|
Name |
Accession |
Description |
Interval |
E-value |
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
3-608 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 1273.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 3 QAREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTGEVIVNADAGRARRPLIVVENGEPLLDDEHVE 82
Cdd:PRK07225 1 MMRKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 83 AVQSGELSFEDLIERGYIEFIDAEEEEDIYVAVDEDDLEPNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQ 162
Cdd:PRK07225 81 KLKNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 163 SLGLPAANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFF 242
Cdd:PRK07225 161 SLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFF 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 243 RTYEGEERRYPGGQEDRFEIPSQDVRGARGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMgGLSPQKRR 322
Cdd:PRK07225 241 RTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDF-GISPEKRR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 323 ETSVTMRSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPH 402
Cdd:PRK07225 320 ETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPH 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 403 ALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKL 482
Cdd:PRK07225 400 AIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKL 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 483 YHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENVE 562
Cdd:PRK07225 480 HHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKK 559
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 525457092 563 QRRVYCPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLKLEDAV 608
Cdd:PRK07225 560 RNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELEDKV 605
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
9-608 |
0e+00 |
|
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: 1110.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 9 VYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTGEVIVNADAGRARRPLIVVENGEPLLDDEHVEAVQSGE 88
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 89 LSFEDLIERGYIEFIDAEEEEDIYVAVDEDDLEPNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPA 168
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 169 ANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGE 248
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 249 ERRYPGGQEDRFEIPSQDVRGARGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMGgLSPQKRRETSVTM 328
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFG-LVTERRRDTSVTV 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 329 RSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRM 408
Cdd:TIGR03670 320 RHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRM 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 409 TVGHVLEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSN 488
Cdd:TIGR03670 400 TVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVAD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 489 KLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENVEQRRVYC 568
Cdd:TIGR03670 480 KIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYC 559
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 525457092 569 PNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLKLEDAV 608
Cdd:TIGR03670 560 PVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGDKV 599
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
120-603 |
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: 676.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 120 LEPNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHLLHYPQLSMVKTQTTEQIG 199
Cdd:cd00653 391 VEKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIA 470
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 200 FDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGEERRYPGGQEDRFEIPSQDVRgargEDAYTHL 279
Cdd:cd00653 471 FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVS----EEKLKNL 546
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 280 DEDGLVNPETVVDENSVLLGKTSPPRFlEEPDDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGE---DGSKLSKVSVR 356
Cdd:cd00653 547 DEDGIIRPGARVEPGDILVGKITPKGE-TESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRElndGGNKLVKVYIR 625
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 357 DERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQG 436
Cdd:cd00653 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDG 705
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 437 ENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLR 516
Cdd:cd00653 706 AEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQR 785
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 517 VGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENveqrrvYCPNCGEETDIHEIEMSYAFKLLLDEMKAL 596
Cdd:cd00653 786 FGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYAFKLLFQELQSM 859
|
....*..
