|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
38-950 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 954.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKGSLPLME---------------LPTDHTVLREKRIPPWMEVVLIp 416
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLErevkeklqkqlskkkDLTPQLLINSKPITSGIKEFLA- 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 417 mTGKPSLYPGLFLFTTPC--------------------------------RLVRP-------------------VQNLAL 445
Cdd:cd00653 298 -TGNWGSKRFLMQRSGLSqvldrlnplselshkrrisslglfrerkgfevRDLHPshwgricpietpegencglVKNLAL 376
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 446 gKEELIGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSD 525
Cdd:cd00653 377 -MARISGRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMD 447
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 526 NKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQG 605
Cdd:cd00653 448 TKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGP 527
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 606 DSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDNIKV 671
Cdd:cd00653 528 EEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDDVKI 607
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 672 CSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMA 751
Cdd:cd00653 608 FSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 752 GKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRT 831
Cdd:cd00653 688 GKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARS 763
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 832 TGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnr 911
Cdd:cd00653 764 TGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA--------------- 828
|
970 980 990
....*....|....*....|....*....|....*....
gi 544346215 912 kYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 950
Cdd:cd00653 829 -NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
487-846 |
1.95e-180 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 526.71 E-value: 1.95e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 487 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 566
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 567 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 645
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 646 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 710
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 711 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 790
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 544346215 791 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 846
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
38-951 |
5.81e-162 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 504.11 E-value: 5.81e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 38 LTRAHVESFNYAVHEGLGLAVQA-------IPPFEFAFKDERI---SFTILDAVISPptvpkgtickeanVYPAECRGRR 107
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVgepEIKEADGSERP-------------ITPMEARLRN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 108 STYRGKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMP 185
Cdd:PRK08565 81 LTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 186 RRnfpiamIRPKWKTRGPGYTqygvsmhcvreeHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFAL 253
Cdd:PRK08565 161 NR------VLVDKGEAGSSIT------------HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILM 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 254 KAL-----------VSfSDYQIFQELIKGKEDdsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQ 322
Cdd:PRK08565 219 RALgletdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIER 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 323 AAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPG----QLFLMFLKGSLPLMEL 394
Cdd:PRK08565 281 AEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGdllaELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 395 PTDHTVLREKRIP-------------------------------------PWMEV------VLIPMT-GKP-----SLYP 425
Cdd:PRK08565 360 QLEKSYARGRKLDlraivrpdiiterirhalatgnwvggrtgvsqlldrtNYLSTlshlrrVVSPLSrGQPhfearDLHG 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 426 G----LFLFTTP----CRLVRpvqNLAL---------------------------GKEELIGTMEQIFMN---------- 460
Cdd:PRK08565 440 TqwgrICPFETPegpnCGLVK---NLALmaqisvgvdeeeveeilyelgvvpveeAREEEYISWSRVYLNgrligyhpdg 516
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 461 ---------------------VAI----------------------------------------------FEDEVFAGV- 472
Cdd:PRK08565 517 eelaekirelrrsgkisdevnVAYietgeinevyvncdsgrvrrplivvengkpkltrehveklkkgeltFDDLVKMGVi 596
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 473 -----------------------TTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLY 529
Cdd:PRK08565 597 eyldaeeeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGH 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 530 RLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK---- 603
Cdd:PRK08565 677 LLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypgg 751
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 604 QGD-----SSLVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKE 662
Cdd:PRK08565 752 QEDkieipEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGE 827
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 663 NCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 742
Cdd:PRK08565 828 KGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 743 IGMLIESMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHM 822
Cdd:PRK08565 905 VGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHM 980
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 823 VSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekpp 902
Cdd:PRK08565 981 VADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH---------- 1050
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....*....
