|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
8-963 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1490.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 8 ITFGKLASVMPMPHLLDVQTRSFSALLspDGDSARTDISLERVFREVFPIADVNGNYSLEFVKFAIGDPKYAVEECIERD 87
Cdd:PRK00405 13 KSFGKIKEVLELPNLLEIQLDSFDWFL--QLDVPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVEECKERG 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 88 MTYSAPLKATLRLVVMETletgvkrpKNIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPGVVFEETVH--PNGQ 165
Cdd:PRK00405 91 LTYSAPLRVKLRLINKET--------GEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDktSSGK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 166 RLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYgTNNDILRLFYATKSLdltqKFEERVLRREVIGA 245
Cdd:PRK00405 163 LLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEKEEF----GKEIEVPVEYLLGK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 246 LIAEqvanletadgeplaregdeltperynalrragvktvrvytryatidlrdddrpvtvrereelpilafDVPEPETGE 325
Cdd:PRK00405 238 VLAE-------------------------------------------------------------------DIVDEETGE 250
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 326 ILLEAGKELTENTkkklvkagvfkvdvlvtsaraESQLIKNTLTKDPTSTEAEALEQIYALLRPGEAPNLETARAALERL 405
Cdd:PRK00405 251 VLAEANDEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENL 309
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 406 FFNPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGYTDDIDHLGNRRVRTVGELIANQFSVGL 485
Cdd:PRK00405 310 FFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGL 389
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 486 SRMARLIKERMSINnDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEV 565
Cdd:PRK00405 390 SRMERAVRERMSLQ-DLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEV 468
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 566 RDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRVTDEIKWLSASEEEEYAVAQANAAVDELG 645
Cdd:PRK00405 469 RDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDG 548
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 646 NFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSVPLLFPRAPLVGTGLEDV 725
Cdd:PRK00405 549 RFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERR 628
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 726 VARDSGAVVVARRAGRVSKVTADEIIVDTGVDVGGSGETplarlmqhDRYRLKKFWRTNQDTAINQRPLIRVGDKVKAEQ 805
Cdd:PRK00405 629 VARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDGV--------DIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGD 700
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 806 VIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITREIPNVSEES 885
Cdd:PRK00405 701 VLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEA 780
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 874574201 886 LVDLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDSSLRVPPGMEGVVIDVKIFSRVED 963
Cdd:PRK00405 781 LRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQ 858
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
3-963 |
0e+00 |
|
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: 1261.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 3 KTLPVITFGKLASVMPMPHLLDVQTRSFSALLSPD-GDSARTDISLERVFREVFPIADVNGNYSLEFVKFAIGDPKYAVE 81
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDtPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 82 ECIERDMTYSAPLKATLRLVVMEtlETGVKrpkNIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPGVVF-EETV 160
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE--EDGTK---EIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFsSEKD 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 161 HPN-GQRLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYGTNNDILrlfyatksldltqkfeervlr 239
Cdd:TIGR02013 156 TTKsGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLIL--------------------- 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 240 revigaliaeqvanletadgeplaregDELTPERYnalrragvktvrvytryatidlrdddrpvtvrereelpilafdvp 319
Cdd:TIGR02013 215 ---------------------------NRLGSGEY--------------------------------------------- 222
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 320 epetgeilleagkeltentkkklvkagvfkvdvlvtsaraesqlIKNTLTKDPTSTEAEALEQIYALLRPGEAPNLETAR 399
Cdd:TIGR02013 223 --------------------------------------------IRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAAR 258
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 400 AALERLFFNPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGYTDDIDHLGNRRVRTVGELIAN 479
Cdd:TIGR02013 259 SLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQN 338
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 480 QFSVGLSRMARLIKERMSINnDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRE 559
Cdd:TIGR02013 339 QFRVGLARMERIVRERMSTQ-DTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRE 417
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 560 RAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRV--TDEIKWLSASEEEEYAVAQA 637
Cdd:TIGR02013 418 RAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQA 497
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 638 NAAVDELGNFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSVPLLFPRAPL 717
Cdd:TIGR02013 498 NAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPL 577
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 718 VGTGLEDVVARDSGAVVVARRAGRVSKVTADEIIVDTGVDVGGSGEtplarlmQHDRYRLKKFWRTNQDTAINQRPLIRV 797
Cdd:TIGR02013 578 VGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDG-------GIDIYRLLKYQRSNQDTCINQRPIVSV 650
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 798 GDKVKAEQVIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITRE 877
Cdd:TIGR02013 651 GDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRD 730
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 878 IPNVSEESLVDLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDSSLRVPPGMEGVVIDVKI 957
Cdd:TIGR02013 731 IPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKV 810
|
....*.