gi 525457092 597 GIAPRLK 603
Cdd:cd00653 860 NIDPRLK 866
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
60-606 |
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: 648.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 60 GRARRPLIVVENGepLLDDEhveavqsgelsfedliergyIEFIDAEEEEDIYVAVDEDDLEPN---------------- 123
Cdd:COG0085 445 GFIETPYRKVENG--KVTDE--------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgee 502
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 124 -------HTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRirpdtrqhLLHYPQLSMVKT-QTT 195
Cdd:COG0085 503 vlvppeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPLQKFQRSnQGT 574
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 196 -----------EQIG------------FDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGEERRY 252
Cdd:COG0085 575 cinqrpivrvgDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDT 654
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 253 PGGQEDR-FEIPSQdvrgarGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMG------GLSPQKRRETS 325
Cdd:COG0085 655 KLGPEEItRDIPNV------SEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERllraifGEKAREVRDTS 728
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 326 VTMRSGEDGVVDTVTLMEGEDGSKLS-------KVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLV 398
Cdd:COG0085 729 LRVPHGEKGKVIDVKVFSREEGDELPpgvnklvRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIV 808
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 399 LNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIF 478
Cdd:COG0085 809 LNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMY 888
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 479 YHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDrefievcGNCGMSAV 558
Cdd:COG0085 889 YLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD-------DVCGRVKV 961
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 525457092 559 ENveqRRVycpncgEETDIHEIEMSYAFKLLLDEMKALGIAPRLKLED 606
Cdd:COG0085 962 YE---AIV------KGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
139-511 |
0e+00 |
|
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: 516.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 139 AGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEG 218
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYTG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 219 FNIEDALVMNKGSVDRAMARSHFFRTYEgeERRYPGGQ-EDRFEIPSQDvrgarGEDAYTHLDEDGLVNPETVVDENSVL 297
Cdd:pfam00562 82 YNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 298 LGKTSPPRFLEEPDDMGGLSPQKRRETSVTMRSGEDGVVDTVTLME-GEDGSKLSKVSVRDERIPELGDKFASRHGQKGV 376
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFElPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 377 VGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENE--DELRGALEEHGFKSS 454
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTevEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 525457092 455 GKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAR 511
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
3-608 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 1273.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 3 QAREAKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTGEVIVNADAGRARRPLIVVENGEPLLDDEHVE 82
Cdd:PRK07225 1 MMRKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 83 AVQSGELSFEDLIERGYIEFIDAEEEEDIYVAVDEDDLEPNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQ 162
Cdd:PRK07225 81 KLKNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 163 SLGLPAANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFF 242
Cdd:PRK07225 161 SLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFF 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 243 RTYEGEERRYPGGQEDRFEIPSQDVRGARGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMgGLSPQKRR 322
Cdd:PRK07225 241 RTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDF-GISPEKRR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 323 ETSVTMRSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPH 402
Cdd:PRK07225 320 ETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPH 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 403 ALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKL 482
Cdd:PRK07225 400 AIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKL 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 483 YHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENVE 562
Cdd:PRK07225 480 HHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKK 559
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 525457092 563 QRRVYCPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLKLEDAV 608
Cdd:PRK07225 560 RNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELEDKV 605
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
9-608 |
0e+00 |
|
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: 1110.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 9 VYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTGEVIVNADAGRARRPLIVVENGEPLLDDEHVEAVQSGE 88
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 89 LSFEDLIERGYIEFIDAEEEEDIYVAVDEDDLEPNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPA 168
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 169 ANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGE 248
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 249 ERRYPGGQEDRFEIPSQDVRGARGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMGgLSPQKRRETSVTM 328
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFG-LVTERRRDTSVTV 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 329 RSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRM 408
Cdd:TIGR03670 320 RHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRM 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 409 TVGHVLEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSN 488
Cdd:TIGR03670 400 TVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVAD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 489 KLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENVEQRRVYC 568
Cdd:TIGR03670 480 KIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDKRKGTAYC 559
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 525457092 569 PNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLKLEDAV 608
Cdd:TIGR03670 560 PVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGDKV 599
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
7-608 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1042.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 7 AKVYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSV--KERTGEVIVNADAGRARRPLIVVENGEPLLDDEHVEAV 84
Cdd:PRK08565 501 SRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYieTGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKL 580
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 85 QSGELSFEDLIERGYIEFIDAEEEEDIYVAVDEDDLEPNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSL 164
Cdd:PRK08565 581 KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSL 660
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 165 GLPAANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRT 244
Cdd:PRK08565 661 GLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRT 740
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 245 YEGEERRYPGGQEDRFEIPSQDVRGARGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMGGLsPQKRRET 324
Cdd:PRK08565 741 YETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLG-LQERRDT 819
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 325 SVTMRSGEDGVVDTVTLMEGEDGSKLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHAL 404
Cdd:PRK08565 820 SVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAI 899
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 405 PSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYH 484
Cdd:PRK08565 900 PSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 485 MVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENVEQR 564
Cdd:PRK08565 980 MVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKN 1059
|
570 580 590 600
....*....|....*....|....*....|....*....|....