gi 544346215 903 PSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 951
Cdd:PRK08565 1051 IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
402-951 |
1.34e-144 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 442.93 E-value: 1.34e-144
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 402 REKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGKEELigtmEQIFMNVAIFEDEVFAGVT--- 473
Cdd:TIGR03670 26 RSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTREHV----EKLKEGELTWDDLVKQGVIeyl 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 474 ---------------------THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ 532
Cdd:TIGR03670 96 daeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLH 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 533 TPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGS---VYKSEFID----LSEKIKQG 605
Cdd:TIGR03670 176 YPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTffrTYEAEERRypggQEDRFEIP 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 606 DSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYLNLNTGE------SFVMyyKSKENCVVDNI 669
Cdd:TIGR03670 256 EPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELREFGLVTerrrdtSVTV--RHGEKGIVDKV 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 670 KVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES 749
Cdd:TIGR03670 331 IITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 750 MAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQV 829
Cdd:TIGR03670 408 IAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHA 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 830 RTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLlspllekpppSWSAMR 909
Cdd:TIGR03670 484 RSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHI----------AWEDKR 553
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 544346215 910 NRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 951
Cdd:TIGR03670 554 KGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
38-949 |
5.15e-109 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 360.58 E-value: 5.15e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFtiLDAVISPPTVpkgtickeanvYPAECRGRRSTYRGKLTAD 117
Cdd:COG0085 16 LLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKY-----------TPEECKERDLTYAAPLYVK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 118 INWAVNGIskGIIKQ---FLGYVPIMVKSklcnlrnlppqaliehheeaeemgGYFIINGIEKVIRMLImprrnfpiami 194
Cdd:COG0085 83 VRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQL----------- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 195 rpkwkTRGPG--YTQYGVSMHcvREEHSA--VNMNLHYLE-----NGTVMLNFIYRKELFFLPLgfaLKALVSFSDYQIF 265
Cdd:COG0085 126 -----VRSPGvyFVEEEDKSG--KDLYSAkvIPSRGAWLEfetdkDGTIYVRIDRKRKIPVTVL---LRALGLETDEEIL 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 266 qELIKGKEDDSFLRNSVsqmlrivMEEGCSTQKQVLNYLGEcfRVKLNVPdwyPNEQAAE-----FLFNQC--------- 331
Cdd:COG0085 196 -EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYR--KLRPGEP---PTIERAEqlldnLFFDPKrydlahvgr 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 332 --------ICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKGSLPLMElptdhTVLRE 403
Cdd:COG0085 263 ykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRME-----RVVRE 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 404 KrippwMEV---------VLI---PMTGK--------------------------------------------------P 421
Cdd:COG0085 338 R-----MTTqdveaitpqSLInirPVVAAikeffgssqlsqfmdqtnplselthkrrlsalgpgglsreragfevrdvhP 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 422 SLY----PglflFTTP----CRLVRpvqNLAL-------------------GKEeligTMEQIFM-------------NV 461
Cdd:COG0085 413 SHYgrmcP----IETPegpnIGLIG---SLALyarvneygfietpyrkvenGKV----TDEIEYLtadeeenyyiaqaNA 481
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 462 AIFEDEVFAGVT-----------------THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLT 519
Cdd:COG0085 482 PLDEDGNFLEERvlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLH 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 520 Y---------QDRSDNklyrlqtpQSPLVR--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIV 576
Cdd:COG0085 562 YplqkfqrsnQGTCIN--------QRPIVRvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIII 629
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 577 NKASWERGfahgsVYKSEFIDLSE----KIKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD----------- 640
Cdd:COG0085 630 SERLVKDD-----VLTSIHIEEYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkge 703
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 641 ----PYYSYLNLNTGEsfvmyyKSK------------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKF 700
Cdd:COG0085 704 teltPEERLLRAIFGE------KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKL 777
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 701 ASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyF 779
Cdd:COG0085 778 AGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----I 852
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 780 GEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMER 859
Cdd:COG0085 853 RELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEV 932
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 860 DALLAHGTSFLLHDRLFNCSDRSVAHVCVkcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAE 939
Cdd:COG0085 933 WALEAYGAAYTLQERLTIKSDDVCGRVKV---------YE---------AIVK--------GENIPEPGIPESFKVLLKE 986
|
1130
....*....|
gi 544346215 940 LAAMNIKVKL 949
Cdd:COG0085 987 LQSLGLDVEV 996
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
1.21e-10 |
|
RNA polymerase Rpb2, 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 61.59 E-value: 1.21e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLENGTVMLNFIYRKELFFLPLGFALKALVSFSDYQIF 265
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREIL 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 266 QELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIHLK 337
Cdd:pfam04561 71 DRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEPFE 147
|
170 180 190
....*....|....*....|....*....|....*...
