|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
48-1168 |
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: 902.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 48 LISHQLNSYNYFIEHGLQNVFQSFGEMlvepsfdvvkKKDNDWRYATVKFGEVTVEKPTFFSDDKELEFLPWHARLQNMT 127
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPI----------TDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 128 YSARIKVNVqvevfkntvvksdkfktgqdNYVEKKILDVKKQDILIGSIPVMVKSILCKTSEKG-KENCKKGDCAFDQGG 206
Cdd:cd00653 71 YSAPLYVDI--------------------RLTVNDKGKIKEQEVFIGEIPIMLRSKLCNLNGLTpEELIKLGECPLDPGG 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 207 YFVIKGAEKVFIAQEQMctkrlwisnspwtvsfrsenKRNRFIVRLSENEK-AEdyKRREKVLTVYFLSTeipvwllffa 285
Cdd:cd00653 131 YFIINGTEKVIINQEQR--------------------SPNVIIVEDSKGKRiYT--KTSIPSYSPYRGSW---------- 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 286 LGVSSDKeamdliafdgDDASITNSLIASIHvadavceafrcgNNALTYVEQQIkstkfppaesvdeclhlylfpglqsl 365
Cdd:cd00653 179 LEVKSDK----------KKDRIYVRIDLKRQ------------EEALKYIGKRF-------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 366 kkkaRFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHARRKMTRAMQKHLSGDGDLKPIeHYLDA 445
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQ-LLINS 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 446 SVITNGLSRAFSTGAWSHPFRKMERvSGVVANLGRANPLQTLIDLRRT-RQQVLYTGKVGDARYPHPSHWGRVCFLSTPD 524
Cdd:cd00653 286 KPITSGIKEFLATGNWGSKRFLMQR-SGLSQVLDRLNPLSELSHKRRIsSLGLFRERKGFEVRDLHPSHWGRICPIETPE 364
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 525 GENCGLVKNMSLLGLVStqslesvveklfacgmeelmddtctplfgkhkvllngdwvglcadsesfvaelksrrrqselp 604
Cdd:cd00653 365 GENCGLVKNLALMARIS--------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 605 remeikrdkddnevriftdaGRLLRPLLVVENLqklkqekpsqypfdhlldhgileligieeeedcntawgikqllkepk 684
Cdd:cd00653 382 --------------------GRIERPYRIVEKE----------------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 685 iYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQKHCQqAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKE 764
Cdd:cd00653 395 -VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQ-AVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFG 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 765 VLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVdakdSEKRKKMDELVQFGKTHSKIGKVDSLED 844
Cdd:cd00653 473 ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIEL----RKTKNGPEEITRGDIPNVSEEKLKNLDE 548
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 845 DGFPFIGANMSTGDIVIGRCTESGA---------------DHSIKLKHTERGIVQKVVLSS---NDEGKNFAAVSLRQVR 906
Cdd:cd00653 549 DGIIRPGARVEPGDILVGKITPKGEtestpifgekardvrDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKR 628
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 907 SPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALSKgiacpiqkegsSAAYTKLT 986
Cdd:cd00653 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGK-----------AGALLGKF 697
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 987 RHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVAD 1066
Cdd:cd00653 698 GDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKG 777
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1067 RKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIertpssgrkirgpYCRVCVSSDHVVRVY 1146
Cdd:cd00653 778 RSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN-------------LCRLCKKGTNISKVG 844
|
1130 1140
....*....|....*....|..
gi 79416709 1147 VPYGAKLLCQELFSMGITLNFD 1168
Cdd:cd00653 845 IPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
41-1163 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 710.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 41 SFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEmlVEPSFDVVKkkdndwryatVKFGEVTVEKPTFF-SDDKELEFLPW 119
Cdd:PRK08565 7 AYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGE--IKTEIPGLK----------IVLGKIRVGEPEIKeADGSERPITPM 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 120 HARLQNMTYSARIKVNVQVevfkntvvksdkfktgqdnYVEKKILdvKKQDILIGSIPVMVKSILCKTSE-KGKENCKKG 198
Cdd:PRK08565 75 EARLRNLTYAAPLYLTMIP-------------------VENGIEY--EPEEVKIGDLPIMVKSKICPLSGlSPDELIEIG 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 199 DCAFDQGGYFVIKGAEKVFIAQEQMCTKRLWI----SNSPWT-----VSFRSeNKRNRFIVRlsenekaedyKRREKVLT 269
Cdd:PRK08565 134 EDPKDPGGYFIINGSERVIVSQEDLAPNRVLVdkgeAGSSIThtakvISSRA-GYRAQVTVE----------RRKDGTIY 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 270 VYF--LSTEIPVWLLFFALGVSSDKEAMDLIAFDGDdasITNSLIASIHVADAVceaFRCGNNALTYVEQQI-----KST 342
Cdd:PRK08565 203 VSFpaVPGKIPFVILMRALGLETDRDIVYAVSLDPE---IQQELLPSLEQASSI---AATVEDALDYIGKRVaigqpREY 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 343 KFPPAESVdecLHLYLFPGL----QSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHA 418
Cdd:PRK08565 277 RIERAEQI---LDKYLLPHLgtspEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQL 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 419 RRKMTRAMQKHLSGDGDLKpIEHYLDASVITNGLSRAFSTGAWshPFRKmervSGVVANLGRANPLQTLIDLRR-----T 493
Cdd:PRK08565 354 VKDLKYQLEKSYARGRKLD-LRAIVRPDIITERIRHALATGNW--VGGR----TGVSQLLDRTNYLSTLSHLRRvvsplS 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 494 RQQVLYtgkvgDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEK-LFACGMEELMDDTCTPLFGKH 572
Cdd:PRK08565 427 RGQPHF-----EARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEiLYELGVVPVEEAREEEYISWS 501
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 573 KVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIK--RDKDDNEVRIFTDAGRLLRPLLVVENLQ-KLKQE-----K 644
Cdd:PRK08565 502 RVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAyiETGEINEVYVNCDSGRVRRPLIVVENGKpKLTREhveklK 581
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 645 PSQYPFDHLLDHGILELIGIEEEEDCNTAWGIKQLLKEpkiYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQKhCQ 724
Cdd:PRK08565 582 KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE---HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAM-AK 657
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 725 QAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQ 804
Cdd:PRK08565 658 QSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTF 737
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 805 IRSYKAEvdakdsEKRKKMDELVQFGKTHSKI----GK--VDSLEDDGFPFIGANMSTGDIVIG-----RCTESGA---- 869
Cdd:PRK08565 738 FRTYETE------ERKYPGGQEDKIEIPEPNVrgyrGEeyYRKLDEDGIVSPEVEVKGGDVLIGktsppRFLEELEelsl 811
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 870 ------DHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPD 943
Cdd:PRK08565 812 glqerrDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPD 891
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 944 IVINPHAFPSRQTPGQLLEAalskgIAcpiqkeGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSG 1023
Cdd:PRK08565 892 LIINPHAIPSRMTVGQLLES-----IA------GKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTG 960
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1024 EMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSS 1103
Cdd:PRK08565 961 EKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKT 1040
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1104 QMHICRKCKTYAnviertpSSGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGI 1163
Cdd:PRK08565 1041 TIYVCELCGHIA-------WYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGI 1093
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
574-1163 |
2.66e-153 |
|
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: 471.43 E-value: 2.66e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 574 VLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKDDNEVRIFTDAGRLLRPLLVVENLQ-KLKQE-----KPSQ 647
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKpKLTREhveklKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 648 YPFDHLLDHGILELIGIEEEEDCNTAWGIKQLLKEpkiYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSqKHCQQAI 727
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE---HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA-AMAKQSL 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 728 GFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRS 807
Cdd:TIGR03670 157 GLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRT 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 808 YKAEvdakdsEKRKKMDELVQFGKTHSKIGKVDS------LEDDGFPFIGANMSTGDIVIGRC---------------TE 866
Cdd:TIGR03670 237 YEAE------ERRYPGGQEDRFEIPEPDVRGYRGeeaykhLDEDGIVYPEVEVKGGDVLIGKTspprfleelrefglvTE 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 867 SGADHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVI 946
Cdd:TIGR03670 311 RRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLII 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 947 NPHAFPSRQTPGQLLEAalskgIAcpiqkeGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMM 1026
Cdd:TIGR03670 391 NPHAIPSRMTVGQLLEM-----IA------GKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKL 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1027 RSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMH 1106
Cdd:TIGR03670 460 EAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVY 539
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*..
