFHTGGV 334
Cdd:cd06528 40 GEAVGIVAAQSIGEPGTQMTLRTFHYAGV 68
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
306-336 |
4.67e-12 |
|
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: 65.52 E-value: 4.67e-12
10 20 30
....*....|....*....|....*....|.
gi 196128985 306 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVGV 336
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVAS 31
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
306-334 |
1.05e-11 |
|
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: 68.54 E-value: 1.05e-11
10 20
....*....|....*....|....*....
gi 196128985 306 GEAVGIIAAQSIGEPGTQLTMRTFHTGGV 334
Cdd:TIGR02389 44 GEAVGIVAAQSIGEPGTQMTMRTFHYAGV 72
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
299-334 |
1.31e-11 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 69.07 E-value: 1.31e-11
10 20 30
....*....|....*....|....*....|....*.
gi 196128985 299 QGKLVCFGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 334
Cdd:PRK14897 175 ERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGV 210
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
306-335 |
8.45e-10 |
|
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: 61.85 E-value: 8.45e-10
10 20 30
....*....|....*....|....*....|
gi 196128985 306 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVG 335
Cdd:cd02736 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVA 39
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
306-335 |
3.08e-09 |
|
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: 60.28 E-value: 3.08e-09
10 20 30
....*....|....*....|....*....|
gi 196128985 306 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVG 335
Cdd:cd02735 10 GEAVGLLAAQSIGEPSTQMTLNTFHFAGRG 39
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
306-335 |
2.38e-08 |
|
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: 57.99 E-value: 2.38e-08
10 20 30
....*....|....*....|....*....|
gi 196128985 306 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVG 335
Cdd:cd02584 27 GEMVGTIAAQSIGEPATQMTLNTFHFAGVS 56
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
125-215 |
7.53e-07 |
|
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: 54.08 E-value: 7.53e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 125 NPVYMMAFSGARG---NISQVRQLVA--------------MRGL---MADPQGAILEFPIQSNFREGLTITEYLLSCYGA 184
Cdd:cd02733 639 NNFKAMVTAGSKGsfiNISQIIACVGqqnvegkripfgfrRRTLphfIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGG 718
|
90 100 110
....*....|....*....|....*....|.
gi 196128985 185 RKGLVDTALRTASAGYLTRRLVDAVQHVVIY 215
Cdd:cd02733 719 REGLIDTAVKTAETGYIQRRLVKAMEDVMVK 749
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
164-208 |
6.66e-06 |
|
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: 51.01 E-value: 6.66e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 196128985 164 IQSNFREGLTITEYLLSCYGARKGLVDTALRTASAGYLTRRLVDA 208
Cdd:cd02583 759 VANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKA 803
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|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
265-334 |
1.14e-05 |
|
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: 50.16 E-value: 1.14e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196128985 265 KKLAAINQKIFV--RSPLTCQTEKTVC--QLCYGLDLAQGK---LVCFGEAVGI----IAAQSIGEpgTQLTMRTFHTGG 333
Cdd:COG0086 29 KKPETINYRTFKpeRDGLFCERIFGPCkdYECYCGKYKRMVykgVVCEKCGVEVtlskVRRERMGH--IELAMPVFHIWG 106
|
.
gi 196128985 334 V 334
Cdd:COG0086 107 L 107
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
1373-1415 |
1.49e-04 |
|
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: 46.19 E-value: 1.49e-04
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 196128985 1373 QRFLVKTLLEAYSNQGVNIAEKHVEVVVRQMTARVRITFGKDT 1415
Cdd:pfam04998 464 RNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
307-326 |
1.12e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.73 E-value: 1.12e-03
|
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