gi 544346215 338 SNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 375
Cdd:pfam04561 148 NERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
38-950 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 954.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKGSLPLME---------------LPTDHTVLREKRIPPWMEVVLIp 416
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLErevkeklqkqlskkkDLTPQLLINSKPITSGIKEFLA- 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 417 mTGKPSLYPGLFLFTTPC--------------------------------RLVRP-------------------VQNLAL 445
Cdd:cd00653 298 -TGNWGSKRFLMQRSGLSqvldrlnplselshkrrisslglfrerkgfevRDLHPshwgricpietpegencglVKNLAL 376
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 446 gKEELIGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSD 525
Cdd:cd00653 377 -MARISGRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMD 447
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 526 NKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQG 605
Cdd:cd00653 448 TKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGP 527
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 606 DSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDNIKV 671
Cdd:cd00653 528 EEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDDVKI 607
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 672 CSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMA 751
Cdd:cd00653 608 FSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 752 GKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRT 831
Cdd:cd00653 688 GKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARS 763
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 832 TGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnr 911
Cdd:cd00653 764 TGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA--------------- 828
|
970 980 990
....*....|....*....|....*....|....*....
gi 544346215 912 kYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 950
Cdd:cd00653 829 -NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
487-846 |
1.95e-180 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 526.71 E-value: 1.95e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 487 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 566
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 567 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 645
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 646 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 710
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 711 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 790
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 544346215 791 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 846
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
38-951 |
5.81e-162 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 504.11 E-value: 5.81e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 38 LTRAHVESFNYAVHEGLGLAVQA-------IPPFEFAFKDERI---SFTILDAVISPptvpkgtickeanVYPAECRGRR 107
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVgepEIKEADGSERP-------------ITPMEARLRN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 108 STYRGKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMP 185
Cdd:PRK08565 81 LTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 186 RRnfpiamIRPKWKTRGPGYTqygvsmhcvreeHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFAL 253
Cdd:PRK08565 161 NR------VLVDKGEAGSSIT------------HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILM 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 254 KAL-----------VSfSDYQIFQELIKGKEDdsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQ 322
Cdd:PRK08565 219 RALgletdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIER 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 323 AAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPG----QLFLMFLKGSLPLMEL 394
Cdd:PRK08565 281 AEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGdllaELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 395 PTDHTVLREKRIP-------------------------------------PWMEV------VLIPMT-GKP-----SLYP 425
Cdd:PRK08565 360 QLEKSYARGRKLDlraivrpdiiterirhalatgnwvggrtgvsqlldrtNYLSTlshlrrVVSPLSrGQPhfearDLHG 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 426 G----LFLFTTP----CRLVRpvqNLAL---------------------------GKEELIGTMEQIFMN---------- 460
Cdd:PRK08565 440 TqwgrICPFETPegpnCGLVK---NLALmaqisvgvdeeeveeilyelgvvpveeAREEEYISWSRVYLNgrligyhpdg 516
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 461 ---------------------VAI----------------------------------------------FEDEVFAGV- 472
Cdd:PRK08565 517 eelaekirelrrsgkisdevnVAYietgeinevyvncdsgrvrrplivvengkpkltrehveklkkgeltFDDLVKMGVi 596
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 473 -----------------------TTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLY 529
Cdd:PRK08565 597 eyldaeeeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGH 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 530 RLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK---- 603
Cdd:PRK08565 677 LLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypgg 751
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 604 QGD-----SSLVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKE 662
Cdd:PRK08565 752 QEDkieipEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGE 827
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 663 NCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMT 742
Cdd:PRK08565 828 KGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 743 IGMLIESMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHM 822
Cdd:PRK08565 905 VGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHM 980
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 823 VSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekpp 902
Cdd:PRK08565 981 VADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH---------- 1050
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....*....