gi 79416709 1107 ICRKCKTYANViertpssGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGI 1163
Cdd:TIGR03670 540 VCENCGHIAWE-------DKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGI 589
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
41-1163 |
2.47e-140 |
|
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: 450.33 E-value: 2.47e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 41 SFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEmlvepsfdvVKKKDNDWRyatVKFGEVTVEKPtffsddkelEFLPWH 120
Cdd:COG0085 9 EPLELPNLLEIQLDSFNWFLEEGLQEIFDEISP---------IEDFTGNLS---LEFGDYRLGEP---------KYTPEE 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 121 ARLQNMTYSARIKVNVQVeVFKNTVvksdkfktgqdnyvekkilDVKKQDILIGSIPVMVKSilcktsekgkenckkgdc 200
Cdd:COG0085 68 CKERDLTYAAPLYVKVRL-VNKETG-------------------EIKEQEVFMGDFPLMTDS------------------ 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 201 afdqgGYFVIKGAEKVFIAQE------------QMCTKRLW----ISNS-PWTVSFRseNKRNRFIVRLsenekaeDYKR 263
Cdd:COG0085 110 -----GTFIINGTERVIVSQLvrspgvyfveeeDKSGKDLYsakvIPSRgAWLEFET--DKDGTIYVRI-------DRKR 175
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 264 RekvltvyflsteIPVWLLFFALGVSSDKEAMDLIAFDGDDASITNSLIA-SIHVADAvceafrcgnnALTYVEQQIKST 342
Cdd:COG0085 176 K------------IPVTVLLRALGLETDEEILEAFGDDPIQEYILATLEKdNTKTQEE----------ALLEIYRKLRPG 233
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 343 KFPPAESVDECLHLYLF----------------------PGLQSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRI 400
Cdd:COG0085 234 EPPTIERAEQLLDNLFFdpkrydlahvgrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRV 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 401 ELAGELLEREIRVHLA----HARRKMTRAMQKHLSgdgdlkpIEHYLDASVITNGLSRAFSTgawshpfrkmervSGVVA 476
Cdd:COG0085 314 RLVGELLQNQFRVGLSrmerVVRERMTTQDVEAIT-------PQSLINIRPVVAAIKEFFGS-------------SQLSQ 373
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 477 NLGRANPLQTLIDLRR---------TRQQVLYtgkvgDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQsles 547
Cdd:COG0085 374 FMDQTNPLSELTHKRRlsalgpgglSRERAGF-----EVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEY---- 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 548 vveklfacGMEElmddtcTPLFGKHKVLLNGDWVGLCADSE--SFVAELKSrrrqselpremeikrDKDDNevriftdaG 625
Cdd:COG0085 445 --------GFIE------TPYRKVENGKVTDEIEYLTADEEenYYIAQANA---------------PLDED--------G 487
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 626 RLLRPLLVVENLQKLKQEKPSQYpfdhlldhgileligieeeedcntawgikqllkepkiyTHCELDLSFLLGVSCAVVP 705
Cdd:COG0085 488 NFLEERVLVRYRGEEVLVPPEEV--------------------------------------DYMDVSPKQIVSVATSLIP 529
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 706 FANHDHGRRVLYQS--QKhcqQAIGFSSTNPNIRCDTLS------QQLFYPQKPLFKTLasECLKK-EVLFN-------- 768
Cdd:COG0085 530 FLEHDDANRALMGAnmQR---QAVPLLRPEAPLLHYPLQkfqrsnQGTCINQRPIVRVG--DRVEKgDVLADgpatdnge 604
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 769 ---GQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYkaEVDAKDSekrkkmdelvqfgkthsKIGKVD----- 840
Cdd:COG0085 605 lalGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEY--EIEARDT-----------------KLGPEEitrdi 665
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 841 ---------SLEDDGFPFIGANMSTGDIVIGRCTESGA----------------------DHSIKLKHTERGIVQKVVLS 889
Cdd:COG0085 666 pnvseealrNLDEDGIIRIGAEVKGGDILVGKVTPKGEteltpeerllraifgekarevrDTSLRVPHGEKGKVIDVKVF 745
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 890 SNDEGKNFAA-------VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLE 962
Cdd:COG0085 746 SREEGDELPPgvnklvrVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLE 825
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 963 AALSKgiacpiqkegssAAYTKLTRHATP-FSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLV 1041
Cdd:COG0085 826 THLGW------------AAALLGRRVATPvFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLH 893
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1042 HMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHIcrkcKTYaNVIert 1121
Cdd:COG0085 894 HMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRV----KVY-EAI--- 965
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|..
