|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
59-1140 |
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: 1159.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 59 LVKQHLDSFNYFVDIDLKKIIKANQTI-LSDVDPEFYLKYVDIRIGK-KSTSSTKDYLTPPHECRLRDMTYSAPIYVDIE 136
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPItDTDDDGRLKLKFGDIYLGKpKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 137 YTRGRNIIM-HKDVEIGRMPIMLRSNKCTLYGCDEAEMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEadEKK 215
Cdd:cd00653 81 LTVNDKGKIkEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 216 GIVQASVTS---------STHERKSKTYVVTKNDKIYLKHnsiseeipivivlkacgvvseleimqlvcgndssyqdifa 286
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 287 vnieeaskfniytQQQALEYIGAKVktmrrqkltvlqegieaiattviahltvealnfrekaLYMAMMTRRVVMAMHNPK 366
Cdd:cd00653 199 -------------QEEALKYIGKRF-------------------------------------EDLIYMIRKLILLVLGKG 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 367 MVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVLKKPNRAMeydalLSINVHSNNITSGLNRAISTGNWSL 446
Cdd:cd00653 229 KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGS 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 447 KRFKMERAGVTHVLSRLSYISALGMMTRISS-QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITtd 525
Cdd:cd00653 304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 526 deeepikklcyvlgvedinlidsaslhlnysvflngtligsarfprkfvshfralrrsckvsafisihtnseqkavhiat 605
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 606 dgGRICRPLIIVtngeshvkahhlkrllegelvfddflklglveyldvneendsfialyekdiDQAVTHLEIEPFTVLGA 685
Cdd:cd00653 382 --GRIERPYRIV---------------------------------------------------EKEVTHIEISPSQILSV 408
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 686 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 765
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYS 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 766 GYDIEDALVLNKASLDRGFGRCETRRKTTTVLKRYPNHTQDIIggmRVDEKGEPIWQHKALGPDGLGEVGMKLDSGQIYI 845
Cdd:cd00653 489 GYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT---RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 846 NKSVPTNSTDAFN--GAAQASYRETPVIYRAPEPSHIDQVMMS---VSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGV 920
Cdd:cd00653 566 GKITPKGETESTPifGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 921 CGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGK 1000
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGK 725
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1001 DMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLE 1080
Cdd:cd00653 726 EVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQE 805
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1081 RLMISSDAFEVDVCAKCGLMGYSGWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRL 1140
Cdd:cd00653 806 RLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
203-380 |
3.10e-47 |
|
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: 167.14 E-value: 3.10e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 203 SKNRIIVEADEKKGIVQASVTSSTHERKSKTYVVTKNDKIYLKHN-SISEEIPIVIVLKACGVVSELEIMQLVCGNDSSY 281
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 282 QDIFAVNIEEASKFNIYTQQQALEYIGaKVKTMRRQKLTVLQEGIEAIATT-----VIAHLTVEAL--NFREKALYMAMM 354
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSRdpkynLNKHLGLNEPfeNERLKAQDILYM 159
|
170 180
....*....|....*....|....*.
gi 372464957 355 TRRVVMAMHNPKMVDDRDYVGNKRLE 380
Cdd:pfam04561 160 IDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
557-617 |
5.98e-28 |
|
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: 107.07 E-value: 5.98e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 372464957 557 VFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISIHTNSEQKAVHIATDGGRICRPLIIV 617
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIV 61
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
639-679 |
2.47e-11 |
|
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: 59.86 E-value: 2.47e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 372464957 639 FDDFLKLGLVEYLDVNEENDSFIALYEKDIDQAV------------THLEIEP 679
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSreeregpyahtyTHCEIHP 53
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
59-1140 |
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: 1159.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 59 LVKQHLDSFNYFVDIDLKKIIKANQTI-LSDVDPEFYLKYVDIRIGK-KSTSSTKDYLTPPHECRLRDMTYSAPIYVDIE 136
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPItDTDDDGRLKLKFGDIYLGKpKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 137 YTRGRNIIM-HKDVEIGRMPIMLRSNKCTLYGCDEAEMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEadEKK 215
Cdd:cd00653 81 LTVNDKGKIkEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 216 GIVQASVTS---------STHERKSKTYVVTKNDKIYLKHnsiseeipivivlkacgvvseleimqlvcgndssyqdifa 286
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 287 vnieeaskfniytQQQALEYIGAKVktmrrqkltvlqegieaiattviahltvealnfrekaLYMAMMTRRVVMAMHNPK 366