gi 874574201 958 FSRVED 963
Cdd:TIGR02013 811 FSREQG 816
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
8-963 |
0e+00 |
|
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: 1201.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 8 ITFGKLASVMPMPHLLDVQTRSFSALLspdgdsartDISLERVFREVFPIADVNGNYSLEFVKFAIGDPKYAVEECIERD 87
Cdd:COG0085 2 WSFAKIKEPLELPNLLEIQLDSFNWFL---------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERD 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 88 MTYSAPLKATLRLVVMETLEtgvkrpknIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPGVVFEETVHPNGQRL 167
Cdd:COG0085 73 LTYAAPLYVKVRLVNKETGE--------IKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 168 YSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYGTNNDILRLFYatksldltqkfeervlrrevigali 247
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETDEEILEAFG------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 248 aeqvanletadgeplaregdeltperynalrragvktvrvytryatidlrdddrpvtvrereelpilafDVPEPEtgeil 327
Cdd:COG0085 200 ---------------------------------------------------------------------DDPIQE----- 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 328 leagkeltentkkklvkagvfkvdvlvtsaraesqLIKNTLTKDPTSTEAEALEQIYALLRPGEAPNLETARAALERLFF 407
Cdd:COG0085 206 -----------------------------------YILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFF 250
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 408 NPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGYTDDIDHLGNRRVRTVGELIANQFSVGLSR 487
Cdd:COG0085 251 DPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSR 330
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 488 MARLIKERMSINnDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRD 567
Cdd:COG0085 331 MERVVRERMTTQ-DVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 409
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 568 VHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRVTDEIKWLSASEEEEYAVAQANAAVDELGNF 647
Cdd:COG0085 410 VHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNF 489
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 648 TTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSVPLLFPRAPLvgtgledvva 727
Cdd:COG0085 490 LEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 728 rdsgavvvarragrvskvtadeiivdtgvdvggsgetplarlmqhDRYRLKKFWRTNQDTAINQRPLIRVGDKVKAEQVI 807
Cdd:COG0085 560 ---------------------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVL 594
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 808 ADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITREIPNVSEESLV 887
Cdd:COG0085 595 ADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALR 674
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 874574201 888 DLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDSSLRVPPGMEGVVIDVKIFSRVED 963
Cdd:COG0085 675 NLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEG 750
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
22-960 |
5.75e-164 |
|
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: 505.95 E-value: 5.75e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 22 LLDVQTRSFSALLspdgdsartDISLERVFREVFPI--ADVNGNYSLEFVKFAIGDPKYA---------VEECIERDMTY 90
Cdd:cd00653 1 LVKQQIDSFNYFL---------NVGLQEIVKSIPPItdTDDDGRLKLKFGDIYLGKPKVEeggvtrkltPNECRLRDLTY 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 91 SAPLKATLRLVVMETletgvkrpKNIIEKEVYLGELPILT------------------------PLGTFVINGAERVVVS 146
Cdd:cd00653 72 SAPLYVDIRLTVNDK--------GKIKEQEVFIGEIPIMLrsklcnlngltpeeliklgecpldPGGYFIINGTEKVIIN 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 147 QLHRSPGVVFEETvhPNGQRLYSARIIP----FRGSWveftvdihdvIYVHIDKKKKfpatallrafgygtnndilrlfy 222
Cdd:cd00653 144 QEQRSPNVIIVED--SKGKRIYTKTSIPsyspYRGSW----------LEVKSDKKKD----------------------- 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 223 atksldltqkfeervlrrevigaliaeqvanletadgeplaregdeltperynalrragvktvrvyTRYATIDLRDDDrp 302
Cdd:cd00653 189 ------------------------------------------------------------------RIYVRIDLKRQE-- 200
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 303 vtvrereelpilafdvpepetgeilleagkeltentkkklvkagvfkvdvlvtsaraesqlikntltkdptsteaEALEQ 382
Cdd:cd00653 201 ---------------------------------------------------------------------------EALKY 205
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 383 IYALLrpgeapnletaraalerlffnpkrydlgrvgrykinqrlkvnvplthtvlteEDFVAIIRYLIELSEGRGYTDDI 462
Cdd:cd00653 206 IGKRF----------------------------------------------------EDLIYMIRKLILLVLGKGKLDDI 233
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 463 DHLGNRRVRTVGELIANQFSVGLSRMARLIKERMS-INNDPEKITLDDLVNARTVSAVIQAFFGSSQ------------L 529
Cdd:cd00653 234 DHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQkQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgL 313
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 530 SQFMDQTNPLAELTHKRRLSAlgpGGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNdlGFIETPY 609
Cdd:cd00653 314 SQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPY 388
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 610 RVVRggrvtdeikwlsaseeeeyavaqanaavdelgnfttdlvlcrkrddypllppSRIDFMDVAPEQLVSIAAALIPFL 689
Cdd:cd00653 389 RIVE----------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 690 EHDDANRALMGSNMQRQSVP----------------LLFPRAPLVGTGLEDVVARdsgavvvarragrvskvtadeiivd 753
Cdd:cd00653 417 EHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAF------------------------- 471
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 754 tgvdvggsgetplarlmqhdryrlkkfwrtnqdtainqrplirvgdkvkaeqviadgpgtegGQIALGANVTVAFMPWYG 833
Cdd:cd00653 472 --------------------------------------------------------------GELPLGQNAIVAVMSYSG 489
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 834 HNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITR-EIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKIT 912
Cdd:cd00653 490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKIT 569
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*...