gi 79416709 1122 pssgrkirgpycrvcVSSDHVVRVYVPYGAKLLCQELFSMGI 1163
Cdd:COG0085 966 ---------------VKGENIPEPGIPESFKVLLKELQSLGL 992
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
701-1069 |
1.21e-132 |
|
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: 408.84 E-value: 1.21e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 701 CAVVPFANHDHGRRVLYQSQkHCQQAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHL 780
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCA-MGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 781 GYNQEDSIVMNKASLERGMFRSEQIRSYKAEvdakdsEKRKKMDELVQFGKTHSKIGKVDSLEDDGFPFIGANMSTGDIV 860
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEAR------KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 861 IGRCTES----------------GADHSIKLKHTERGIVQKV-VLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGV 923
Cdd:pfam00562 155 VGKVGPTeltkllraifgekardVKDTSLKVPPGEEGVVDDViVFELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 924 LGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALSKgiacpiqkegsSAAYTKLTRHATPFSTPG--VTEIT 1001
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGK-----------AAALLGVFVDATPFDGASteVEDIG 303
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 79416709 1002 EQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKR 1069
Cdd:pfam00562 304 ELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
574-635 |
3.81e-23 |
|
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: 93.58 E-value: 3.81e-23
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79416709 574 VLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKDDNEVRIFTDAGRLLRPLLVVE 635
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
48-1168 |
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: 902.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 48 LISHQLNSYNYFIEHGLQNVFQSFGEMlvepsfdvvkKKDNDWRYATVKFGEVTVEKPTFFSDDKELEFLPWHARLQNMT 127
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPI----------TDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 128 YSARIKVNVqvevfkntvvksdkfktgqdNYVEKKILDVKKQDILIGSIPVMVKSILCKTSEKG-KENCKKGDCAFDQGG 206
Cdd:cd00653 71 YSAPLYVDI--------------------RLTVNDKGKIKEQEVFIGEIPIMLRSKLCNLNGLTpEELIKLGECPLDPGG 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 207 YFVIKGAEKVFIAQEQMctkrlwisnspwtvsfrsenKRNRFIVRLSENEK-AEdyKRREKVLTVYFLSTeipvwllffa 285
Cdd:cd00653 131 YFIINGTEKVIINQEQR--------------------SPNVIIVEDSKGKRiYT--KTSIPSYSPYRGSW---------- 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 286 LGVSSDKeamdliafdgDDASITNSLIASIHvadavceafrcgNNALTYVEQQIkstkfppaesvdeclhlylfpglqsl 365
Cdd:cd00653 179 LEVKSDK----------KKDRIYVRIDLKRQ------------EEALKYIGKRF-------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 366 kkkaRFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHARRKMTRAMQKHLSGDGDLKPIeHYLDA 445
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQ-LLINS 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 446 SVITNGLSRAFSTGAWSHPFRKMERvSGVVANLGRANPLQTLIDLRRT-RQQVLYTGKVGDARYPHPSHWGRVCFLSTPD 524
Cdd:cd00653 286 KPITSGIKEFLATGNWGSKRFLMQR-SGLSQVLDRLNPLSELSHKRRIsSLGLFRERKGFEVRDLHPSHWGRICPIETPE 364
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 525 GENCGLVKNMSLLGLVStqslesvveklfacgmeelmddtctplfgkhkvllngdwvglcadsesfvaelksrrrqselp 604
Cdd:cd00653 365 GENCGLVKNLALMARIS--------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 605 remeikrdkddnevriftdaGRLLRPLLVVENLqklkqekpsqypfdhlldhgileligieeeedcntawgikqllkepk 684
Cdd:cd00653 382 --------------------GRIERPYRIVEKE----------------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 685 iYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQKHCQqAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKE 764
Cdd:cd00653 395 -VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQ-AVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFG 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 765 VLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVdakdSEKRKKMDELVQFGKTHSKIGKVDSLED 844
Cdd:cd00653 473 ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIEL----RKTKNGPEEITRGDIPNVSEEKLKNLDE 548
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 845 DGFPFIGANMSTGDIVIGRCTESGA---------------DHSIKLKHTERGIVQKVVLSS---NDEGKNFAAVSLRQVR 906
Cdd:cd00653 549 DGIIRPGARVEPGDILVGKITPKGEtestpifgekardvrDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKR 628
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 907 SPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALSKgiacpiqkegsSAAYTKLT 986
Cdd:cd00653 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGK-----------AGALLGKF 697
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 987 RHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVAD 1066
Cdd:cd00653 698 GDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKG 777
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1067 RKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIertpssgrkirgpYCRVCVSSDHVVRVY 1146
Cdd:cd00653 778 RSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN-------------LCRLCKKGTNISKVG 844
|
1130 1140
....*....|....*....|..
gi 79416709 1147 VPYGAKLLCQELFSMGITLNFD 1168
Cdd:cd00653 845 IPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
41-1163 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 710.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 41 SFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEmlVEPSFDVVKkkdndwryatVKFGEVTVEKPTFF-SDDKELEFLPW 119
Cdd:PRK08565 7 AYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGE--IKTEIPGLK----------IVLGKIRVGEPEIKeADGSERPITPM 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 120 HARLQNMTYSARIKVNVQVevfkntvvksdkfktgqdnYVEKKILdvKKQDILIGSIPVMVKSILCKTSE-KGKENCKKG 198
Cdd:PRK08565 75 EARLRNLTYAAPLYLTMIP-------------------VENGIEY--EPEEVKIGDLPIMVKSKICPLSGlSPDELIEIG 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 199 DCAFDQGGYFVIKGAEKVFIAQEQMCTKRLWI----SNSPWT-----VSFRSeNKRNRFIVRlsenekaedyKRREKVLT 269
Cdd:PRK08565 134 EDPKDPGGYFIINGSERVIVSQEDLAPNRVLVdkgeAGSSIThtakvISSRA-GYRAQVTVE----------RRKDGTIY 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 270 VYF--LSTEIPVWLLFFALGVSSDKEAMDLIAFDGDdasITNSLIASIHVADAVceaFRCGNNALTYVEQQI-----KST 342
Cdd:PRK08565 203 VSFpaVPGKIPFVILMRALGLETDRDIVYAVSLDPE---IQQELLPSLEQASSI---AATVEDALDYIGKRVaigqpREY 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 343 KFPPAESVdecLHLYLFPGL----QSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHA 418
Cdd:PRK08565 277 RIERAEQI---LDKYLLPHLgtspEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQL 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 419 RRKMTRAMQKHLSGDGDLKpIEHYLDASVITNGLSRAFSTGAWshPFRKmervSGVVANLGRANPLQTLIDLRR-----T 493
Cdd:PRK08565 354 VKDLKYQLEKSYARGRKLD-LRAIVRPDIITERIRHALATGNW--VGGR----TGVSQLLDRTNYLSTLSHLRRvvsplS 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 494 RQQVLYtgkvgDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEK-LFACGMEELMDDTCTPLFGKH 572
Cdd:PRK08565 427 RGQPHF-----EARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEiLYELGVVPVEEAREEEYISWS 501
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 573 KVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIK--RDKDDNEVRIFTDAGRLLRPLLVVENLQ-KLKQE-----K 644
Cdd:PRK08565 502 RVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAyiETGEINEVYVNCDSGRVRRPLIVVENGKpKLTREhveklK 581
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 645 PSQYPFDHLLDHGILELIGIEEEEDCNTAWGIKQLLKEpkiYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQKhCQ 724
Cdd:PRK08565 582 KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE---HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAM-AK 657
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 725 QAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQ 804
Cdd:PRK08565 658 QSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTF 737
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 805 IRSYKAEvdakdsEKRKKMDELVQFGKTHSKI----GK--VDSLEDDGFPFIGANMSTGDIVIG-----RCTESGA---- 869
Cdd:PRK08565 738 FRTYETE------ERKYPGGQEDKIEIPEPNVrgyrGEeyYRKLDEDGIVSPEVEVKGGDVLIGktsppRFLEELEelsl 811
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 870 ------DHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPD 943
Cdd:PRK08565 812 glqerrDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPD 891
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 944 IVINPHAFPSRQTPGQLLEAalskgIAcpiqkeGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSG 1023
Cdd:PRK08565 892 LIINPHAIPSRMTVGQLLES-----IA------GKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTG 960
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1024 EMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSS 1103
Cdd:PRK08565 961 EKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKT 1040
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1104 QMHICRKCKTYAnviertpSSGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGI 1163
Cdd:PRK08565 1041 TIYVCELCGHIA-------WYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGI 1093
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
574-1163 |
2.66e-153 |
|
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: 471.43 E-value: 2.66e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 574 VLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKDDNEVRIFTDAGRLLRPLLVVENLQ-KLKQE-----KPSQ 647
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKpKLTREhveklKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 648 YPFDHLLDHGILELIGIEEEEDCNTAWGIKQLLKEpkiYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSqKHCQQAI 727
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE---HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA-AMAKQSL 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 728 GFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRS 807
Cdd:TIGR03670 157 GLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRT 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 808 YKAEvdakdsEKRKKMDELVQFGKTHSKIGKVDS------LEDDGFPFIGANMSTGDIVIGRC---------------TE 866
Cdd:TIGR03670 237 YEAE------ERRYPGGQEDRFEIPEPDVRGYRGeeaykhLDEDGIVYPEVEVKGGDVLIGKTspprfleelrefglvTE 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 867 SGADHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVI 946
Cdd:TIGR03670 311 RRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLII 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 947 NPHAFPSRQTPGQLLEAalskgIAcpiqkeGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMM 1026
Cdd:TIGR03670 391 NPHAIPSRMTVGQLLEM-----IA------GKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKL 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1027 RSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMH 1106
Cdd:TIGR03670 460 EAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVY 539
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*..