gi 525457092 565 RVYCPNCGEETDIHEIEMSYAFKLLLDEMKALGIAPRLKLEDAV 608
Cdd:PRK08565 1060 KYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGDKV 1103
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
120-603 |
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: 676.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 120 LEPNHTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHLLHYPQLSMVKTQTTEQIG 199
Cdd:cd00653 391 VEKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIA 470
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 200 FDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGEERRYPGGQEDRFEIPSQDVRgargEDAYTHL 279
Cdd:cd00653 471 FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVS----EEKLKNL 546
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 280 DEDGLVNPETVVDENSVLLGKTSPPRFlEEPDDMGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGE---DGSKLSKVSVR 356
Cdd:cd00653 547 DEDGIIRPGARVEPGDILVGKITPKGE-TESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRElndGGNKLVKVYIR 625
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 357 DERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQG 436
Cdd:cd00653 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDG 705
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 437 ENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLR 516
Cdd:cd00653 706 AEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQR 785
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 517 VGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENveqrrvYCPNCGEETDIHEIEMSYAFKLLLDEMKAL 596
Cdd:cd00653 786 FGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYAFKLLFQELQSM 859
|
....*..
gi 525457092 597 GIAPRLK 603
Cdd:cd00653 860 NIDPRLK 866
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
60-606 |
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: 648.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 60 GRARRPLIVVENGepLLDDEhveavqsgelsfedliergyIEFIDAEEEEDIYVAVDEDDLEPN---------------- 123
Cdd:COG0085 445 GFIETPYRKVENG--KVTDE--------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgee 502
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 124 -------HTHLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRirpdtrqhLLHYPQLSMVKT-QTT 195
Cdd:COG0085 503 vlvppeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------LLHYPLQKFQRSnQGT 574
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 196 -----------EQIG------------FDERPAAQNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGEERRY 252
Cdd:COG0085 575 cinqrpivrvgDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDT 654
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 253 PGGQEDR-FEIPSQdvrgarGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEEPDDMG------GLSPQKRRETS 325
Cdd:COG0085 655 KLGPEEItRDIPNV------SEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERllraifGEKAREVRDTS 728
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 326 VTMRSGEDGVVDTVTLMEGEDGSKLS-------KVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLV 398
Cdd:COG0085 729 LRVPHGEKGKVIDVKVFSREEGDELPpgvnklvRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIV 808
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 399 LNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIF 478
Cdd:COG0085 809 LNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMY 888
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 479 YHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDrefievcGNCGMSAV 558
Cdd:COG0085 889 YLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD-------DVCGRVKV 961
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 525457092 559 ENveqRRVycpncgEETDIHEIEMSYAFKLLLDEMKALGIAPRLKLED 606
Cdd:COG0085 962 YE---AIV------KGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
139-511 |
0e+00 |
|
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: 516.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 139 AGMIPYPEHNASPRITMGAGMMKQSLGLPAANYRIRPDTRQHLLHYPQLSMVKTQTTEQIGFDERPAAQNFVVAVMSYEG 218
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYTG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 219 FNIEDALVMNKGSVDRAMARSHFFRTYEgeERRYPGGQ-EDRFEIPSQDvrgarGEDAYTHLDEDGLVNPETVVDENSVL 297