Cdd:cd00653 199 -------------QEEALKYIGKRF-------------------------------------EDLIYMIRKLILLVLGKG 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 367 MVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVLKKPNRAMeydalLSINVHSNNITSGLNRAISTGNWSL 446
Cdd:cd00653 229 KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGS 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 447 KRFKMERAGVTHVLSRLSYISALGMMTRISS-QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITtd 525
Cdd:cd00653 304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 526 deeepikklcyvlgvedinlidsaslhlnysvflngtligsarfprkfvshfralrrsckvsafisihtnseqkavhiat 605
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 606 dgGRICRPLIIVtngeshvkahhlkrllegelvfddflklglveyldvneendsfialyekdiDQAVTHLEIEPFTVLGA 685
Cdd:cd00653 382 --GRIERPYRIV---------------------------------------------------EKEVTHIEISPSQILSV 408
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 686 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 765
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYS 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 766 GYDIEDALVLNKASLDRGFGRCETRRKTTTVLKRYPNHTQDIIggmRVDEKGEPIWQHKALGPDGLGEVGMKLDSGQIYI 845
Cdd:cd00653 489 GYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT---RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 846 NKSVPTNSTDAFN--GAAQASYRETPVIYRAPEPSHIDQVMMS---VSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGV 920
Cdd:cd00653 566 GKITPKGETESTPifGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 921 CGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGK 1000
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGK 725
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1001 DMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLE 1080
Cdd:cd00653 726 EVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQE 805
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1081 RLMISSDAFEVDVCAKCGLMGYSGWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRL 1140
Cdd:cd00653 806 RLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
46-1146 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1059.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 46 KWHLLPAFLKVKGLVKQHLDSFNYFVDIDLKKIIKANQTILSDVdPEFYLKYVDIRIGK---KSTSSTKDYLTPpHECRL 122
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEpeiKEADGSERPITP-MEARL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 123 RDMTYSAPIYVDIEYTRGRNIIMHKDVEIGRMPIMLRSNKCTLYGCDEAEMAKLNECPLDPGGYFIVNGTEKVILVQEQL 202
Cdd:PRK08565 79 RNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 203 SKNRIIVEADEKKGIVQ--ASVTSSTHERKSKTYVVTKNDK-IYLKHNSISEEIPIVIVLKACGVVSELEIMQLVcGNDS 279
Cdd:PRK08565 159 APNRVLVDKGEAGSSIThtAKVISSRAGYRAQVTVERRKDGtIYVSFPAVPGKIPFVILMRALGLETDRDIVYAV-SLDP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 280 SYQDIFAVNIEEASKFNIyTQQQALEYIGAKV-----KTMRRQKLTvlqegiEAIATTVIAHLTVEALNFREKALYMAMM 354
Cdd:PRK08565 238 EIQQELLPSLEQASSIAA-TVEDALDYIGKRVaigqpREYRIERAE------QILDKYLLPHLGTSPEDRIKKAYFLGQM 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 355 TRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVLKKpnramEYDALLSINVHSNNITSG 434
Cdd:PRK08565 311 ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYAR-----GRKLDLRAIVRPDIITER 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 435 LNRAISTGNWSlkrfkMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVK 514
Cdd:PRK08565 386 IRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVK 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 515 NLALMTHITTDDEEEPIKKLCYVLGVEDI-NLIDSASLHLnYSVFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISI- 592
Cdd:PRK08565 461 NLALMAQISVGVDEEEVEEILYELGVVPVeEAREEEYISW-SRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 593 -HTNSEQKAVHIATDGGRICRPLIIVTNGESHVKAHHLKRLLEGELVFDDFLKLGLVEYLDVNEENDSFIALYEKDIDQA 671
Cdd:PRK08565 540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 672 VTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKL 751
Cdd:PRK08565 620 HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDR 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 752 PAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCETRRKTTTVLKRYPNHTQDII----GGMRvDEKGEPIWQHkaLG 827
Cdd:PRK08565 700 PAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIeipePNVR-GYRGEEYYRK--LD 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 828 PDGLGEVGMKLDSGQIYINKSVP---TNSTDAFNGAAQASyRETPVIYRAPEPSHIDQVMMSVSDNDQALIKVLLRQHRR 904
Cdd:PRK08565 777 EDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRI 855
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 905 PELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLE 984
Cdd:PRK08565 856 PELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEE 935
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 985 DMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEM 1064
Cdd:PRK08565 936 ELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEM 1015
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1065 ERDCVIAYGASQLLLERLMISSDAFEVDVCAKCGLMGYSG------WCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAP 1138
Cdd:PRK08565 1016 ERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISP 1095
|
....*...