gi 79416709 1107 ICRKCKTYANViertpssGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGI 1163
Cdd:TIGR03670 540 VCENCGHIAWE-------DKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGI 589
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
571-1163 |
8.78e-145 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 449.41 E-value: 8.78e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 571 KHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKDDNEVRIFTDAGRLLRPLLVVEN---------LQKLK 641
Cdd:PRK07225 4 KAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENgepllteehIEKLK 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 642 QEKPSqypFDHLLDHGILELIGIEEEEDCNTAWGIKQLLKEpkiYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQS-- 719
Cdd:PRK07225 84 NGELT---FDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE---HTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAgm 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 720 QKhcqQAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGM 799
Cdd:PRK07225 158 IK---QSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 800 FRSEQIRSYKAEvdakdsEKRKKMDELVQF-----------GKTHSKigkvdSLEDDGFPFIGANMSTGDIVIGRC---- 864
Cdd:PRK07225 235 GRSHFFRTYEGE------ERRYPGGQEDRFeipdkdvrgyrGEEAYR-----HLDEDGLVNPETEVKEGDVLIGKTsppr 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 865 -----TESGA------DHSIKLKHTERGIVQKVVLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNF 933
Cdd:PRK07225 304 fleepDDFGIspekrrETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDM 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 934 PFTIQGIVPDIVINPHAFPSRQTPGQLLEAALSKgIACpiqKEGSSAAytkltrhATPFSTPGVTEITEQLHRAGFSRWG 1013
Cdd:PRK07225 384 PFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGK-VGS---LEGRRVD-------GTAFSGEDEEDLREALEKLGFEHTG 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1014 NERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLH 1093
Cdd:PRK07225 453 KEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLK 532
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1094 ERLFTLSDSSQMHICRKCKTYANViertpssGRKIRGPYCRVCVSSDHVVRVYVPYGAKLLCQELFSMGI 1163
Cdd:PRK07225 533 ERLLDESDKVEIYVCAKCGMIAIY-------DKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGI 595
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
41-1163 |
2.47e-140 |
|
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: 450.33 E-value: 2.47e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 41 SFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEmlvepsfdvVKKKDNDWRyatVKFGEVTVEKPtffsddkelEFLPWH 120
Cdd:COG0085 9 EPLELPNLLEIQLDSFNWFLEEGLQEIFDEISP---------IEDFTGNLS---LEFGDYRLGEP---------KYTPEE 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 121 ARLQNMTYSARIKVNVQVeVFKNTVvksdkfktgqdnyvekkilDVKKQDILIGSIPVMVKSilcktsekgkenckkgdc 200
Cdd:COG0085 68 CKERDLTYAAPLYVKVRL-VNKETG-------------------EIKEQEVFMGDFPLMTDS------------------ 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 201 afdqgGYFVIKGAEKVFIAQE------------QMCTKRLW----ISNS-PWTVSFRseNKRNRFIVRLsenekaeDYKR 263
Cdd:COG0085 110 -----GTFIINGTERVIVSQLvrspgvyfveeeDKSGKDLYsakvIPSRgAWLEFET--DKDGTIYVRI-------DRKR 175
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 264 RekvltvyflsteIPVWLLFFALGVSSDKEAMDLIAFDGDDASITNSLIA-SIHVADAvceafrcgnnALTYVEQQIKST 342
Cdd:COG0085 176 K------------IPVTVLLRALGLETDEEILEAFGDDPIQEYILATLEKdNTKTQEE----------ALLEIYRKLRPG 233
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 343 KFPPAESVDECLHLYLF----------------------PGLQSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRI 400
Cdd:COG0085 234 EPPTIERAEQLLDNLFFdpkrydlahvgrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRV 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 401 ELAGELLEREIRVHLA----HARRKMTRAMQKHLSgdgdlkpIEHYLDASVITNGLSRAFSTgawshpfrkmervSGVVA 476
Cdd:COG0085 314 RLVGELLQNQFRVGLSrmerVVRERMTTQDVEAIT-------PQSLINIRPVVAAIKEFFGS-------------SQLSQ 373
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 477 NLGRANPLQTLIDLRR---------TRQQVLYtgkvgDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQsles 547
Cdd:COG0085 374 FMDQTNPLSELTHKRRlsalgpgglSRERAGF-----EVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEY---- 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 548 vveklfacGMEElmddtcTPLFGKHKVLLNGDWVGLCADSE--SFVAELKSrrrqselpremeikrDKDDNevriftdaG 625
Cdd:COG0085 445 --------GFIE------TPYRKVENGKVTDEIEYLTADEEenYYIAQANA---------------PLDED--------G 487
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 626 RLLRPLLVVENLQKLKQEKPSQYpfdhlldhgileligieeeedcntawgikqllkepkiyTHCELDLSFLLGVSCAVVP 705
Cdd:COG0085 488 NFLEERVLVRYRGEEVLVPPEEV--------------------------------------DYMDVSPKQIVSVATSLIP 529
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 706 FANHDHGRRVLYQS--QKhcqQAIGFSSTNPNIRCDTLS------QQLFYPQKPLFKTLasECLKK-EVLFN-------- 768
Cdd:COG0085 530 FLEHDDANRALMGAnmQR---QAVPLLRPEAPLLHYPLQkfqrsnQGTCINQRPIVRVG--DRVEKgDVLADgpatdnge 604
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 769 ---GQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYkaEVDAKDSekrkkmdelvqfgkthsKIGKVD----- 840
Cdd:COG0085 605 lalGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEY--EIEARDT-----------------KLGPEEitrdi 665
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 841 ---------SLEDDGFPFIGANMSTGDIVIGRCTESGA----------------------DHSIKLKHTERGIVQKVVLS 889
Cdd:COG0085 666 pnvseealrNLDEDGIIRIGAEVKGGDILVGKVTPKGEteltpeerllraifgekarevrDTSLRVPHGEKGKVIDVKVF 745
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 890 SNDEGKNFAA-------VSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLE 962
Cdd:COG0085 746 SREEGDELPPgvnklvrVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLE 825
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 963 AALSKgiacpiqkegssAAYTKLTRHATP-FSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLV 1041
Cdd:COG0085 826 THLGW------------AAALLGRRVATPvFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLH 893
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1042 HMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHIcrkcKTYaNVIert 1121
Cdd:COG0085 894 HMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRV----KVY-EAI--- 965
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|..