Cdd:pfam00562 82 YNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 298 LGKTSPPRFLEEPDDMGGLSPQKRRETSVTMRSGEDGVVDTVTLME-GEDGSKLSKVSVRDERIPELGDKFASRHGQKGV 376
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFElPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 377 VGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENE--DELRGALEEHGFKSS 454
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTevEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 525457092 455 GKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAR 511
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
65-598 |
3.20e-72 |
|
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: 251.12 E-value: 3.20e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 65 PLIVVENGEPLLDDEhveavqsgelsfedliergyIEFIDAEEEEDIYVA-----VDEDD-----------------LEP 122
Cdd:TIGR02013 466 PYRKVKDGKVVVTDE--------------------IDYLTADEEDNYVIAqanapLDENGrfvedlvvaryrgeitlVSP 525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 123 NH-THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGL----------------------------------- 166
Cdd:TIGR02013 526 DQvDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLlrseaplvgtgmeakvardsgavivakrggvveyv 605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 167 PAANYRIRPDTRQHLLHYPQL--SMVKTQTTEQ-IGFDERPA--------------------------AQNFVVAVMSYE 217
Cdd:TIGR02013 606 DAKRIVIRYDEDEEEPDGGIDiyRLLKYQRSNQdTCINQRPIvsvgdrveagdvladgpstdlgelalGRNVLVAFMPWN 685
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 218 GFNIEDALVMNKGSVDRAMARSHFFRTYEGEERRYPGGQED-RFEIPsqDVrgarGEDAYTHLDEDGLVNPETVVDENSV 296
Cdd:TIGR02013 686 GYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEiTRDIP--NV----SEEALRNLDENGIVRIGAEVKAGDI 759
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 297 LLGKTSPPRFLEepddmggLSPQKR-------------RETSVTMRSGEDGVVDTVTLMEGEDG-------SKLSKVSVR 356
Cdd:TIGR02013 760 LVGKVTPKGETE-------LTPEEKllraifgekardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIA 832
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 357 DERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEM-LG--GKVGALEGRRVDGTA 433
Cdd:TIGR02013 833 QKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThLGwaGKRLGRKGVPIATPV 912
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 434 FQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREG 513
Cdd:TIGR02013 913 FDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 992
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 514 GLRVGEMEREVLIGHGAAMALKERLLDSSDrefiEVCGNcgMSAVENVEQrrvycpncGEetDIHEIEMSYAFKLLLDEM 593
Cdd:TIGR02013 993 GQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVVGR--TKAYEAIVK--------GE--NVPEPGIPESFNVLIKEL 1056
|
....*
gi 525457092 594 KALGI 598
Cdd:TIGR02013 1057 QSLGL 1061
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
207-598 |
5.60e-60 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 216.51 E-value: 5.60e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 207 QNFVVAVMSYEGFNIEDALVMNKGSV--DR----------AMARShffrTYEGEErrypggqEDRFEIPsqDVrgarGED 274
Cdd:PRK00405 717 QNVLVAFMPWNGYNFEDAILISERLVkeDVftsihieeyeIEARD----TKLGPE-------EITRDIP--NV----SEE 779
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 275 AYTHLDEDGLVNPETVVDENSVLLGKTSPPRflEEPddmggLSPQKR-------------RETSVTMRSGEDG-VVDTVT 340
Cdd:PRK00405 780 ALRNLDESGIVRIGAEVKPGDILVGKVTPKG--ETE-----LTPEEKllraifgekardvKDTSLRVPHGEEGtVIDVKV 852
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 341 LMEGEDGS-------KLSKVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHV 413
Cdd:PRK00405 853 FTRIEQGDelppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQI 932
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 414 LEMLGGKVGALEGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHAR 493
Cdd:PRK00405 933 LETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHAR 1012
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 494 SRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSDrefievcgncgmsaveNVEQR-RVYcpNC- 571
Cdd:PRK00405 1013 STGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----------------DVVGRtKVY--EAi 1074
|
410 420
....*....|....*....|....*....