gi 874574201 913 PKGETELSPeeklltaIFGEKAKDVKDSSLRVPPGMEGVVIDVKIFSR 960
Cdd:cd00653 570 PKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSR 610
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
775-981 |
4.42e-64 |
|
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: 221.63 E-value: 4.42e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 775 YRLKKFWRTNQDT---AINQRPLIRVGdKVKAEQViadgpgtegGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDT 851
Cdd:pfam00562 30 YTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGF 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 852 YSSIHIQELElhVRDTKRGQ-EEITREIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKItpkGETELSpeeKLLTAIF 930
Cdd:pfam00562 100 FTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKV---GPTELT---KLLRAIF 171
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 874574201 931 GEKAKDVKDSSLRVPPGMEGVVIDVKIFSrvedqvvEKDRGE-----RIGEVRRLE 981
Cdd:pfam00562 172 GEKARDVKDTSLKVPPGEEGVVDDVIVFE-------LPPGGIkmvkvYIRQKRKPE 220
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
8-963 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1490.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 8 ITFGKLASVMPMPHLLDVQTRSFSALLspDGDSARTDISLERVFREVFPIADVNGNYSLEFVKFAIGDPKYAVEECIERD 87
Cdd:PRK00405 13 KSFGKIKEVLELPNLLEIQLDSFDWFL--QLDVPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVEECKERG 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 88 MTYSAPLKATLRLVVMETletgvkrpKNIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPGVVFEETVH--PNGQ 165
Cdd:PRK00405 91 LTYSAPLRVKLRLINKET--------GEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDktSSGK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 166 RLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYgTNNDILRLFYATKSLdltqKFEERVLRREVIGA 245
Cdd:PRK00405 163 LLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEKEEF----GKEIEVPVEYLLGK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 246 LIAEqvanletadgeplaregdeltperynalrragvktvrvytryatidlrdddrpvtvrereelpilafDVPEPETGE 325
Cdd:PRK00405 238 VLAE-------------------------------------------------------------------DIVDEETGE 250
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 326 ILLEAGKELTENTkkklvkagvfkvdvlvtsaraESQLIKNTLTKDPTSTEAEALEQIYALLRPGEAPNLETARAALERL 405
Cdd:PRK00405 251 VLAEANDEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENL 309
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 406 FFNPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGYTDDIDHLGNRRVRTVGELIANQFSVGL 485
Cdd:PRK00405 310 FFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGL 389
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 486 SRMARLIKERMSINnDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEV 565
Cdd:PRK00405 390 SRMERAVRERMSLQ-DLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEV 468
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 566 RDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRVTDEIKWLSASEEEEYAVAQANAAVDELG 645
Cdd:PRK00405 469 RDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDG 548
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 646 NFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSVPLLFPRAPLVGTGLEDV 725
Cdd:PRK00405 549 RFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERR 628
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 726 VARDSGAVVVARRAGRVSKVTADEIIVDTGVDVGGSGETplarlmqhDRYRLKKFWRTNQDTAINQRPLIRVGDKVKAEQ 805
Cdd:PRK00405 629 VARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDGV--------DIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGD 700
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 806 VIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITREIPNVSEES 885
Cdd:PRK00405 701 VLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEA 780
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 874574201 886 LVDLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDSSLRVPPGMEGVVIDVKIFSRVED 963
Cdd:PRK00405 781 LRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQ 858
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
3-963 |
0e+00 |
|
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: 1261.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 3 KTLPVITFGKLASVMPMPHLLDVQTRSFSALLSPD-GDSARTDISLERVFREVFPIADVNGNYSLEFVKFAIGDPKYAVE 81
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDtPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 82 ECIERDMTYSAPLKATLRLVVMEtlETGVKrpkNIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPGVVF-EETV 160
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE--EDGTK---EIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFsSEKD 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 161 HPN-GQRLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYGTNNDILrlfyatksldltqkfeervlr 239
Cdd:TIGR02013 156 TTKsGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLIL--------------------- 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 240 revigaliaeqvanletadgeplaregDELTPERYnalrragvktvrvytryatidlrdddrpvtvrereelpilafdvp 319
Cdd:TIGR02013 215 ---------------------------NRLGSGEY--------------------------------------------- 222
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 320 epetgeilleagkeltentkkklvkagvfkvdvlvtsaraesqlIKNTLTKDPTSTEAEALEQIYALLRPGEAPNLETAR 399
Cdd:TIGR02013 223 --------------------------------------------IRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAAR 258
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 400 AALERLFFNPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGYTDDIDHLGNRRVRTVGELIAN 479
Cdd:TIGR02013 259 SLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQN 338
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 480 QFSVGLSRMARLIKERMSINnDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRE 559
Cdd:TIGR02013 339 QFRVGLARMERIVRERMSTQ-DTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRE 417
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 560 RAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRV--TDEIKWLSASEEEEYAVAQA 637
Cdd:TIGR02013 418 RAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQA 497
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 638 NAAVDELGNFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSVPLLFPRAPL 717
Cdd:TIGR02013 498 NAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPL 577
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 718 VGTGLEDVVARDSGAVVVARRAGRVSKVTADEIIVDTGVDVGGSGEtplarlmQHDRYRLKKFWRTNQDTAINQRPLIRV 797
Cdd:TIGR02013 578 VGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDG-------GIDIYRLLKYQRSNQDTCINQRPIVSV 650
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 798 GDKVKAEQVIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITRE 877
Cdd:TIGR02013 651 GDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRD 730
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 878 IPNVSEESLVDLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDSSLRVPPGMEGVVIDVKI 957
Cdd:TIGR02013 731 IPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKV 810
|
....*.