gi 79416709 1122 pssgrkirgpycrvcVSSDHVVRVYVPYGAKLLCQELFSMGI 1163
Cdd:COG0085 966 ---------------VKGENIPEPGIPESFKVLLKELQSLGL 992
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
701-1069 |
1.21e-132 |
|
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: 408.84 E-value: 1.21e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 701 CAVVPFANHDHGRRVLYQSQkHCQQAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKEVLFNGQNAIVAVNVHL 780
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCA-MGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 781 GYNQEDSIVMNKASLERGMFRSEQIRSYKAEvdakdsEKRKKMDELVQFGKTHSKIGKVDSLEDDGFPFIGANMSTGDIV 860
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEAR------KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 861 IGRCTES----------------GADHSIKLKHTERGIVQKV-VLSSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGV 923
Cdd:pfam00562 155 VGKVGPTeltkllraifgekardVKDTSLKVPPGEEGVVDDViVFELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 924 LGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALSKgiacpiqkegsSAAYTKLTRHATPFSTPG--VTEIT 1001
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGK-----------AAALLGVFVDATPFDGASteVEDIG 303
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 79416709 1002 EQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKR 1069
Cdd:pfam00562 304 ELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
41-558 |
4.80e-61 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 217.51 E-value: 4.80e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 41 SFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEmlVEpsFDVVKkkdndwrYATVKFGEVTVEKP-TFFSDDKELEFLPW 119
Cdd:PRK09606 11 AYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGP--IE--TEIED-------GVYVELGKIRVGKPvVKEADGSEREIYPM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 120 HARLQNMTYSARIKVNVqvevfknTVVKSDKfktgqdnyvEKKILDVKkqdilIGSIPVMVKSILCKTSEKG-KENCKKG 198
Cdd:PRK09606 80 EARLRNLTYSAPLYLEM-------SPVEGGE---------EEEPEEVY-----IGELPVMVGSKICNLYGLSeEELIEVG 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 199 DCAFDQGGYFVIKGAEKVFIAQEQMctkrlwisnSPwtvsfrsenkrNRFIVrlsenEKAEDYKRREKV----------- 267
Cdd:PRK09606 139 EDPLDPGGYFIVNGSERVLMTLEDL---------AP-----------NKILV-----EKDERYGDRIEVakvfsqrrgyr 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 268 ------------LTVYF--LSTEIPVWLLFFALGVSSDKEAMDLIafdGDDASITNSLIASIHVADAVCEafrcgNNALT 333
Cdd:PRK09606 194 alvtvernrdglLEVSFpsVPGSIPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEAEVDTQ-----EEALE 265
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 334 YVEQ-----QIKSTKFPPAESVdecLHLYLFPGL----QSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAG 404
Cdd:PRK09606 266 YIGKrvapgQTKEYRIKRAEYV---IDRYLLPHLgvepEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAG 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 405 ELLEREIRVHLAHARRKMTRAMQKHLSGDGDLKpIEHYLDASVITNGLSRAFSTGAWshpfrkmerV---SGVVANLGRA 481
Cdd:PRK09606 343 DLMEDLFRVAFNRLARDVKYQLERANMRNRELS-IKTAVRSDVLTERLEHAMATGNW---------VggrTGVSQLLDRT 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 482 NPLQTLIDLRR-----TRQQVLYtgkvgDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQS-LESVVEKLFAC 555
Cdd:PRK09606 413 DYMATLSHLRRvvsplSRSQPHF-----EARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEdEEEVKEILKEL 487
|
...
gi 79416709 556 GME 558
Cdd:PRK09606 488 GVE 490
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
48-1125 |
2.49e-59 |
|
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: 222.62 E-value: 2.49e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 48 LISHQLNSYNYFI----------EHGLQNVFQSF-------GEMLVEpsfdvvkkkdndwrYATVKFGE--VTVEKptff 108
Cdd:TIGR02013 20 LLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIfpiedytGNIELE--------------YLSYRLGEpkYSVEE---- 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 109 sddkeleflpwhARLQNMTYSARIKVNVQVEVFKNTVVKsdkfktgqdnyvekkilDVKKQDILIGSIPVMVKSilckts 188
Cdd:TIGR02013 82 ------------CKERGLTYSAPLKVKLRLINKEEDGTK-----------------EIKEQDVYMGDIPLMTDR------ 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 189 ekgkenckkgdcafdqgGYFVIKGAEKVFIAQeqmctkrlwISNSPwTVSFRSE---NKRNRFIV-------RLSENEKA 258
Cdd:TIGR02013 127 -----------------GTFIINGAERVVVSQ---------LHRSP-GVFFSSEkdtTKSGKVLFsariipyRGSWLEFE 179
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 259 EDYKrreKVLTVYFLST-EIPVWLLFFALGVSSDKEAMDLIafdGDDASITNSLIA--SIHVADAVCEAF---RCGNNAL 332
Cdd:TIGR02013 180 TDKK---DVLYVRIDRKrKLPATVLLRALGYTIDTLILNRL---GSGEYIRNTLRKdpTNSEEEALVEIYrklRPGEPPT 253
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 333 TYVEQQ-IKSTKFPPAE---------SVDECLHLYLFPGLQSLKKKArFLGYMvKCLLNSYAGKRKCENRDSFRNKRIEL 402
Cdd:TIGR02013 254 VEAARSlLENLFFDPKRydlgrvgryKLNKKLGLDVPESIGVLTKED-IIATI-KYLIKLRNGKGEIDDIDHLGNRRIRS 331
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 403 AGELLEREIRVHLAharrKMTRAMQKHLS-GDGD-LKPIEhYLDASVITNGLSRAFSTGAWSHpFrkMERVsgvvanlgr 480
Cdd:TIGR02013 332 VGELLQNQFRVGLA----RMERIVRERMStQDTDtLTPQD-LINAKPISAAIKEFFGSSQLSQ-F--MDQT--------- 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 481 aNPLQTLIDLRR---------TRQQVLYtgkvgDARYPHPSHWGRVCFLSTPDGENCGLVKNMSL------LGLVSTQSL 545
Cdd:TIGR02013 395 -NPLAELTHKRRlsalgpgglTRERAGF-----EVRDVHPTHYGRICPIETPEGPNIGLINSLSTyarvneYGFIETPYR 468
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 546 ESVVEKlfacgmeelmddtctplfgkhkVLLNGDWVGLCADSES--FVAelksrrrQSELPRemeikrdkDDNevriftd 623
Cdd:TIGR02013 469 KVKDGK----------------------VVVTDEIDYLTADEEDnyVIA-------QANAPL--------DEN------- 504
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 624 aGRLLRPLLVVenlqKLKQEKPsqypfdhlldhgileligieeeedcntawgikqlLKEPKIYTHCELDLSFLLGVSCAV 703
Cdd:TIGR02013 505 -GRFVEDLVVA----RYRGEIT----------------------------------LVSPDQVDYMDVSPKQVVSVAASL 545
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 704 VPFANHDHGRRVLYQSQKHcQQAIGF----------------------------------------------SSTNPNIR 737
Cdd:TIGR02013 546 IPFLEHDDANRALMGSNMQ-RQAVPLlrseaplvgtgmeakvardsgavivakrggvveyvdakrivirydeDEEEPDGG 624