gi 372464957 1139 RLRLEDIF 1146
Cdd:PRK08565 1096 RLKLGDKV 1103
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
557-1144 |
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: 697.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 557 VFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISIHTNSEQKAVHIATDGGRICRPLIIVTNGESHVKAHHLKRLLEGE 636
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 637 LVFDDFLKLGLVEYLDVNEENDSFIALYEKDIDQAVTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIA 716
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 717 YNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCETRRKTTTV 796
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 797 LKRYPNHTQDII----GGMRvDEKGEPIWQHkaLGPDGLGEVGMKLDSGQIYINKSVPT---NSTDAFNGAAQASyRETP 869
Cdd:TIGR03670 241 ERRYPGGQEDRFeipePDVR-GYRGEEAYKH--LDEDGIVYPEVEVKGGDVLIGKTSPPrflEELREFGLVTERR-RDTS 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 870 VIYRAPEPSHIDQVMMSVSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFP 949
Cdd:TIGR03670 317 VTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIP 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 950 SRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHM 1029
Cdd:TIGR03670 397 SRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHM 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1030 VLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCAKCGLMGY------S 1103
Cdd:TIGR03670 477 VADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgT 556
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 372464957 1104 GWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRLRLED 1144
Cdd:TIGR03670 557 AYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
51-1144 |
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: 600.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 51 PAFLKVKGLVKQHLDSFNYFVDIDLKKIIKANQTIlSDVDPEFYLKYVDIRIGK-KSTsstkdyltpPHECRLRDMTYSA 129
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPI-EDFTGNLSLEFGDYRLGEpKYT---------PEECKERDLTYAA 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 130 PIYVDIEYT-RGRNIIMHKDVEIGRMPIMLRSnkctlygcdeaemaklnecpldpgGYFIVNGTEKVILVQEQLSKNRII 208
Cdd:COG0085 78 PLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVYF 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 209 VEADEKKG--IVQASVTSStheRKSKTYVVT-KNDKIYLKhnsISE--EIPIVIVLKACGVVSELEIMQLVcgNDSSYQD 283
Cdd:COG0085 134 VEEEDKSGkdLYSAKVIPS---RGAWLEFETdKDGTIYVR---IDRkrKIPVTVLLRALGLETDEEILEAF--GDDPIQE 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 284 IFAVNIEeasKFNIYTQQQALEYIGAKV-----KTMRRQKlTVLQEGIEAIATTVIAHLTVEALNFR-----------EK 347
Cdd:COG0085 206 YILATLE---KDNTKTQEEALLEIYRKLrpgepPTIERAE-QLLDNLFFDPKRYDLAHVGRYKINKKlgldvppedrvLT 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 348 ALYMAMMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKasiDKVLKKPNRAMEYDALLSINVh 427
Cdd:COG0085 282 AEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVR---ERMTTQDVEAITPQSLINIRP- 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 428 snnITSGLNRAISTGNwsLKRFkMER----AGVTHvLSRLSyisALGM--MTRISSQFEksrkVsgpRALQPSQFGMLCT 501
Cdd:COG0085 358 ---VVAAIKEFFGSSQ--LSQF-MDQtnplSELTH-KRRLS---ALGPggLSRERAGFE----V---RDVHPSHYGRMCP 420
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 502 ADTPEGEACGLVKNLALMthittddeeepikklcyvlgvedinlidsaslhlnysvflngtligsarfprkfvshfralr 581
Cdd:COG0085 421 IETPEGPNIGLIGSLALY-------------------------------------------------------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 582 rsCKVSAFisihtnseqkavhiatdgGRICRPLIIVTNGeshvkahhlkrllegeLVFDDflklglVEYLDVNEENDSFI 661
Cdd:COG0085 439 --ARVNEY------------------GFIETPYRKVENG----------------KVTDE------IEYLTADEEENYYI 476
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 662 ALYEKDIDQA-----------------------VTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYN 718
Cdd:COG0085 477 AQANAPLDEDgnfleervlvryrgeevlvppeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE 556
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 719 -QFKRIDTLLYL-----MIYPQQPMVKT----KTIELI------DYDKLPAGQNATVAVMSYSGYDIEDALVLNKASLDR 782
Cdd:COG0085 557 aPLLHYPLQKFQrsnqgTCINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKD 636
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 783 GFGRCETRRKTTTVLKRYP----NHTQDIiggmrvDEKGEPIWQHkaLGPDGLGEVGMKLDSGQIYINKSVPTNSTD--- 855
Cdd:COG0085 637 DVLTSIHIEEYEIEARDTKlgpeEITRDI------PNVSEEALRN--LDEDGIIRIGAEVKGGDILVGKVTPKGETEltp 708
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 856 -------AFNGAAQaSYRETPVIYRAPEPSHIDQVMMSVSDNDQAL-------IKVLLRQHRRPELGDKFSSRHGQKGVC 921
Cdd:COG0085 709 eerllraIFGEKAR-EVRDTSLRVPHGEKGKVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKLAGRHGNKGVI 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 922 GIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGKD 1001
Cdd:COG0085 788 SRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1002 MLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLER 1081
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 372464957 1082 LMISSDafevDVCakcglmGYSGWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRLRLED 1144
Cdd:COG0085 948 LTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
686-1055 |
3.60e-176 |
|
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: 521.70 E-value: 3.60e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 686 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 765
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 766 GYDIEDALVLNKASLDRGFGRCETRRktTTVLKRYPNHTQDIIGGmrvDEKGEPIWQHKALGPDGLGEVGMKLDSGQIYI 845
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITR---DIPNVSEEALKKLDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 846 NKSVPTNST---DAFNGAAQASYRETPVIYRAPEPSHIDQVMM-SVSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGVC 921
Cdd:pfam00562 156 GKVGPTELTkllRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 922 GIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSK--LEDMSKILVEKGFNYSG 999
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYYG 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 372464957 1000 KDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1055
Cdd:pfam00562 316 KEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
203-380 |
3.10e-47 |
|
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: 167.14 E-value: 3.10e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 203 SKNRIIVEADEKKGIVQASVTSSTHERKSKTYVVTKNDKIYLKHN-SISEEIPIVIVLKACGVVSELEIMQLVCGNDSSY 281
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 282 QDIFAVNIEEASKFNIYTQQQALEYIGaKVKTMRRQKLTVLQEGIEAIATT-----VIAHLTVEAL--NFREKALYMAMM 354
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSRdpkynLNKHLGLNEPfeNERLKAQDILYM 159
|
170 180
....*....|....*....|....*.