gi 525457092 572 --GEetDIHEIEMSYAFKLLLDEMKALGI 598
Cdd:PRK00405 1075 vkGE--NIPEPGIPESFNVLVKELQSLGL 1101
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
129-598 |
1.28e-56 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 206.48 E-value: 1.28e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 129 IDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGL---------------------------------PAANYRI-- 173
Cdd:CHL00207 512 ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLlypekpivgtgyekqialdsgmtiisltegivvSVSAYKIii 591
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 174 RPDTRQHLLHYPQLSMVKTQTT-----------EQI------------GFDERPAAQNFVVAVMSYEGFNIEDALVMNKG 230
Cdd:CHL00207 592 QDDNNRYIHYYLQKYQRSNQNTcinyrpivwvgEKInigqiladgsdiDNSELALGQNVLVAYMPWEGYNFEDAILINKR 671
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 231 SVDRAMARSHFFRTYEGEERRYPGGQED-RFEIPSQdvrgarGEDAYTHLDEDGLVNPETVVDENSVLLGKTSPPRFLEE 309
Cdd:CHL00207 672 LVYEDLFTSIHIEKYEIELRQTKLGSEEiTRNIPNV------SEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQ 745
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 310 PDD------MGGLSPQKRRETSVTMRSGEDG-VVDTVTLMEgEDGSKLS-------KVSVRDERIPELGDKFASRHGQKG 375
Cdd:CHL00207 746 LPEgkllraIFGEKAKDVKDTSLRMPNGGYGrVIKVEIFSR-SKGDELKfgyylkiRVFIAQIRKIQVGDKLAGRHGNKG 824
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 376 VVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGTAFQGENEDE---------LRGAL 446
Cdd:CHL00207 825 IISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEysrilinnkLNQAS 904
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 447 EEHGFK------SSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEM 520
Cdd:CHL00207 905 IKNNEYwlfnsyHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEM 984
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 521 EREVLIGHGAAMALKERLLDSSD----REFIevcgncgMSAVENVEQrrvycpncgeetdIHEIEMSYAFKLLLDEMKAL 596
Cdd:CHL00207 985 EVWALEAFGAAYTLKELLTIKSDdmqgRNET-------LNAIVKGQP-------------IPKPGTPESFKVLMRELQSL 1044
|
..
gi 525457092 597 GI 598
Cdd:CHL00207 1045 GL 1046
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
207-543 |
1.51e-47 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 179.71 E-value: 1.51e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 207 QNFVVAVMSYEGFNIEDALVMNKGSVDRAMARSHFFRTYEGEERRYPGGQEdRF--EIPSQDVRGARgedaytHLDEDGL 284
Cdd:CHL00001 653 KNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPE-RItkEIPHLEAHLLR------NLDKNGI 725
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 285 VNPETVVDENSVLLGKTSP---PRFLEEPDD-----MGGLSPQKRRETSVTMRSGEDGVVDTVTLMEGEDGSKLSKVSVR 356
Cdd:CHL00001 726 VMLGSWVETGDILVGKLTPqeaEESSYAPEGrllraIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPETIH 805
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 357 ----DERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEMLGGKVGALEGRRVDGT 432
Cdd:CHL00001 806 vyilQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIA 885
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 433 AFQGENEDE---------LRGALEEHG----FK--SSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGP 497
Cdd:CHL00001 886 PFDERYEQEasrklvfseLYEASKQTAnpwvFEpeYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGP 965
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 525457092 498 VQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSD 543
Cdd:CHL00001 966 YALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
513-605 |
1.41e-36 |
|
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: 131.17 E-value: 1.41e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 513 GGLRVGEMEREVLIGHGAAMALKERLLDSSDREFIEVCGNCGMSAVENveqrrvYCPNCGEETDIHEIEMSYAFKLLLDE 592
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYN------KCPICKGETDISPGYIPESFKLLFQE 74
|
90
....*....|...