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 738 CDTLSQQLF--------YPQKPLFKtLASECLKKEVLFN-----------GQNAIVAVNVHLGYNQEDSIVMNKASLERG 798
Cdd:TIGR02013 625 IDIYRLLKYqrsnqdtcINQRPIVS-VGDRVEAGDVLADgpstdlgelalGRNVLVAFMPWNGYNYEDAILISERLVKDD 703
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 799 MFRSEQIRSYkaEVDAKDSekrKKMDElvQFGKTHSKIGK--VDSLEDDGFPFIGANMSTGDIVIGRCTESGA------- 869
Cdd:TIGR02013 704 VFTSIHIEEY--EVEARDT---KLGPE--EITRDIPNVSEeaLRNLDENGIVRIGAEVKAGDILVGKVTPKGEteltpee 776
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 870 ---------------DHSIKLKHTERGIVQKVVLSSNDEGKNFAA-------VSLRQVRSPCLGDKFSSMHGQKGVLGYL 927
Cdd:TIGR02013 777 kllraifgekardvrDTSLRVPPGVEGTVIDVKVFSREQGDELPPgvnklvkVYIAQKRKIQVGDKMAGRHGNKGVVSKI 856
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 928 EEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALskGIACpiqkegssaayTKLTRHATPFSTPGV-----TEITE 1002
Cdd:TIGR02013 857 LPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHL--GWAG-----------KRLGRKGVPIATPVFdgaseEEIKE 923
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1003 QLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDC 1082
Cdd:TIGR02013 924 YLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWA 1003
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|....*
gi 79416709 1083 LIAHGASANLHERLFTLSDSsqmhICRKCKTYANVI--ERTPSSG 1125
Cdd:TIGR02013 1004 LEAYGAAYTLQEMLTVKSDD----VVGRTKAYEAIVkgENVPEPG 1044
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
47-435 |
5.46e-51 |
|
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: 185.28 E-value: 5.46e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 47 GLISHQLNSYNYFIEHGLQNVFQSfgEMLVEPSFDVVKKKDNDWRYaTVKFGEVTVEKPTFFSDDKELEFLPWH-ARLQN 125
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDE--NALIESEFEIQHPGENGDKL-SLKFGQIRLGKPMFDETDGSTREIYPQeCRLRN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 126 MTYSARIKVNVQvevfkntvvksdkfktgqdnYVEKKILDVKKQDILIGSIPVMVKSILCKTSEKG-KENCKKGDCAFDQ 204
Cdd:pfam04563 78 LTYSAPLYVDLE--------------------LSVYNGEDIKPIEVFIGRLPIMLRSNACILSGATeSELVKLGECPLDP 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 205 GGYFVIKGAEKVFIAQEQMCTkrlwisNSPWTVSFRSENKRN-----RFIVRLSENEKAE---DYKRREKVLTVYF---- 272
Cdd:pfam04563 138 GGYFIINGSEKVIVAQEHRSR------NHPIVFKKADPKKRGsvasvRSSAEISVRPDSTswvNVLEYLSNGTIYFkfpy 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 273 LSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDASITNSLIASIHvadavcEAFRCGNN----ALTY------VEQQIKST 342
Cdd:pfam04563 212 IKKEIPIVIILRALGFTSDREIFELICYDVNDQQLQEELLPSLE------EGFKIRIQtqeqALDYiggrgrAIFRMGRP 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 343 KFPPAESVDECLHLYLFPGLQ----SLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHA 418
Cdd:pfam04563 286 REPRIKYAEEILQKEVLPHLGtyelDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKL 365
|
410
....*....|....*..
gi 79416709 419 RRKMTRAMQKHLsGDGD 435
Cdd:pfam04563 366 VRDVRERLQKVL-GSPD 381
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
48-1104 |
8.68e-51 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 195.69 E-value: 8.68e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 48 LISHQLNSYNYFIEHGLQNVFQSFGEMlvepsFDVVKKKDNdwryatVKFG-EVTVEKPTFfsddkELEFlpwhARLQNM 126
Cdd:CHL00207 10 FLEIQRTSFCWFLNEGLNEELNIFSKI-----FDYTGNLEL------LLFGkNYKLKYPKY-----NLLS----AKSYDS 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 127 TYSarIKVNVQVEvFKNtvvksdkfktgqdnyveKKILDVKKQDILIGSIPVMvksilcktsekgkenckkgdcafDQGG 206
Cdd:CHL00207 70 NYS--IQIYLPLK-FIN-----------------LKTNKIKFINYLIGNLPKM-----------------------TQRG 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 207 YFVIKGAEKVFIAQeqmctkrlwISNSPwTVSFRSENKRNR-------------FIVRLSENEKAEDYKRREKVltvyfl 273
Cdd:CHL00207 107 TFIINGLERVIVSQ---------IIRSP-GIYFKKEIKKNSnkiysatlipnrgSWIKFELDKNKEIWIRIDKN------ 170
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 274 sTEIPVWLLFFALGVSsDKEAMDLIAFDGDDASITNSL--IASIHVADAVCEAF---RCGNNALTYVEQQIKSTKFPPAE 348
Cdd:CHL00207 171 -RKKPLIIFLKALGLT-DQDIYSRLTKSEFLKKLKPILlnSNSYTNEEILLEIYknlSPIEPATVNDANQNLFSRFFDPK 248
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 349 SVDEC---LHLYLFPGLQSLKKKARFLGYM-----VKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHARR 420
Cdd:CHL00207 249 NYDLGkvgRYKINNKLNLNIPERVRNLTYEdilsiIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLER 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 421 KMTRAMQKHlsgdgdlkPIEHYLDASVITNGLSRAFstgawshpFRKMERVSGVVANLGRANPLQTLIDLRRTR---QQV 497
Cdd:CHL00207 329 ILRNRMTIC--------DIDSLSKFNLINPKPLIAL--------IREFFGSSQLSQYMDQTNPLSELTHKRRISilgPGG 392
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 498 LYTGKVGDA-RYPHPSHWGRVCFLSTPDGENCGLVknmsllglvSTQSLESVVEKLfacgmeELMDDTCTPLFgKHKVLL 576
Cdd:CHL00207 393 LDKDRISFAvRDIHPSHYGRICPIETPEGPNCGLI---------GSLATNARINKF------GFIETPFYKVI-NGKVKK 456
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 577 NGDWVGLCADSESFVaelksrrrqSELPREMEIKRDKddnevriftdagRLLRPLLVVENLQKLKQEKPSQY-------- 648
Cdd:CHL00207 457 FGNPIYLTADSEDLY---------RIAPNDINLNKNN------------YFKKNIIPVRYKQEFKTVNPSKVdfiaispi 515
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 649 ----------PFdhlLDHGileligieeeeDCNTA-WGIKQ------LL--KEPKIYTHCE----LDLSFLLGVSCA-VV 704
Cdd:CHL00207 516 qvfsiaesliPF---LEHN-----------DANRAlMGSNMqrqavpLLypEKPIVGTGYEkqiaLDSGMTIISLTEgIV 581
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 705 PFAN-------HDHGRRVLYQSQKHcqqaigfsstnpnircDTLSQQLFYPQKPLF---------KTLAS-ECLKKEVLF 767
Cdd:CHL00207 582 VSVSaykiiiqDDNNRYIHYYLQKY----------------QRSNQNTCINYRPIVwvgekinigQILADgSDIDNSELA 645
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 768 NGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVDakdseKRKKMDElvQFGKTHSKIGK--VDSLEDD 845
Cdd:CHL00207 646 LGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELR-----QTKLGSE--EITRNIPNVSEysLKNLDEN 718
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 846 GFPFIGANMSTGDIVIGRCTESGA----------------------DHSIKLKHTERGIVQKVVL---SSNDEGKNFAAV 900