gi 874574201 958 FSRVED 963
Cdd:TIGR02013 811 FSREQG 816
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
8-963 |
0e+00 |
|
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: 1201.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 8 ITFGKLASVMPMPHLLDVQTRSFSALLspdgdsartDISLERVFREVFPIADVNGNYSLEFVKFAIGDPKYAVEECIERD 87
Cdd:COG0085 2 WSFAKIKEPLELPNLLEIQLDSFNWFL---------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERD 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 88 MTYSAPLKATLRLVVMETLEtgvkrpknIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPGVVFEETVHPNGQRL 167
Cdd:COG0085 73 LTYAAPLYVKVRLVNKETGE--------IKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 168 YSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYGTNNDILRLFYatksldltqkfeervlrrevigali 247
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETDEEILEAFG------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 248 aeqvanletadgeplaregdeltperynalrragvktvrvytryatidlrdddrpvtvrereelpilafDVPEPEtgeil 327
Cdd:COG0085 200 ---------------------------------------------------------------------DDPIQE----- 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 328 leagkeltentkkklvkagvfkvdvlvtsaraesqLIKNTLTKDPTSTEAEALEQIYALLRPGEAPNLETARAALERLFF 407
Cdd:COG0085 206 -----------------------------------YILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFF 250
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 408 NPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGYTDDIDHLGNRRVRTVGELIANQFSVGLSR 487
Cdd:COG0085 251 DPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSR 330
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 488 MARLIKERMSINnDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRD 567
Cdd:COG0085 331 MERVVRERMTTQ-DVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRD 409
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 568 VHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRVTDEIKWLSASEEEEYAVAQANAAVDELGNF 647
Cdd:COG0085 410 VHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNF 489
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 648 TTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSVPLLFPRAPLvgtgledvva 727
Cdd:COG0085 490 LEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 728 rdsgavvvarragrvskvtadeiivdtgvdvggsgetplarlmqhDRYRLKKFWRTNQDTAINQRPLIRVGDKVKAEQVI 807
Cdd:COG0085 560 ---------------------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVL 594
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 808 ADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITREIPNVSEESLV 887
Cdd:COG0085 595 ADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALR 674
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 874574201 888 DLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDSSLRVPPGMEGVVIDVKIFSRVED 963
Cdd:COG0085 675 NLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEG 750
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-1048 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 895.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 1 MTKTLPV-----ITFGKLASVMPMPHLLDVQTRSFSALLSPDGDSartDISLERVFREVFPIADVNGNYSLEFVKFAIGD 75
Cdd:PRK09603 1 MSKKIPLknrlrADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGK---ESGIEKVFKSIFPIQDEHNRITLEYAGCEFGK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 76 PKYAVEECIERDMTYSAPLKATLRLVVMETLE-TGVKRP-KNIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPG 153
Cdd:PRK09603 78 SKYTVREAMERGITYSIPLKIKVRLILWEKDTkSGEKNGiKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPG 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 154 VVF--EETVHPNGQRLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYgTNNDILRLFYATKSLdltq 231
Cdd:PRK09603 158 VIFkeEESSTSLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDY-QKQDIIKMFYPLVKV---- 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 232 KFE-ERVLRREVIGALIAEQVANLETADGEPLAREGDELTPERYNALRRAGVKTVRvYTRYATIDlRDDDRPVTVREree 310
Cdd:PRK09603 233 RYEnDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVE-YPMDILLN-RHLAEPVMVGK--- 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 311 lpilafdvpepetgEILLEAGKELTENTKKKLVKAGVFKVDVLVTSARAESQLIKNTLTKDPTS----TEAEALE----- 381
Cdd:PRK09603 308 --------------EVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESlkllKQTEKIDdenal 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 382 ---QIYALLRPGEAPNLETARAALERLFFNPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGY 458
Cdd:PRK09603 374 aaiRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGK 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 459 TDDIDHLGNRRVRTVGELIANQFSVGLSRMARLIKERM-SINNDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTN 537
Cdd:PRK09603 454 IDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLtTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTN 533
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 538 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRV 617
Cdd:PRK09603 534 PLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKV 613
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 618 TDEIKWLSASEEEEYAVAQANAAVDELGNFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRA 697
Cdd:PRK09603 614 VGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRA 693
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 698 LMGSNMQRQSVPLLFPRAPLVGTGLEDVVARDSGAVVVARRAGRVSKVTADEIIVdTGVDVGGSgetplarlmQHDRYRL 777
Cdd:PRK09603 694 LMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI-LGEGKEEA---------YIDAYSL 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 778 KKFWRTNQDTAINQRPLIRVGDKVKAEQVIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHI 857
Cdd:PRK09603 764 QKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHI 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 858 QELELHVRDTKRGQEEITREIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDV 937
Cdd:PRK09603 844 YEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHV 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 938 KDSSLRVPPGMEGVVIDVKIFSRvedQVVEKDRgerigEVRRLENEEKARISAVLFEEVTELLQgqevalmlkngtvEEY 1017
Cdd:PRK09603 924 VNKSLYCPPSLEGTVIDVKVFTK---KGYEKDA-----RVLSAYEEEKAKLDMEHFDRLTMLNR-------------EEL 982
|
1050 1060 1070
....*....|....*....|....*....|..
gi 874574201 1018 LPAGTKLTKSTL-EEVDLADVDLKTLRVVNKA 1048
Cdd:PRK09603 983 LRVSSLLSQAILeEPFSHNGKDYKEGDQIPKE 1014
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
22-1000 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 835.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 22 LLDVQTRSFSALLSPDGDSARtdisLERVFREVFPIADVNGNYSLEFVKFAIGDPKYAVEECIERDMTYSAPLKATLRLV 101
Cdd:PRK14844 32 LVKVQKESYDSFTPKNKGNER----LEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRLV 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 102 VME---TLE--TGVKRP----------KNIIEKEVYLGELPILTPLGTFVINGAERVVVSQLHRSPGVVFEE---TVHPN 163
Cdd:PRK14844 108 IMQdgiSLDeyKSIKESgdhsklatviKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSdkgKTYNS 187
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 164 GQRLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYgTNNDILRLFYatksldltqkfeervlrrevi 243
Cdd:PRK14844 188 GKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGL-SNNDILDRFY--------------------- 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 244 galiaEQVANLETADGEPLAREGDELTPERY---------NALRRAgvkTVRVYTRYATiDLRDDDRPVTVREREELP-- 312
Cdd:PRK14844 246 -----EKIKYIKHKDGWKVPFVPDKFKGVRLpfdlmdvegNVLLKA---NVRITSRLAK-KLYDNELKEYLVPFDSICgl 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 313 ILAFDVPEPETGEILLEAGKELTENTKKKLVKAGVFKVDVLVTSARAESQLIKNTLTKDPTSTEAEALEQIYALLRPGEA 392
Cdd:PRK14844 317 FLAEDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEV 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 393 PNLETARAALERLFFNPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELSEGRGYTDDIDHLGNRRVRT 472
Cdd:PRK14844 397 PVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRS 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 473 VGELIANQFSVGLSRMARLIKERMSINNdPEKITLDDLVNARTVSAVIQAFFGSSQLSQFMDQTNPLAELTHKRRLSALG 552
Cdd:PRK14844 477 VGEFIENQFRTGLLKLERAVVDSMSTSS-LDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALG 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 553 PGGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVRGGRVTDEIKWLSASEEEEY 632
Cdd:PRK14844 556 PGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLY 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 633 AVAQANAAVDELGNFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSVPLLF 712
Cdd:PRK14844 636 YIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLK 715
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 713 PRAPLVGTGLEDVVARDSGAVVVARRAGRVSKVTADEIIVdTGVDVGGsgetplARLMQHDRYRLKKFWRTNQDTAINQR 792
Cdd:PRK14844 716 PTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVI-RAFDKER------VNYLDVDIYHLRKFQRSNHNTCINQK 788
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 793 PLIRVGDKVKAEQVIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQE 872
Cdd:PRK14844 789 PLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSE 868
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 873 EITREIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLLTAIFGEKAKDVKDSSLRVPPGMEGVV 952
Cdd:PRK14844 869 KITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTV 948
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....