gi 525457092 593 MKALGIAPRLKLE 605
Cdd:pfam04560 75 LQSLGIDPRLLLE 87
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
125-598 |
2.98e-35 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 142.76 E-value: 2.98e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 125 THLEIDPQLIFGIGAGMIPYPEHNASPRITMGAGMMKQSLGL-----------------------------------PAA 169
Cdd:PRK09603 665 TLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLlrsdapivgtgiekiiardswgaikanragvvekiDSK 744
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 170 NYRI--RPDTRQHLLHYP--------------QLSMVK---TQTTEQIGFD-------ERPAAQNFVVAVMSYEGFNIED 223
Cdd:PRK09603 745 NIYIlgEGKEEAYIDAYSlqknlrtnqntsfnQVPIVKvgdKVEAGQIIADgpsmdrgELALGKNVRVAFMPWNGYNFED 824
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 224 ALVMNKGSV-DRAMARSHFFRTyEGEERRYPGGQEdrfEIpSQDVRGARgEDAYTHLDEDGLVNPETVVDENSVLLGKTS 302
Cdd:PRK09603 825 AIVVSERITkDDIFTSTHIYEK-EVDARELKHGVE---EF-TADIPDVK-EEALAHLDESGIVKVGTYVSAGMILVGKTS 898
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 303 P-------------------------------PRFLE--------------EPDD--MGGLSPQKR-------------- 321
Cdd:PRK09603 899 PkgeikstpeerllraifgdkaghvvnkslycPPSLEgtvidvkvftkkgyEKDArvLSAYEEEKAkldmehfdrltmln 978
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 322 RETSVTMRS-------GEDGVVDTVTLMEG-----------------------------------------------EDG 347
Cdd:PRK09603 979 REELLRVSSllsqailEEPFSHNGKDYKEGdqipkeeiasinrftlaslvkkyskevqnhyeitknnfleqkkvlgeEHE 1058
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 348 SKLS----------------KVSVRDERIPELGDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVG 411
Cdd:PRK09603 1059 EKLSilekddilpngvikkvKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIG 1138
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 412 HVLEMLGGKVGALEGRRVDGT----------------------------------------------------------A 433
Cdd:PRK09603 1139 QILEMHLGLVGKEFGKQIASMledktkdfakelrakmleianainekdpltihalencsdeelleyakdwskgvkmaipV 1218
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 434 FQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYHKLYHMVSNKLHARSRGPVQVLTRQPTEGRAREG 513
Cdd:PRK09603 1219 FEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFG 1298
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 514 GLRVGEMEREVLIGHGAAMALKERLLDSSDrefievcgncgmsaveNVEQRRVYCPNCGEETDIHEIEMSYAFKLLLDEM 593
Cdd:PRK09603 1299 GQRFGEMEVWALEAYGAAHTLKEMLTIKSD----------------DIRGRENAYRAIAKGEQVGESEIPETFYVLTKEL 1362
|
....*
gi 525457092 594 KALGI 598
Cdd:PRK09603 1363 QSLAL 1367
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
364-543 |
1.02e-26 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 116.26 E-value: 1.02e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 364 GDKFASRHGQKGVVGHLAPQEDMPFTQEGVVPDLVLNPHALPSRMTVGHVLEM--------LGGKVGAL----------- 424
Cdd:PRK14844 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILEThvgwackkLGEKVGNIldeinkiksaf 1163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 --------------------------------------------------------------------------------
Cdd:PRK14844 1164 ckgirslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnscksaysnlrnflievyscgs 1243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 525457092 425 ------------------------EGRRVDGTAFQGENEDELRGALEEHGFKSSGKEVMYSGVTGEKIDAEIFVGTIFYH 480
Cdd:PRK14844 1244 nvsicnnirdisdnnliefarklrDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 525457092 481 KLYHMVSNKLHARSRGPVQVLTRQPTEGRAREGGLRVGEMEREVLIGHGAAMALKERLLDSSD 543
Cdd:PRK14844 1324 KLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
9-70 |
5.63e-25 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 97.82 E-value: 5.63e-25
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 525457092 9 VYVNGSLVGTHPDPNQLAAQIREARRRGDVSQMVNVSVKERTGEVIVNADAGRARRPLIVVE 70
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
91-131 |
8.03e-13 |
|
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pssm-ID: 428013 [Multi-domain] Cd Length: 53 Bit Score: 62.94 E-value: 8.03e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 525457092 91 FEDLIERGYIEFIDAEEEEDIYVAVDEDDLEP------------NHTHLEIDP 131
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEEssreeregpyahTYTHCEIHP 53
|
|
| OrfB_Zn_ribbon |
pfam07282 |
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a ... |
550-576 |
6.29e-03 |
|
Putative transposase DNA-binding domain; This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding.
Pssm-ID: 284650 [Multi-domain] Cd Length: 69 Bit Score: 35.65 E-value: 6.29e-03
10 20
....*....|....*....|....*..
gi 525457092 550 CGNCGMSAVENVEQRRVYCPNCGEETD 576
Cdd:pfam07282 31 CSVCGHKNKESLSGRTFVCPNCGFVAD 57
|
|
| |