Cdd:CHL00207 719 GIISIGSKVLAGDILVGKITPKGEsdqlpegkllraifgekakdvkDTSLRMPNGGYGRVIKVEIfsrSKGDELKFGYYL 798
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 901 SLR----QVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALskGIAC----- 971
Cdd:CHL00207 799 KIRvfiaQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLL--GLAGdnlnk 876
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 972 -----PIQKEGSSAA-----YTKLTRhatpfstpgVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLV 1041
Cdd:CHL00207 877 rfkilPFDEMYGSEYsriliNNKLNQ---------ASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLI 947
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79416709 1042 HMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQ 1104
Cdd:CHL00207 948 HLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQ 1010
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1071-1170 |
4.35e-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: 131.56 E-value: 4.35e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1071 GGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIertpssgrkirgpYCRVCVSSDHVVRVYVPYG 1150
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYN-------------KCPICKGETDISPGYIPES 67
|
90 100
....*....|....*....|
gi 79416709 1151 AKLLCQELFSMGITLNFDTK 1170
Cdd:pfam04560 68 FKLLFQELQSLGIDPRLLLE 87
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
769-1101 |
7.54e-30 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 128.68 E-value: 7.54e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 769 GQNAIVAV---NvhlGYNQEDSIVMNKASLERGMFRSEQIRSYkaEVDAKDS----------------EKRKKMDElvqf 829
Cdd:PRK00405 716 GQNVLVAFmpwN---GYNFEDAILISERLVKEDVFTSIHIEEY--EIEARDTklgpeeitrdipnvseEALRNLDE---- 786
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 830 gkthskigkvdsledDGFPFIGANMSTGDIVIGRCT-------------------ESGADH---SIKLKHTERGIVQKV- 886
Cdd:PRK00405 787 ---------------SGIVRIGAEVKPGDILVGKVTpkgeteltpeekllraifgEKARDVkdtSLRVPHGEEGTVIDVk 851
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 887 VLSSNDEGKNFAAVSLRQVR---------SPclGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTP 957
Cdd:PRK00405 852 VFTRIEQGDELPPGVNKLVKvyiaqkrkiQV--GDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNI 929
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 958 GQLLEAALskGIACpiqkegssaayTKLTRHatpFSTP---GVTE--ITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFM 1032
Cdd:PRK00405 930 GQILETHL--GWAA-----------KGLGIK---FATPvfdGAKEeeIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTV 993
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 79416709 1033 GPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSD 1101
Cdd:PRK00405 994 GYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1062
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
376-1166 |
1.02e-23 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 109.24 E-value: 1.02e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 376 VKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAharrKMTRAMQKHL---SGDGD-LKPIEhYLDASVITNG 451
Cdd:PRK09603 441 VKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLV----KMQKTIKDKLttmSGAFDsLMPHD-LVNSKMITST 515
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 452 LSRAFSTGAWSHpFrkmervsgvvanLGRANPLQTLIDLRRTR---QQVLYTGKVG-DARYPHPSHWGRVCFLSTPDGEN 527
Cdd:PRK09603 516 IMEFFMGGQLSQ-F------------MDQTNPLSEVTHKRRLSalgEGGLVKDRVGfEARDVHPTHYGRICPIETPEGQN 582
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 528 CGLVKNMSL------LGLVST---QSLESVV--EKLFACGMEE---LMDDTCTPLFGKHKVLlnGDWVGLCADSESFVAE 593
Cdd:PRK09603 583 IGLINTLSTftrvndLGFIEApykKVVDGKVvgETIYLTAIQEdshIIAPASTPIDEEGNIL--GDLIETRVEGEIVLNE 660
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 594 lKSRRRQSELPREMEIKRDKDDNEVRIFTDAGRLLrpllVVENLQKlkQEKPsqypfdhLLDHGILELIGIEEEEDCNTA 673
Cdd:PRK09603 661 -KSKVTLMDLSSSMLVGVAASLIPFLEHDDANRAL----MGTNMQR--QAVP-------LLRSDAPIVGTGIEKIIARDS 726
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 674 WG-IKQllKEPKIYTHCELDLSFLLGVSCAVVpFANHDHGRRVLYQSQKHCqqaigFSSTnPNIRC-DTLSQQLFYPQKP 751
Cdd:PRK09603 727 WGaIKA--NRAGVVEKIDSKNIYILGEGKEEA-YIDAYSLQKNLRTNQNTS-----FNQV-PIVKVgDKVEAGQIIADGP 797
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 752 lfktlaseCLKKEVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIrsYKAEVDAKdsEKRKKMDELVQfGK 831
Cdd:PRK09603 798 --------SMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHI--YEKEVDAR--ELKHGVEEFTA-DI 864
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 832 THSKIGKVDSLEDDGFPFIGANMSTGDIVIGRCTESG------------------ADHSIK------------------- 874
Cdd:PRK09603 865 PDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGeikstpeerllraifgdkAGHVVNkslycppslegtvidvkvf 944
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 875 -----------------------LKHTER-------------GIVQKVVLSSN--------DEGK-----------NFAA 899
Cdd:PRK09603 945 tkkgyekdarvlsayeeekakldMEHFDRltmlnreellrvsSLLSQAILEEPfshngkdyKEGDqipkeeiasinRFTL 1024
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 900 VSL------------RQVRSPCL-------------------------------------------GDKFSSMHGQKGVL 924
Cdd:PRK09603 1025 ASLvkkyskevqnhyEITKNNFLeqkkvlgeeheeklsilekddilpngvikkvklyiatkrklkvGDKMAGRHGNKGIV 1104
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 925 GYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAAL------------------SKG-----------IACPIQK 975
Cdd:PRK09603 1105 SNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLglvgkefgkqiasmledkTKDfakelrakmleIANAINE 1184
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 976 EGSSA-------------AYTKLTRHATPFSTP---GVTEitEQLHR----AGFSRWGNERVYNGRSGEMMRSMIFMGPT 1035
Cdd:PRK09603 1185 KDPLTihalencsdeellEYAKDWSKGVKMAIPvfeGISQ--EKFYKlfelAKIAMDGKMDLYDGRTGEKMRERVNVGYM 1262
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 1036 FYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQmhicrkcktya 1115
Cdd:PRK09603 1263 YMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR----------- 1331
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|.