gi 874574201 953 IDVKIFSRveDQVVEKDRGERIGEvRRLENEEKAR------ISAVLFEEVTELL 1000
Cdd:PRK14844 949 IDVQVFTR--RGVEENERALLIKQ-KEINDFEKERdyiinvTSEYFYDELKKLL 999
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
56-960 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 762.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 56 PIADVNGNYSLEFVK--FAIGDPKYAVEECIERDMTYSAPLKATLRLVvmeTLETGVkrpknIIEKEVYLGELPILTPLG 133
Cdd:CHL00207 35 KIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFI---NLKTNK-----IKFINYLIGNLPKMTQRG 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 134 TFVINGAERVVVSQLHRSPGVVFEETVHPNGQRLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGYgT 213
Cdd:CHL00207 107 TFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGL-T 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 214 NNDILrlfyatksldltqkfeervlrrevigaliaeqvanletadgeplaregdeltperynalrragvktvrvytryat 293
Cdd:CHL00207 186 DQDIY--------------------------------------------------------------------------- 190
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 294 idlrdddrpvtvrereelpilafdvpepetgeilleagKELTENTKKKLvkagvfkvdvlvtsaraesqLIKNTLTKDPT 373
Cdd:CHL00207 191 --------------------------------------SRLTKSEFLKK--------------------LKPILLNSNSY 212
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 374 STEaEALEQIYALLRPGEAPNLETARAALERLFFNPKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIELS 453
Cdd:CHL00207 213 TNE-EILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLK 291
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 454 EGRGYTDDIDHLGNRRVRTVGELIANQFSVGLSRMARLIKERMSINnDPEKITLDDLVNARTVSAVIQAFFGSSQLSQFM 533
Cdd:CHL00207 292 INKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTIC-DIDSLSKFNLINPKPLIALIREFFGSSQLSQYM 370
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 534 DQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETPYRVVR 613
Cdd:CHL00207 371 DQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVI 450
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 614 GGRV--TDEIKWLSASEEEEYAVAQANAAVDELGNFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPFLEH 691
Cdd:CHL00207 451 NGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEH 530
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 692 DDANRALMGSNMQRQSVPLLFPRAPLVGTGLEDVVARDSGAVVVARRAGRVSKVTADEIIVdtgvdvggsgetplarlmQ 771
Cdd:CHL00207 531 NDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIII------------------Q 592
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 772 HDR-----YRLKKFWRTNQDTAINQRPLIRVGDKVKAEQVIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERL 846
Cdd:CHL00207 593 DDNnryihYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRL 672
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 847 VKDDTYSSIHIQELELHVRDTKRGQEEITREIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKITPKGETELSPEEKLL 926
Cdd:CHL00207 673 VYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLL 752
|
890 900 910
....*....|....*....|....*....|....