gi 372464957 355 TRRVVMAMHNPKMVDDRDYVGNKRLE 380
Cdd:pfam04561 160 IDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
557-617 |
5.98e-28 |
|
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: 107.07 E-value: 5.98e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 372464957 557 VFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISIHTNSEQKAVHIATDGGRICRPLIIV 617
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIV 61
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
639-679 |
2.47e-11 |
|
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: 59.86 E-value: 2.47e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 372464957 639 FDDFLKLGLVEYLDVNEENDSFIALYEKDIDQAV------------THLEIEP 679
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSreeregpyahtyTHCEIHP 53
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
59-1140 |
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: 1159.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 59 LVKQHLDSFNYFVDIDLKKIIKANQTI-LSDVDPEFYLKYVDIRIGK-KSTSSTKDYLTPPHECRLRDMTYSAPIYVDIE 136
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPItDTDDDGRLKLKFGDIYLGKpKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 137 YTRGRNIIM-HKDVEIGRMPIMLRSNKCTLYGCDEAEMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEadEKK 215
Cdd:cd00653 81 LTVNDKGKIkEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 216 GIVQASVTS---------STHERKSKTYVVTKNDKIYLKHnsiseeipivivlkacgvvseleimqlvcgndssyqdifa 286
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 287 vnieeaskfniytQQQALEYIGAKVktmrrqkltvlqegieaiattviahltvealnfrekaLYMAMMTRRVVMAMHNPK 366
Cdd:cd00653 199 -------------QEEALKYIGKRF-------------------------------------EDLIYMIRKLILLVLGKG 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 367 MVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVLKKPNRAMeydalLSINVHSNNITSGLNRAISTGNWSL 446
Cdd:cd00653 229 KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGS 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 447 KRFKMERAGVTHVLSRLSYISALGMMTRISS-QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITtd 525
Cdd:cd00653 304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 526 deeepikklcyvlgvedinlidsaslhlnysvflngtligsarfprkfvshfralrrsckvsafisihtnseqkavhiat 605
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 606 dgGRICRPLIIVtngeshvkahhlkrllegelvfddflklglveyldvneendsfialyekdiDQAVTHLEIEPFTVLGA 685
Cdd:cd00653 382 --GRIERPYRIV---------------------------------------------------EKEVTHIEISPSQILSV 408
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 686 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 765
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYS 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 766 GYDIEDALVLNKASLDRGFGRCETRRKTTTVLKRYPNHTQDIIggmRVDEKGEPIWQHKALGPDGLGEVGMKLDSGQIYI 845
Cdd:cd00653 489 GYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT---RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 846 NKSVPTNSTDAFN--GAAQASYRETPVIYRAPEPSHIDQVMMS---VSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGV 920
Cdd:cd00653 566 GKITPKGETESTPifGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 921 CGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGK 1000
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGK 725
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1001 DMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLE 1080
Cdd:cd00653 726 EVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQE 805
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1081 RLMISSDAFEVDVCAKCGLMGYSGWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRL 1140
Cdd:cd00653 806 RLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
46-1146 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1059.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 46 KWHLLPAFLKVKGLVKQHLDSFNYFVDIDLKKIIKANQTILSDVdPEFYLKYVDIRIGK---KSTSSTKDYLTPpHECRL 122
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEpeiKEADGSERPITP-MEARL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 123 RDMTYSAPIYVDIEYTRGRNIIMHKDVEIGRMPIMLRSNKCTLYGCDEAEMAKLNECPLDPGGYFIVNGTEKVILVQEQL 202
Cdd:PRK08565 79 RNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 203 SKNRIIVEADEKKGIVQ--ASVTSSTHERKSKTYVVTKNDK-IYLKHNSISEEIPIVIVLKACGVVSELEIMQLVcGNDS 279
Cdd:PRK08565 159 APNRVLVDKGEAGSSIThtAKVISSRAGYRAQVTVERRKDGtIYVSFPAVPGKIPFVILMRALGLETDRDIVYAV-SLDP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 280 SYQDIFAVNIEEASKFNIyTQQQALEYIGAKV-----KTMRRQKLTvlqegiEAIATTVIAHLTVEALNFREKALYMAMM 354
Cdd:PRK08565 238 EIQQELLPSLEQASSIAA-TVEDALDYIGKRVaigqpREYRIERAE------QILDKYLLPHLGTSPEDRIKKAYFLGQM 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 355 TRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVLKKpnramEYDALLSINVHSNNITSG 434
Cdd:PRK08565 311 ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYAR-----GRKLDLRAIVRPDIITER 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 435 LNRAISTGNWSlkrfkMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVK 514
Cdd:PRK08565 386 IRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVK 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 515 NLALMTHITTDDEEEPIKKLCYVLGVEDI-NLIDSASLHLnYSVFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISI- 592