gi 544346215 903 PSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 951
Cdd:PRK08565 1051 IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
402-951 |
1.34e-144 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 442.93 E-value: 1.34e-144
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 402 REKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGKEELigtmEQIFMNVAIFEDEVFAGVT--- 473
Cdd:TIGR03670 26 RSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTREHV----EKLKEGELTWDDLVKQGVIeyl 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 474 ---------------------THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ 532
Cdd:TIGR03670 96 daeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLH 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 533 TPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGS---VYKSEFID----LSEKIKQG 605
Cdd:TIGR03670 176 YPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTffrTYEAEERRypggQEDRFEIP 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 606 DSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYLNLNTGE------SFVMyyKSKENCVVDNI 669
Cdd:TIGR03670 256 EPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELREFGLVTerrrdtSVTV--RHGEKGIVDKV 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 670 KVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES 749
Cdd:TIGR03670 331 IITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 750 MAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQV 829
Cdd:TIGR03670 408 IAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHA 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 830 RTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLlspllekpppSWSAMR 909
Cdd:TIGR03670 484 RSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHI----------AWEDKR 553
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 544346215 910 NRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 951
Cdd:TIGR03670 554 KGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
401-951 |
6.85e-130 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 404.73 E-value: 6.85e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 401 LREKR----IPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN-----------------------LALGKEEL 450
Cdd:PRK07225 27 IREARrsgeISEEVNVSYKEETNE------VIINTDAGRARRPlivVENgepllteehieklkngeltfddlVKQGVIEY 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 451 IGTMEQIFMNVAIFEDEVFAGvTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYR 530
Cdd:PRK07225 101 LDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHL 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 531 LQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSefIDLSEKIKQGDSSLV 610
Cdd:PRK07225 180 LHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRT--YEGEERRYPGGQEDR 257
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 611 FGIKPGDPR------VLQKLDDDGLPFIGAKLQYGD--------PyySYLNLNTGE----------SFVMyyKSKENCVV 666
Cdd:PRK07225 258 FEIPDKDVRgyrgeeAYRHLDEDGLVNPETEVKEGDvligktspP--RFLEEPDDFgispekrretSVTM--RSGEEGIV 333
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 667 DNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGML 746
Cdd:PRK07225 334 DTVILTETEEGS---RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHV 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 747 IESMAGKSAALHGLCHDATPFifSEENSalEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDK 826
Cdd:PRK07225 411 LEMIGGKVGSLEGRRVDGTAF--SGEDE--EDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANK 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 827 FQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLlspllekpppsws 906
Cdd:PRK07225 487 LHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMI------------- 553
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 544346215 907 AMRNRKYN---CTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 951
Cdd:PRK07225 554 AIYDKKRNrkyCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
38-949 |
5.15e-109 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 360.58 E-value: 5.15e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFtiLDAVISPPTVpkgtickeanvYPAECRGRRSTYRGKLTAD 117
Cdd:COG0085 16 LLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKY-----------TPEECKERDLTYAAPLYVK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 118 INWAVNGIskGIIKQ---FLGYVPIMVKSklcnlrnlppqaliehheeaeemgGYFIINGIEKVIRMLImprrnfpiami 194
Cdd:COG0085 83 VRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQL----------- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 195 rpkwkTRGPG--YTQYGVSMHcvREEHSA--VNMNLHYLE-----NGTVMLNFIYRKELFFLPLgfaLKALVSFSDYQIF 265