gi 874574201 927 TAIFGEKAKDVKDSSLRVPPGMEGVVIDVKIFSR 960
Cdd:CHL00207 753 RAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSR 786
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
55-956 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 736.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 55 FP-IADVNGNYSLEFV--KFAIGDPKYAVEECIERDMTYSAPLKATLRLVVmetletgvKRPKNIIEKEVYLGELPILTP 131
Cdd:CHL00001 38 FPkIEDTDQEIEFQLFveTYQLVEPLIKERDAVYESLTYSSELYVPAGLIW--------KKSRDMQEQTVFIGNIPLMNS 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 132 LGTFVINGAERVVVSQLHRSPGVVFEETVHPNGQRLYSARIIPFRGSWVEFTVDIHDVIYVHIDKKKKFPATALLRAFGy 211
Cdd:CHL00001 110 LGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMG- 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 212 gtnndilrlfyatksldltqkfeervlrrevigaliaeqvanletadgeplaregdeltperynalrragvktvrvytry 291
Cdd:CHL00001 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 292 atIDLRDddrpvtvrereelpILAFdVPEPEtgeILLEagkelTENTKKKlvkagvfkvdvlvtsaraesqlikntltKD 371
Cdd:CHL00001 189 --LNLRE--------------ILDN-VCYPE---IFLS-----FLNDKEK----------------------------KK 215
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 372 PTSTEAEALEqIYALL--RPGEAPNLETARAALERLFFNpKRYDLGRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYL 449
Cdd:CHL00001 216 IGSKENAILE-FYQQFacVGGDPVFSESLCKELQKKFFQ-QRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYL 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 450 IELSEGRGYTDDIDHLGNRRVRTVGELIANQFSVGLSRMARLIKERMS-INNDPEKITLDDLVNARTVSAVIQAFFGSSQ 528
Cdd:CHL00001 294 IGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICgAIRRKLIPTPQNLVTSTPLTTTYESFFGSHP 373
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 529 LSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNDLGFIETP 608
Cdd:CHL00001 374 LSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESP 453
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 609 YRVVRGGRVTDEIKWLSASEEEEYAVAQANAAVDELGNFTTDLVLCRKRDDYPLLPPSRIDFMDVAPEQLVSIAAALIPF 688
Cdd:CHL00001 454 FYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPF 533
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 689 LEHDDANRALMGSNMQRQSVPLLFPRAPLVGTGLEDVVARDSGAVVVARRAGRVSKVTADEIIVDtgvdvgGSGETplar 768
Cdd:CHL00001 534 LEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILS------GNGDT---- 603
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 769 lmqhDRYRLKKFWRTNQDTAINQRPLIRVGDKVKAEQVIADGPGTEGGQIALGANVTVAFMPWYGHNFEDAIVLSERLVK 848
Cdd:CHL00001 604 ----LSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVY 679
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 849 DDTYSSIHIQELELHVRDTKRGQEEITREIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKITPK--GETELSPEEKLL 926
Cdd:CHL00001 680 EDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYAPEGRLL 759
|
890 900 910
....*....|....*....|....*....|
gi 874574201 927 TAIFGEKAKDVKDSSLRVPPGMEGVVIDVK 956
Cdd:CHL00001 760 RAIFGIQVSTSKETCLKLPIGGRGRVIDVR 789
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
22-960 |
5.75e-164 |
|
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: 505.95 E-value: 5.75e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 22 LLDVQTRSFSALLspdgdsartDISLERVFREVFPI--ADVNGNYSLEFVKFAIGDPKYA---------VEECIERDMTY 90
Cdd:cd00653 1 LVKQQIDSFNYFL---------NVGLQEIVKSIPPItdTDDDGRLKLKFGDIYLGKPKVEeggvtrkltPNECRLRDLTY 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 91 SAPLKATLRLVVMETletgvkrpKNIIEKEVYLGELPILT------------------------PLGTFVINGAERVVVS 146
Cdd:cd00653 72 SAPLYVDIRLTVNDK--------GKIKEQEVFIGEIPIMLrsklcnlngltpeeliklgecpldPGGYFIINGTEKVIIN 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 147 QLHRSPGVVFEETvhPNGQRLYSARIIP----FRGSWveftvdihdvIYVHIDKKKKfpatallrafgygtnndilrlfy 222
Cdd:cd00653 144 QEQRSPNVIIVED--SKGKRIYTKTSIPsyspYRGSW----------LEVKSDKKKD----------------------- 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 223 atksldltqkfeervlrrevigaliaeqvanletadgeplaregdeltperynalrragvktvrvyTRYATIDLRDDDrp 302
Cdd:cd00653 189 ------------------------------------------------------------------RIYVRIDLKRQE-- 200
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 303 vtvrereelpilafdvpepetgeilleagkeltentkkklvkagvfkvdvlvtsaraesqlikntltkdptsteaEALEQ 382
Cdd:cd00653 201 ---------------------------------------------------------------------------EALKY 205
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 383 IYALLrpgeapnletaraalerlffnpkrydlgrvgrykinqrlkvnvplthtvlteEDFVAIIRYLIELSEGRGYTDDI 462
Cdd:cd00653 206 IGKRF----------------------------------------------------EDLIYMIRKLILLVLGKGKLDDI 233
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 463 DHLGNRRVRTVGELIANQFSVGLSRMARLIKERMS-INNDPEKITLDDLVNARTVSAVIQAFFGSSQ------------L 529
Cdd:cd00653 234 DHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQkQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgL 313
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 530 SQFMDQTNPLAELTHKRRLSAlgpGGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRVNdlGFIETPY 609
Cdd:cd00653 314 SQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPY 388
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 610 RVVRggrvtdeikwlsaseeeeyavaqanaavdelgnfttdlvlcrkrddypllppSRIDFMDVAPEQLVSIAAALIPFL 689
Cdd:cd00653 389 RIVE----------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 690 EHDDANRALMGSNMQRQSVP----------------LLFPRAPLVGTGLEDVVARdsgavvvarragrvskvtadeiivd 753
Cdd:cd00653 417 EHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAF------------------------- 471
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 754 tgvdvggsgetplarlmqhdryrlkkfwrtnqdtainqrplirvgdkvkaeqviadgpgtegGQIALGANVTVAFMPWYG 833
Cdd:cd00653 472 --------------------------------------------------------------GELPLGQNAIVAVMSYSG 489
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 834 HNFEDAIVLSERLVKDDTYSSIHIQELELHVRDTKRGQEEITR-EIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKIT 912
Cdd:cd00653 490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKIT 569
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*...