Cdd:PRK08565 461 NLALMAQISVGVDEEEVEEILYELGVVPVeEAREEEYISW-SRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 593 -HTNSEQKAVHIATDGGRICRPLIIVTNGESHVKAHHLKRLLEGELVFDDFLKLGLVEYLDVNEENDSFIALYEKDIDQA 671
Cdd:PRK08565 540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 672 VTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKL 751
Cdd:PRK08565 620 HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDR 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 752 PAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCETRRKTTTVLKRYPNHTQDII----GGMRvDEKGEPIWQHkaLG 827
Cdd:PRK08565 700 PAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIeipePNVR-GYRGEEYYRK--LD 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 828 PDGLGEVGMKLDSGQIYINKSVP---TNSTDAFNGAAQASyRETPVIYRAPEPSHIDQVMMSVSDNDQALIKVLLRQHRR 904
Cdd:PRK08565 777 EDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRI 855
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 905 PELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLE 984
Cdd:PRK08565 856 PELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEE 935
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 985 DMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEM 1064
Cdd:PRK08565 936 ELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEM 1015
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1065 ERDCVIAYGASQLLLERLMISSDAFEVDVCAKCGLMGYSG------WCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAP 1138
Cdd:PRK08565 1016 ERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISP 1095
|
....*...
gi 372464957 1139 RLRLEDIF 1146
Cdd:PRK08565 1096 RLKLGDKV 1103
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
557-1144 |
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: 697.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 557 VFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISIHTNSEQKAVHIATDGGRICRPLIIVTNGESHVKAHHLKRLLEGE 636
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 637 LVFDDFLKLGLVEYLDVNEENDSFIALYEKDIDQAVTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIA 716
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 717 YNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCETRRKTTTV 796
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 797 LKRYPNHTQDII----GGMRvDEKGEPIWQHkaLGPDGLGEVGMKLDSGQIYINKSVPT---NSTDAFNGAAQASyRETP 869
Cdd:TIGR03670 241 ERRYPGGQEDRFeipePDVR-GYRGEEAYKH--LDEDGIVYPEVEVKGGDVLIGKTSPPrflEELREFGLVTERR-RDTS 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 870 VIYRAPEPSHIDQVMMSVSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFP 949
Cdd:TIGR03670 317 VTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIP 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 950 SRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHM 1029
Cdd:TIGR03670 397 SRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHM 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1030 VLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCAKCGLMGY------S 1103
Cdd:TIGR03670 477 VADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgT 556
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 372464957 1104 GWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRLRLED 1144
Cdd:TIGR03670 557 AYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
557-1144 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 695.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 557 VFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISIHTNSEQKAVHIATDGGRICRPLIIVTNGESHVKAHHLKRLLEGE 636
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 637 LVFDDFLKLGLVEYLDVNEENDSFIALYEKDIDQAVTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIA 716
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 717 YNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCETRRKTTTV 796
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 797 LKRYPNHTQDII----GGMRvDEKGEPIWQHkaLGPDGLGEVGMKLDSGQIYINKSVPT---NSTDAFNGAAQASyRETP 869
Cdd:PRK07225 247 ERRYPGGQEDRFeipdKDVR-GYRGEEAYRH--LDEDGLVNPETEVKEGDVLIGKTSPPrflEEPDDFGISPEKR-RETS 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 870 VIYRAPEPSHIDQVMMSVSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFP 949
Cdd:PRK07225 323 VTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIP 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 950 SRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHM 1029
Cdd:PRK07225 403 SRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHM 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1030 VLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCAKCGLMGY------S 1103
Cdd:PRK07225 483 VANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIydkkrnR 562
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 372464957 1104 GWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRLRLED 1144
Cdd:PRK07225 563 KYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELED 603
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
51-1144 |
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: 600.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 51 PAFLKVKGLVKQHLDSFNYFVDIDLKKIIKANQTIlSDVDPEFYLKYVDIRIGK-KSTsstkdyltpPHECRLRDMTYSA 129
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPI-EDFTGNLSLEFGDYRLGEpKYT---------PEECKERDLTYAA 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 130 PIYVDIEYT-RGRNIIMHKDVEIGRMPIMLRSnkctlygcdeaemaklnecpldpgGYFIVNGTEKVILVQEQLSKNRII 208