Cdd:COG0085 126 -----VRSPGvyFVEEEDKSG--KDLYSAkvIPSRGAWLEfetdkDGTIYVRIDRKRKIPVTVL---LRALGLETDEEIL 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 266 qELIKGKEDDSFLRNSVsqmlrivMEEGCSTQKQVLNYLGEcfRVKLNVPdwyPNEQAAE-----FLFNQC--------- 331
Cdd:COG0085 196 -EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYR--KLRPGEP---PTIERAEqlldnLFFDPKrydlahvgr 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 332 --------ICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKGSLPLMElptdhTVLRE 403
Cdd:COG0085 263 ykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRME-----RVVRE 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 404 KrippwMEV---------VLI---PMTGK--------------------------------------------------P 421
Cdd:COG0085 338 R-----MTTqdveaitpqSLInirPVVAAikeffgssqlsqfmdqtnplselthkrrlsalgpgglsreragfevrdvhP 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 422 SLY----PglflFTTP----CRLVRpvqNLAL-------------------GKEeligTMEQIFM-------------NV 461
Cdd:COG0085 413 SHYgrmcP----IETPegpnIGLIG---SLALyarvneygfietpyrkvenGKV----TDEIEYLtadeeenyyiaqaNA 481
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 462 AIFEDEVFAGVT-----------------THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLT 519
Cdd:COG0085 482 PLDEDGNFLEERvlvryrgeevlvppeevDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLH 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 520 Y---------QDRSDNklyrlqtpQSPLVR--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIV 576
Cdd:COG0085 562 YplqkfqrsnQGTCIN--------QRPIVRvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIII 629
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 577 NKASWERGfahgsVYKSEFIDLSE----KIKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD----------- 640
Cdd:COG0085 630 SERLVKDD-----VLTSIHIEEYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkge 703
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 641 ----PYYSYLNLNTGEsfvmyyKSK------------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKF 700
Cdd:COG0085 704 teltPEERLLRAIFGE------KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKL 777
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 701 ASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyF 779
Cdd:COG0085 778 AGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----I 852
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 780 GEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMER 859
Cdd:COG0085 853 RELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEV 932
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 860 DALLAHGTSFLLHDRLFNCSDRSVAHVCVkcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAE 939
Cdd:COG0085 933 WALEAYGAAYTLQERLTIKSDDVCGRVKV---------YE---------AIVK--------GENIPEPGIPESFKVLLKE 986
|
1130
....*....|
gi 544346215 940 LAAMNIKVKL 949
Cdd:COG0085 987 LQSLGLDVEV 996
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
37-386 |
2.56e-65 |
|
RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 224.95 E-value: 2.56e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 37 ELTRAHVESFNYAVHEGLGLAVQAIPPFEFAFK-------DERISFTILDAVISPPTVPKGTIcKEANVYPAECRGRRST 109
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEiqhpgenGDKLSLKFGQIRLGKPMFDETDG-STREIYPQECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 110 YRGKLTADINWAVNGISKGI-IKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRN 188
Cdd:pfam04563 80 YSAPLYVDLELSVYNGEDIKpIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRN 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 189 FPIAMIRPKWKTRGPGYTQYGVSMHCVRE-EHSAVNMnLHYLENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqE 267
Cdd:pfam04563 160 HPIVFKKADPKKRGSVASVRSSAEISVRPdSTSWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-E 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 268 LIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNV-PDWYPNEQAAEFLFNQCICIHLK----SNTEK 342
Cdd:pfam04563 236 LICYDVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKK 315
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 544346215 343 FYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLK 386
Cdd:pfam04563 316 AYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFR 359
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
554-880 |
6.31e-50 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 191.80 E-value: 6.31e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 554 IGTNAIVAVISYTGYDMEDAMIVNkaswERGF---AHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 630
Cdd:TIGR02013 673 LGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 631 FIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSKEncVVDN--------------IKVCSNDTGS--- 678