gi 874574201 913 PKGETELSPeeklltaIFGEKAKDVKDSSLRVPPGMEGVVIDVKIFSR 960
Cdd:cd00653 570 PKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSR 610
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
775-981 |
4.42e-64 |
|
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: 221.63 E-value: 4.42e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 775 YRLKKFWRTNQDT---AINQRPLIRVGdKVKAEQViadgpgtegGQIALGANVTVAFMPWYGHNFEDAIVLSERLVKDDT 851
Cdd:pfam00562 30 YTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGF 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 852 YSSIHIQELElhVRDTKRGQ-EEITREIPNVSEESLVDLDERGIVRIGAHVKPGDILVGKItpkGETELSpeeKLLTAIF 930
Cdd:pfam00562 100 FTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKV---GPTELT---KLLRAIF 171
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 874574201 931 GEKAKDVKDSSLRVPPGMEGVVIDVKIFSrvedqvvEKDRGE-----RIGEVRRLE 981
Cdd:pfam00562 172 GEKARDVKDTSLKVPPGEEGVVDDVIVFE-------LPPGGIkmvkvYIRQKRKPE 220
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
51-957 |
6.97e-36 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 147.80 E-value: 6.97e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 51 FREVFPIAdvnGNYSLEFVKFAIGDPKYAvE-----------ECIERDMTYSAPLKATLRLVVmetletgvkrpKNIIEK 119
Cdd:PRK08565 37 FGEIKTEI---PGLKIVLGKIRVGEPEIK-EadgserpitpmEARLRNLTYAAPLYLTMIPVE-----------NGIEYE 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 120 --EVYLGELPILT------------------------PLGTFVINGAERVVVSQLHRSPGVVFEETVHPNGQRLYSARII 173
Cdd:PRK08565 102 peEVKIGDLPIMVkskicplsglspdelieigedpkdPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVI 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 174 PFR-GSWVEFTVDIHD--VIYVHIDK-KKKFPATALLRAFGYGTNNDILrlfYATKSLDLTQKfeervlrrevigaliaE 249
Cdd:PRK08565 182 SSRaGYRAQVTVERRKdgTIYVSFPAvPGKIPFVILMRALGLETDRDIV---YAVSLDPEIQQ----------------E 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 250 QVANLETAdgeplaregdeltperynalrragvktvrvytryatidlrdddrpvtvrereelpilafdvpepetgeille 329
Cdd:PRK08565 243 LLPSLEQA------------------------------------------------------------------------ 250
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 330 agkeltentkkklvkagvfkvdvlvtsaraesqlikntltKDPTSTEAEALEQIYALLRPGEapnletaraalerlffnP 409
Cdd:PRK08565 251 ----------------------------------------SSIAATVEDALDYIGKRVAIGQ-----------------P 273
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 410 KRYDLGRVGRYkINQRLkvnvpLTHTVLTEED------FVA-IIRYLIELSEGRGYTDDIDHLGNRRVRTVGELIANQFS 482
Cdd:PRK08565 274 REYRIERAEQI-LDKYL-----LPHLGTSPEDrikkayFLGqMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFR 347
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 483 VGLSRMARLIKERMSIN-NDPEKITLDDLVNARTVSA-VIQAFF------GSSQLSQFMDQTNPLAELTHKRRLsaLGPg 554
Cdd:PRK08565 348 VAFKQLVKDLKYQLEKSyARGRKLDLRAIVRPDIITErIRHALAtgnwvgGRTGVSQLLDRTNYLSTLSHLRRV--VSP- 424
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 555 gLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLSCYGRV-------------NDLGFI------ETPY----RV 611
Cdd:PRK08565 425 -LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQIsvgvdeeeveeilYELGVVpveearEEEYiswsRV 503
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 612 VRGGR----------VTDEIKWLSASEEEEYAVaqaNAAVDELGNFTTDLVLCR------------------KRDDYPLL 663
Cdd:PRK08565 504 YLNGRligyhpdgeeLAEKIRELRRSGKISDEV---NVAYIETGEINEVYVNCDsgrvrrplivvengkpklTREHVEKL 580
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 664 PPSRIDF-----------------------------------MDVAPEQLVSIAAALIPFLEHDDANRALMGSNMQRQSV 708
Cdd:PRK08565 581 KKGELTFddlvkmgvieyldaeeeenayvaldpedltpehthLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSL 660
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 709 P----------------LLFPRAPLVGTgledvvardsgavvvarragrvskvtadeiivdtgvdvggsgetplaRLMQH 772
Cdd:PRK08565 661 GlyaanfrirtdtrghlLHYPQRPLVQT-----------------------------------------------RALEI 693
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 773 DRYrlkkfwrtnqdtaiNQRPlirvgdkvkaeqviadgpgteggqiaLGANVTVAFMPWYGHNFEDAIVLSERLVKDDTY 852
Cdd:PRK08565 694 IGY--------------NDRP--------------------------AGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA 733
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 853 SSIHIQELELHVRDTKRGQE-EITREIPNVS----EESLVDLDERGIVRIGAHVKPGDILVGKITPKgetELSPEEKLLT 927
Cdd:PRK08565 734 RSTFFRTYETEERKYPGGQEdKIEIPEPNVRgyrgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELS 810
|
1050 1060 1070
....*....|....*....|....*....|
gi 874574201 928 AIFGEKakdvKDSSLRVPPGMEGVVIDVKI 957
Cdd:PRK08565 811 LGLQER----RDTSVTVRHGEKGIVDTVLI 836
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
22-518 |
6.48e-34 |
|
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: 135.20 E-value: 6.48e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 22 LLDVQTRSFSALLSpdgDSARTDISLERVFREVFPIADVNGN---YSLEFVKFAIGDPKYAV----------EECIERDM 88
Cdd:pfam04563 2 LVRQQLDSFNEFVD---NDLQKIIDENALIESEFEIQHPGENgdkLSLKFGQIRLGKPMFDEtdgstreiypQECRLRNL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 89 TYSAPLKATLRLVVMETLEtgvkrpknIIEKEVYLGELPILT------------------------PLGTFVINGAERVV 144