Cdd:COG0085 78 PLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVYF 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 209 VEADEKKG--IVQASVTSStheRKSKTYVVT-KNDKIYLKhnsISE--EIPIVIVLKACGVVSELEIMQLVcgNDSSYQD 283
Cdd:COG0085 134 VEEEDKSGkdLYSAKVIPS---RGAWLEFETdKDGTIYVR---IDRkrKIPVTVLLRALGLETDEEILEAF--GDDPIQE 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 284 IFAVNIEeasKFNIYTQQQALEYIGAKV-----KTMRRQKlTVLQEGIEAIATTVIAHLTVEALNFR-----------EK 347
Cdd:COG0085 206 YILATLE---KDNTKTQEEALLEIYRKLrpgepPTIERAE-QLLDNLFFDPKRYDLAHVGRYKINKKlgldvppedrvLT 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 348 ALYMAMMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKasiDKVLKKPNRAMEYDALLSINVh 427
Cdd:COG0085 282 AEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVR---ERMTTQDVEAITPQSLINIRP- 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 428 snnITSGLNRAISTGNwsLKRFkMER----AGVTHvLSRLSyisALGM--MTRISSQFEksrkVsgpRALQPSQFGMLCT 501
Cdd:COG0085 358 ---VVAAIKEFFGSSQ--LSQF-MDQtnplSELTH-KRRLS---ALGPggLSRERAGFE----V---RDVHPSHYGRMCP 420
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 502 ADTPEGEACGLVKNLALMthittddeeepikklcyvlgvedinlidsaslhlnysvflngtligsarfprkfvshfralr 581
Cdd:COG0085 421 IETPEGPNIGLIGSLALY-------------------------------------------------------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 582 rsCKVSAFisihtnseqkavhiatdgGRICRPLIIVTNGeshvkahhlkrllegeLVFDDflklglVEYLDVNEENDSFI 661
Cdd:COG0085 439 --ARVNEY------------------GFIETPYRKVENG----------------KVTDE------IEYLTADEEENYYI 476
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 662 ALYEKDIDQA-----------------------VTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYN 718
Cdd:COG0085 477 AQANAPLDEDgnfleervlvryrgeevlvppeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE 556
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 719 -QFKRIDTLLYL-----MIYPQQPMVKT----KTIELI------DYDKLPAGQNATVAVMSYSGYDIEDALVLNKASLDR 782
Cdd:COG0085 557 aPLLHYPLQKFQrsnqgTCINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKD 636
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 783 GFGRCETRRKTTTVLKRYP----NHTQDIiggmrvDEKGEPIWQHkaLGPDGLGEVGMKLDSGQIYINKSVPTNSTD--- 855
Cdd:COG0085 637 DVLTSIHIEEYEIEARDTKlgpeEITRDI------PNVSEEALRN--LDEDGIIRIGAEVKGGDILVGKVTPKGETEltp 708
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 856 -------AFNGAAQaSYRETPVIYRAPEPSHIDQVMMSVSDNDQAL-------IKVLLRQHRRPELGDKFSSRHGQKGVC 921
Cdd:COG0085 709 eerllraIFGEKAR-EVRDTSLRVPHGEKGKVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKLAGRHGNKGVI 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 922 GIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSKLEDMSKILVEKGFNYSGKD 1001
Cdd:COG0085 788 SRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1002 MLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLER 1081
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 372464957 1082 LMISSDafevDVCakcglmGYSGWCTTCKSAENVIKMTIPYAAKLLFQELLSMNIAPRLRLED 1144
Cdd:COG0085 948 LTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
686-1055 |
3.60e-176 |
|
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: 521.70 E-value: 3.60e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 686 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 765
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 766 GYDIEDALVLNKASLDRGFGRCETRRktTTVLKRYPNHTQDIIGGmrvDEKGEPIWQHKALGPDGLGEVGMKLDSGQIYI 845
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITR---DIPNVSEEALKKLDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 846 NKSVPTNST---DAFNGAAQASYRETPVIYRAPEPSHIDQVMM-SVSDNDQALIKVLLRQHRRPELGDKFSSRHGQKGVC 921
Cdd:pfam00562 156 GKVGPTELTkllRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 922 GIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGSLEYGTCFGGSK--LEDMSKILVEKGFNYSG 999
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYYG 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 372464957 1000 KDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1055
Cdd:pfam00562 316 KEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
58-433 |
4.97e-153 |
|
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: 462.62 E-value: 4.97e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 58 GLVKQHLDSFNYFVDIDLKKIIKANQTILSDVDPE--------FYLKYVDIRIGKKSTSSTKDY--LTPPHECRLRDMTY 127
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQhpgengdkLSLKFGQIRLGKPMFDETDGStrEIYPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 128 SAPIYVDIEYTR-GRNIIMHKDVEIGRMPIMLRSNKCTLYGCDEAEMAKLNECPLDPGGYFIVNGTEKVILVQEQLSKNR 206
Cdd:pfam04563 81 SAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 207 IIV--EADEKKGIVQASVTSSTHE--RKSKTYVV-----TKNDKIYLKHNSISEEIPIVIVLKACGVVSELEIMQLVCG- 276
Cdd:pfam04563 161 PIVfkKADPKKRGSVASVRSSAEIsvRPDSTSWVnvleyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYd 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 277 -NDSSYQDIFAVNIEEASKFNIYTQQQALEYIGAKVKT---MRRQKLTVLQEGIEAIATTVIAHLTVEALNFREKALYMA 352
Cdd:pfam04563 241 vNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYFIG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 353 MMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVLKKPNRAMeydalLSINVHSNNIT 432
Cdd:pfam04563 321 YMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLM-----LQLLVNAKPIT 395
|
.