Cdd:TIGR02013 749 RIGAEVKAGDilvgkvtpkgeteltPEEKLLRAIFGE------KARD--VRDTslrvppgvegtvidVKVFSREQGDelp 820
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 679 -GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKS 754
Cdd:TIGR02013 821 pGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKR 900
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 755 AALHGLCHdATPfIFseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGA 834
Cdd:TIGR02013 901 LGRKGVPI-ATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGP 976
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 544346215 835 RDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 880
Cdd:TIGR02013 977 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
480-880 |
2.58e-42 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 167.96 E-value: 2.58e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 480 PHSLLSVIANFIPFSDHNQSPRnmyqCQMGK--QTMGFPLL--------------------------------------- 518
Cdd:CHL00207 514 PIQVFSIAESLIPFLEHNDANR----ALMGSnmQRQAVPLLypekpivgtgyekqialdsgmtiisltegivvsvsayki 589
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 519 TYQDRSDNKL-YRLQ----------TPQSPLVRPS--------MYDYYDMDN--YPIGTNAIVAVISYTGYDMEDAMIVN 577
Cdd:CHL00207 590 IIQDDNNRYIhYYLQkyqrsnqntcINYRPIVWVGekinigqiLADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILIN 669
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 578 KAswergFAHGSVYKSEFIDLSEKI----KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGD-------PYYSYL 646
Cdd:CHL00207 670 KR-----LVYEDLFTSIHIEKYEIElrqtKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDilvgkitPKGESD 744
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 647 NLNTGESFVMYYKSKENCVVDN--------------IKVCSNDTGSGKFKCVCITMRV----PRNPTIGDKFASRHGQKG 708
Cdd:CHL00207 745 QLPEGKLLRAIFGEKAKDVKDTslrmpnggygrvikVEIFSRSKGDELKFGYYLKIRVfiaqIRKIQVGDKLAGRHGNKG 824
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 709 ILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAalHGLCHDATPFIFSEENSALE---YFGEMLKA 785
Cdd:CHL00207 825 IISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAG--DNLNKRFKILPFDEMYGSEYsriLINNKLNQ 902
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 786 AG--------YNFY--GTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFG 855
Cdd:CHL00207 903 ASiknneywlFNSYhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFG 982
|
490 500
....*....|....*....|....*
gi 544346215 856 EMERDALLAHGTSFLLHDRLFNCSD 880
Cdd:CHL00207 983 EMEVWALEAFGAAYTLKELLTIKSD 1007
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
695-871 |
1.86e-36 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 149.10 E-value: 1.86e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 695 TIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKsaalhGL-CHDATPfIF- 769
Cdd:PRK00405 881 QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAAK-----GLgIKFATP-VFd 954
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 770 --SEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRN 847
Cdd:PRK00405 955 gaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029
|
170 180
....*....|....*....|....
gi 544346215 848 VQGGIRFGEMERDALLAHGTSFLL 871
Cdd:PRK00405 1030 QFGGQRFGEMEVWALEAYGAAYTL 1053
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
555-880 |
2.94e-31 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 132.33 E-value: 2.94e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 555 GTNAIVAVISYTGYDMEDAMIVNkaswERgFAHGSVYKSEFIDLSE----KIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 630
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLIS----ER-LVYEDIYTSFHIRKYEiqthVTSQGPERITKEIPHLEAHLLRNLDKNGIV 726
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 631 FIGAKLQYGD-------PYYSYLNLNTGESFVMY-------YKSKENC----------VVDNIKVCSNDTGSGKFKCVCI 686
Cdd:CHL00001 727 MLGSWVETGDilvgkltPQEAEESSYAPEGRLLRaifgiqvSTSKETClklpiggrgrVIDVRWIQKKGGSSYNPETIHV 806
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 687 TMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATP 766
Cdd:CHL00001 807 YILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAP 886
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 767 F--IFSEENSALEYFGEMLKA---AGY------NFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGAR 835
Cdd:CHL00001 887 FdeRYEQEASRKLVFSELYEAskqTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPY 966
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 544346215 836 DRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 880
Cdd:CHL00001 967 ALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
678-880 |