gi 79416709 1116 nviertpssGRkiRGPYcRVCVSSDHVVRVYVPYGAKLLCQELFSMGITLN 1166
Cdd:PRK09603 1332 ---------GR--ENAY-RAIAKGEQVGESEIPETFYVLTKELQSLALDIN 1370
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
574-635 |
3.81e-23 |
|
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: 93.58 E-value: 3.81e-23
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79416709 574 VLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKDDNEVRIFTDAGRLLRPLLVVE 635
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
47-1107 |
7.46e-22 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 102.67 E-value: 7.46e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 47 GLISHQLNSYNYFIEHGL--------------QNV-FQSFGE--MLVEPSFdvvKKKDndwryatvkfgevtvekptffs 109
Cdd:CHL00001 14 GFNQIQFEGFCRFIDQGLteelskfpkiedtdQEIeFQLFVEtyQLVEPLI---KERD---------------------- 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 110 ddkeleflpwhARLQNMTYSARIKVNVQVevfkntvvksdkfktgqdnyVEKKILDVKKQDILIGSIPVMvksilcktse 189
Cdd:CHL00001 69 -----------AVYESLTYSSELYVPAGL--------------------IWKKSRDMQEQTVFIGNIPLM---------- 107
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 190 kgkenckkgdcafDQGGYFVIKGAEKVFIAQeqmctkrlwISNSPwTVSFRSENKRNRFIV-------------RLSENE 256
Cdd:CHL00001 108 -------------NSLGTFIINGIYRVVINQ---------ILRSP-GIYYRSELDHNGISVytgtiisdwggrlELEIDR 164
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 257 KAEDYKRREKVltvyflsTEIPVWLLFFALGvSSDKEAMDliafdgddaSITNSLIASIHVADAVCEAFRCGNNALTYVE 336
Cdd:CHL00001 165 KARIWARVSRK-------QKISILVLLSAMG-LNLREILD---------NVCYPEIFLSFLNDKEKKKIGSKENAILEFY 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 337 QQIKSTKFPPAESVDECLHLY--LFP--------GLQSLKKK--------ARFL---------GYMVKCllnSYaGKRKC 389
Cdd:CHL00001 228 QQFACVGGDPVFSESLCKELQkkFFQqrcelgriGRRNMNRKlnldipenNTFLlpqdvlaaaDYLIGM---KF-GMGTL 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 390 ENRDSFRNKRIELAGELLEREIR---VHLAHARRKMTRAMQKHlsgdgDLKPIEHYLdasVITNGLSRAFSTGAWSHPfr 466
Cdd:CHL00001 304 DDIDHLKNKRIRSVADLLQDQFGlalNRLENAVRGTICGAIRR-----KLIPTPQNL---VTSTPLTTTYESFFGSHP-- 373
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 467 kmerVSGVvanLGRANPLQTLIDLRRtrqqVLYTGKVG--------DARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLG 538
Cdd:CHL00001 374 ----LSQF---LDQTNPLTEIVHGRK----LSSLGPGGltgrtasfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHA 442
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 539 LVSTQ-SLESVVEKLFACGMEELMddtctplfgkhkVLLngdwvglcadsesfvaelksrrrqseLPREmeikrdkdDNE 617
Cdd:CHL00001 443 RIGHWgSLESPFYEISERSKEERM------------VYL--------------------------SPSE--------DEY 476
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 618 VRIFTDAgrllrPLLVVENLQKlKQEKPSQYPFDHLldhgileligieeeedcNTAWGikqllkepkiythcELDL---- 693
Cdd:CHL00001 477 YMIAAGN-----SLALNQGIQE-EQVVPARYRQEFL-----------------TIAWE--------------QIHLrsif 519
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 694 ---SFLLGVScaVVPFANHDHGRRVLYQS--QKhcqQAIGFSSTNpniRC------------------------------ 738
Cdd:CHL00001 520 pfqYFSIGAS--LIPFLEHNDANRALMGSnmQR---QAVPLSRSE---KCivgtglerqvaldsgvvaiaehegkiiytd 591
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 739 ----------DTLSQQL-FYP---------QKPLFKtlASECLKK-EVLFN-----------GQNAIVAVNVHLGYNQED 786
Cdd:CHL00001 592 tdkiilsgngDTLSIPLvMYQrsnkntcmhQKPQVR--RGKCVKKgQILADgaatvggelalGKNVLVAYMPWEGYNFED 669
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 787 SIVMNKASLERGMFRSEQIRSYKAEVdAKDSEKRKKMDelvqfgkthSKIGKVDS-----LEDDGFPFIGANMSTGDIVI 861
Cdd:CHL00001 670 AVLISERLVYEDIYTSFHIRKYEIQT-HVTSQGPERIT---------KEIPHLEAhllrnLDKNGIVMLGSWVETGDILV 739
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 862 GRCTESGADHS--------------IKLKHTE----------RGIV------QKVVLSSNDEGKnfAAVSLRQVRSPCLG 911
Cdd:CHL00001 740 GKLTPQEAEESsyapegrllraifgIQVSTSKetclklpiggRGRVidvrwiQKKGGSSYNPET--IHVYILQKREIQVG 817
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 912 DKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALskGIAcpiqkeGSSaaytkLTRH--A 989
Cdd:CHL00001 818 DKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL--GLA------GDL-----LNRHyrI 884
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 990 TPFStpgvtEITEQ----------LHRAGFSR---W-------GNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVK 1049
Cdd:CHL00001 885 APFD-----ERYEQeasrklvfseLYEASKQTanpWvfepeypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIH 959
|
1210 1220 1230 1240 1250
....*....|....*....|....*....|....*....|....*....|....*...
gi 79416709 1050 FRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDssqmHI 1107
Cdd:CHL00001 960 ARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD----HI 1013
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
478-537 |
4.50e-16 |
|
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: 73.71 E-value: 4.50e-16
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79416709 478 LGRANPLQTLIDLRR---TRQQVLYTGKVGDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLL 537
Cdd:pfam04565 3 LDRTNYLSTLSHLRRvnsPRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALY 65
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
989-1119 |
6.91e-14 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 76.97 E-value: 6.91e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 989 ATPFSTPGVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRK 1068
Cdd:PRK14844 1274 APVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKS 1353
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 79416709 1069 RFGGIKFGEMERDCLIAHGASANLHERLFTLSDSsqmhICRKCKTYANVIE 1119
Cdd:PRK14844 1354 HFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDD----INGRVKIYESIIK 1400
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
231-401 |
5.53e-12 |
|
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: 65.83 E-value: 5.53e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 231 SNSPWTVSFRSENKRNRFIVRLSENEKA----EDYKRREKVLTVYFLSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDAS 306
Cdd:pfam04561 2 SNGIYVEKELDKNGIIATYTSSLISNRGswlkLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDPQ 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79416709 307 ITNSLIASIHVADAVCEA----------FRCGNNALTYVE--QQIKSTKFPPAESVDeclHLYLFPGLQSLKKKARFLGY 374
Cdd:pfam04561 82 MLELLKPELEEAENIYTQeealdyigkgFALRRGEEPRLQraREILYSRDPKYNLNK---HLGLNEPFENERLKAQDILY 158
|
170 180
....*....|....*....|....*..
gi 79416709 375 MVKCLLNSYAGKRKCENRDSFRNKRIE 401
Cdd:pfam04561 159 MIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