gi 372464957 433 S 433
Cdd:pfam04563 396 S 396
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
44-543 |
3.53e-114 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 363.89 E-value: 3.53e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 44 EDKWHLLPAFLKVKGLVKQHLDSFNYFVDIDLKKIIKANQTILSDVDPEFYLKYVDIRIGKKST-----SSTKDYltpPH 118
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVkeadgSEREIY---PM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 119 ECRLRDMTYSAPIYVDIEYTRGRNIIMHKDVEIGRMPIMLRSNKCTLYGCDEAEMAKLNECPLDPGGYFIVNGTEKVILV 198
Cdd:PRK09606 80 EARLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMT 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 199 QEQLSKNRIIVEADEKKG--IVQASVTSSTHERKSKTYVVTKNDKI-YLKHNSISEEIPIVIVLKACGVVSELEIMQLVc 275
Cdd:PRK09606 160 LEDLAPNKILVEKDERYGdrIEVAKVFSQRRGYRALVTVERNRDGLlEVSFPSVPGSIPFVILMRALGLETDEEIVEAV- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 276 GNDSSYQDIFAVNIEEAskfNIYTQQQALEYIGAKV-----KTMRRQKltvlqegieaiATTVIA-----HLTVEALNFR 345
Cdd:PRK09606 239 SDDPEIVKFMLENLEEA---EVDTQEEALEYIGKRVapgqtKEYRIKR-----------AEYVIDryllpHLGVEPEVRR 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 346 EKALYMAMMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVLKKpNRAmeydalLSIN 425
Cdd:PRK09606 305 AKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMR-NRE------LSIK 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 426 --VHSNNITSGLNRAISTGNWslkrfKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTAD 503
Cdd:PRK09606 378 taVRSDVLTERLEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSE 452
|
490 500 510 520
....*....|....*....|....*....|....*....|
gi 372464957 504 TPEGEACGLVKNLALMTHITTDDEEEPIKKLCYVLGVEDI 543
Cdd:PRK09606 453 TPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
51-1136 |
6.61e-67 |
|
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: 245.73 E-value: 6.61e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 51 PAFLKVKGLVKQHLDSFNYFVDID----------LKKIIKANQTIlSDVDPEFYLKYVDIRIGKKSTSstkdyltpPHEC 120
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPI-EDYTGNIELEYLSYRLGEPKYS--------VEEC 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 121 RLRDMTYSAPIYVDIEYT----RGRNIIMHKDVEIGRMPIMLRSnkctlygcdeaemaklnecpldpgGYFIVNGTEKVI 196
Cdd:TIGR02013 83 KERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLMTDR------------------------GTFIINGAERVV 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 197 LVQEQLSKNRIIVEA----DEKKGIVQASVTSStheRKSKTYVVT-KNDKIYLKHNSiSEEIPIVIVLKACGvvseLEIM 271
Cdd:TIGR02013 139 VSQLHRSPGVFFSSEkdttKSGKVLFSARIIPY---RGSWLEFETdKKDVLYVRIDR-KRKLPATVLLRALG----YTID 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 272 QLVCGNDSSYQDIFAV------NIEEASKFNIYTQ------------QQALE--------YIGAKVKTMRRQKltVLQEG 325
Cdd:TIGR02013 211 TLILNRLGSGEYIRNTlrkdptNSEEEALVEIYRKlrpgepptveaaRSLLEnlffdpkrYDLGRVGRYKLNK--KLGLD 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 326 IEAIATTVIAHLTVEALNFrekalymammtrrvVMAMHNPKM-VDDRDYVGNKRLELAGQLisllfedLFKKFNSDFkAS 404
Cdd:TIGR02013 289 VPESIGVLTKEDIIATIKY--------------LIKLRNGKGeIDDIDHLGNRRIRSVGEL-------LQNQFRVGL-AR 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 405 IDKVLKKPNRAMEYDALLSIN-VHSNNITSGLNRAISTGnwSLKRFkMER----AGVTHVlSRLSyisALGM--MTRISS 477
Cdd:TIGR02013 347 MERIVRERMSTQDTDTLTPQDlINAKPISAAIKEFFGSS--QLSQF-MDQtnplAELTHK-RRLS---ALGPggLTRERA 419
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 478 QFEKsrkvsgpRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITtddeeepikklcyvlgveDINLIDSAslhlnYSV 557
Cdd:TIGR02013 420 GFEV-------RDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN------------------EYGFIETP-----YRK 469
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 558 FLNGTLIGSARfprkfVSHFRALRRSCKVSAFISIHTNseqkavhiatDGGRICRPliivtngesHVKAHHlkrllEGEl 637
Cdd:TIGR02013 470 VKDGKVVVTDE-----IDYLTADEEDNYVIAQANAPLD----------ENGRFVED---------LVVARY-----RGE- 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 638 vfddflklglveyldvneendsfIALYEKDidqAVTHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAI----- 712