3.55e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 123.11 E-value: 3.55e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 678 SGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE---SMAGK- 753
Cdd:PRK09603 1072 NGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlGLVGKe 1151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 754 ----------------------------------------------SAALHGLCHD-------ATPfIFseENSALEYFG 780
Cdd:PRK09603 1152 fgkqiasmledktkdfakelrakmleianainekdpltihalencsDEELLEYAKDwskgvkmAIP-VF--EGISQEKFY 1228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 781 EMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERD 860
Cdd:PRK09603 1229 KLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
|
250 260
....*....|....*....|
gi 544346215 861 ALLAHGTSFLLHDRLFNCSD 880
Cdd:PRK09603 1309 ALEAYGAAHTLKEMLTIKSD 1328
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
38-381 |
2.14e-22 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 101.95 E-value: 2.14e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKD-ERISFTilDAVISPPTVpkgticKEAN-----VYPAECRGRRSTYR 111
Cdd:PRK09606 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDgVYVELG--KIRVGKPVV------KEADgsereIYPMEARLRNLTYS 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 112 GKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML-------IM 184
Cdd:PRK09606 90 APLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLedlapnkIL 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 185 PRRNFPIAMIRPKWKTrgpgYTQY-GVSMHCVREEHSavnmnlhyleNGTVMLNFIY-RKELFFLPLgfaLKALVSFSDy 262
Cdd:PRK09606 170 VEKDERYGDRIEVAKV----FSQRrGYRALVTVERNR----------DGLLEVSFPSvPGSIPFVIL---MRALGLETD- 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 263 qifQELIKGKEDDsflRNSVSQMLRIVMEEGCSTQKQVLNYLGEcfRVKLNVPDWYPNEQaAEFLFNQCICIHLKSNTEK 342
Cdd:PRK09606 232 ---EEIVEAVSDD---PEIVKFMLENLEEAEVDTQEEALEYIGK--RVAPGQTKEYRIKR-AEYVIDRYLLPHLGVEPEV 302
|
330 340 350 360
....*....|....*....|....*....|....*....|...
gi 544346215 343 F----YMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLF 381
Cdd:PRK09606 303 RrakaHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLM 345
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
850-952 |
2.72e-22 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 91.88 E-value: 2.72e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 850 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGsllspllekpppswsAMRNRKYnCTLCSRSDTIDTVSV 929
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCG---------------LYAAYNK-CPICKGETDISPGYI 64
|
90 100
....*....|....*....|...
gi 544346215 930 PYVFRYFVAELAAMNIKVKLDVV 952
Cdd:pfam04560 65 PESFKLLFQELQSLGIDPRLLLE 87
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
697-880 |
1.85e-20 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 98.16 E-value: 1.85e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 697 GDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAG--------------------KSAA 756
Cdd:PRK14844 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgekvgnildeinkiKSAF 1163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 757 LHGL--------------------------------------------------------CHDATPFIFS---------- 770
Cdd:PRK14844 1164 CKGIrslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnsCKSAYSNLRNflievyscgs 1243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 771 -----------EENSALEY----------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 817
Cdd:PRK14844 1244 nvsicnnirdiSDNNLIEFarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544346215 818 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 880
Cdd:PRK14844 1324 KLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
400-438 |
3.22e-13 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 64.81 E-value: 3.22e-13
10 20 30
....*....|....*....|....*....|....*....
gi 544346215 400 VLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 438
Cdd:pfam06883 21 VEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
1.21e-10 |
|
RNA polymerase Rpb2, 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 61.59 E-value: 1.21e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLENGTVMLNFIYRKELFFLPLGFALKALVSFSDYQIF 265
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREIL 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346215 266 QELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIHLK 337
Cdd:pfam04561 71 DRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEPFE 147
|
170 180 190
....*....|....*....|....*....|....*...
gi 544346215 338 SNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 375
Cdd:pfam04561 148 NERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