Cdd:pfam04563 79 TYSAPLYVDLELSVYNGED--------IKPIEVFIGRLPIMLrsnacilsgateselvklgecpldPGGYFIINGSEKVI 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 145 VSQLHRS---PGVVFEET---VHPNGQRLYSARI--IPFRGSWVEF-TVDIHDVIYVHIDK-KKKFPATALLRAFGYGTN 214
Cdd:pfam04563 151 VAQEHRSrnhPIVFKKADpkkRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYiKKEIPIVIILRALGFTSD 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 215 NDILRLfyatksldltqkfeervlrrevigaliaeqvanletadgeplaregdeltperynalrragvktvrvytryati 294
Cdd:pfam04563 231 REIFEL-------------------------------------------------------------------------- 236
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 295 dlrdddrpvtvrereelpiLAFDVPEPETGEILLEagkELTEntkkklvkagVFKVDVlvtsaraesqlikntltkdptS 374
Cdd:pfam04563 237 -------------------ICYDVNDQQLQEELLP---SLEE----------GFKIRI---------------------Q 263
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 375 TEAEALEQIYALLR------PGEAPNLETARAAL-ERLFFNPKRYDLGRVGRYKInqrlkvnvplthtvlteedFVAIIR 447
Cdd:pfam04563 264 TQEQALDYIGGRGRaifrmgRPREPRIKYAEEILqKEVLPHLGTYELDETKKAYF-------------------IGYMIR 324
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 874574201 448 YLIELSEGRGYTDDIDHLGNRRVRTVGELIANQFSVGLSRMARLIKERMSIN-NDPEKITLDDLVNARTVSA 518
Cdd:pfam04563 325 RLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVlGSPDDLMLQLLVNAKPITS 396
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
531-594 |
3.49e-33 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 122.25 E-value: 3.49e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 874574201 531 QFMDQTNPLAELTHKRRLSAlGPGGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSLS 594
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLA 63
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
609-674 |
2.94e-28 |
|
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.
Pssm-ID: 463067 [Multi-domain] Cd Length: 66 Bit Score: 108.22 E-value: 2.94e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 874574201 609 YRVVRGGRVTDEIKWLSASEEEEYAVAQANAAVDELGNFTTDLVLCRKRDDYPLLPPSRIDFMDVA 674
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
21-593 |
2.96e-27 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 116.97 E-value: 2.96e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 21 HLLDVQTRSFSALLspdgdsartDISLERVFREVFPI-ADVNGNYSLEFVKFAIGDPK-----------YAVEECIeRDM 88
Cdd:PRK09606 17 RLVRHHIDSYNDFV---------DNGLQKIIDEQGPIeTEIEDGVYVELGKIRVGKPVvkeadgsereiYPMEARL-RNL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 89 TYSAPLKATLRLVVMETLETGVkrpkniiekEVYLGELPI------------------------LTPLGTFVINGAERVV 144
Cdd:PRK09606 87 TYSAPLYLEMSPVEGGEEEEPE---------EVYIGELPVmvgskicnlyglseeelievgedpLDPGGYFIVNGSERVL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 145 VSQLHRSPGVVFEETVHPNGQRLYSARIIP-FRGSWVEFTVDIHDVIYVHIDkkkkFPATA-------LLRAFGYGTNND 216
Cdd:PRK09606 158 MTLEDLAPNKILVEKDERYGDRIEVAKVFSqRRGYRALVTVERNRDGLLEVS----FPSVPgsipfviLMRALGLETDEE 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 217 IlrlfyatksldltqkfeervlrrevigaliAEQVANletadgeplaregdeltperynalrragvktvrvytryatidl 296
Cdd:PRK09606 234 I------------------------------VEAVSD------------------------------------------- 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 297 rdddrpvtvrereelpilafdvpEPETGEILLEagkeltentkkKLVKAGVfkvdvlvtsaraesqlikntltkdptSTE 376
Cdd:PRK09606 241 -----------------------DPEIVKFMLE-----------NLEEAEV--------------------------DTQ 260
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 377 AEALEQIYALLRPGEApnletaraalerlffnpKRYDLGRvGRYKINQRLkvnvpLTHTVLTEEDFVAIIRYL------- 449
Cdd:PRK09606 261 EEALEYIGKRVAPGQT-----------------KEYRIKR-AEYVIDRYL-----LPHLGVEPEVRRAKAHYLgrmaeac 317
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 450 IELSEGRGYTDDIDHLGNRRVRTVGELIANQFSVGLSRMARLIK---ERMSI-NNDPEKITL--DDLVNARTVSAVIQAF 523
Cdd:PRK09606 318 FELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKyqlERANMrNRELSIKTAvrSDVLTERLEHAMATGN 397
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 874574201 524 F--GSSQLSQFMDQTNPLAELTHKRRLSAlgpgGLTRERAGFEVRDVHYSQYGRMCPIETPEGPNIGLITSL 593
Cdd:PRK09606 398 WvgGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNF 465
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
375-471 |
1.94e-16 |
|
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: 78.54 E-value: 1.94e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 874574201 375 TEAEALEQIYAL--LRPGEAPNLETARAALERlffnpkrydlgRVGRYKINQRLKVNVPLTHTVLTEEDFVAIIRYLIEL 452
Cdd:pfam04561 98 TQEEALDYIGKGfaLRRGEEPRLQRAREILYS-----------RDPKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNL 166
|
90
....*....|....*....
gi 874574201 453 SEGRGYTDDIDHLGNRRVR 471
Cdd:pfam04561 167 KLGRRKPDDIDHLGNKRVR 185
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
314-352 |
7.99e-04 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 43.52 E-value: 7.99e-04
10 20 30
....*....|....*....|....*....|....*....
gi 874574201 314 LAFDVPEPETGEILLEAGKELTENTKKKLVKAGVFKVDV 352
Cdd:PRK00566 811 LAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKI 849
|
|
| |