Cdd:TIGR02013 520 -----------------------ITLVSPD---QVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllrs 573
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 713 --------------------------GAIAYNQFKRI---------DTLLYLMIYP--------------QQPMV----K 739
Cdd:TIGR02013 574 eaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRllkyqrsnqdtcinQRPIVsvgdR 653
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 740 TKTIELI------DYDKLPAGQNATVAVMSYSGYDIEDALVLNKASL-DRGFGRCETRRKTTTV--LKRYPNH-TQDIig 809
Cdd:TIGR02013 654 VEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISERLVkDDVFTSIHIEEYEVEArdTKLGPEEiTRDI-- 731
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 810 gmrvDEKGEPIWQHkaLGPDGLGEVGMKLDSGQIYINKSVPTNSTD---------AFNGAAQASYRETPViyRAP---EP 877
Cdd:TIGR02013 732 ----PNVSEEALRN--LDENGIVRIGAEVKAGDILVGKVTPKGETEltpeekllrAIFGEKARDVRDTSL--RVPpgvEG 803
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 878 SHIDQVMMSVSDNDQ------ALIKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSR 951
Cdd:TIGR02013 804 TVIDVKVFSREQGDElppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 952 MTVGKMIELVSGKAGVLNGslEYGTC-----FGGSKLEDMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKL 1026
Cdd:TIGR02013 884 MNIGQILETHLGWAGKRLG--RKGVPiatpvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKL 961
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1027 KHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDafevDVcakcglmgySGWC 1106
Cdd:TIGR02013 962 HHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DV---------VGRT 1028
|
1210 1220 1230
....*....|....*....|....*....|....*
gi 372464957 1107 TTCKS---AENVIKMTIPYAAKLLFQEL--LSMNI 1136
Cdd:TIGR02013 1029 KAYEAivkGENVPEPGIPESFNVLIKELqsLGLDI 1063
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
55-1136 |
4.87e-53 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 203.01 E-value: 4.87e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 55 KVKGLVKQHLDSFNYFVDIDLKKIIKANQTIlsdVDPEFYLKYVDIRIGKKstssTKDYLTPPHECRLRDMTYSAPIYVD 134
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKI---FDYTGNLELLLFGKNYK----LKYPKYNLLSAKSYDSNYSIQIYLP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 135 IEYTRGR-NIIMHKDVEIGRMPIMLRSnkctlygcdeaemaklnecpldpgGYFIVNGTEKVILVQE--------QLSKN 205
Cdd:CHL00207 79 LKFINLKtNKIKFINYLIGNLPKMTQR------------------------GTFIINGLERVIVSQIirspgiyfKKEIK 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 206 RIiveadeKKGIVQASVTSsthERKS-KTYVVTKNDKIYLKHNSISEeIPIVIVLKACGVvSELEIMQLVCGNDSSYQDI 284
Cdd:CHL00207 135 KN------SNKIYSATLIP---NRGSwIKFELDKNKEIWIRIDKNRK-KPLIIFLKALGL-TDQDIYSRLTKSEFLKKLK 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 285 F-----AVNIEEASKFNIY---------TQQQALEYIGAKVKTMRRQKLTVLQEGIeaiattVIAHLTVEALNFREKALY 350
Cdd:CHL00207 204 PillnsNSYTNEEILLEIYknlspiepaTVNDANQNLFSRFFDPKNYDLGKVGRYK------INNKLNLNIPERVRNLTY 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 351 MAMM--TRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNSDFKASIDKVlkkpnramEYDALLSINVHS 428
Cdd:CHL00207 278 EDILsiIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTIC--------DIDSLSKFNLIN 349
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 429 NNITSGLNRAISTGNwSLKRFkMERagvTHVLSRLSY---ISALGmmtriSSQFEKSRKVSGPRALQPSQFGMLCTADTP 505
Cdd:CHL00207 350 PKPLIALIREFFGSS-QLSQY-MDQ---TNPLSELTHkrrISILG-----PGGLDKDRISFAVRDIHPSHYGRICPIETP 419
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 506 EGEACGLVKNLAlmTHITtddeeepikklcyvlgVEDINLIDSaslhlNYSVFLNGTLIGSARFprkfvshfralrrsck 585
Cdd:CHL00207 420 EGPNCGLIGSLA--TNAR----------------INKFGFIET-----PFYKVINGKVKKFGNP---------------- 460
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 586 vsafisIHTNSEQKAVHIATdggricrPLIIVTNGESHVKAHHLKRLLEGELVFddflklglveyldVNEENDSFIAlye 665
Cdd:CHL00207 461 ------IYLTADSEDLYRIA-------PNDINLNKNNYFKKNIIPVRYKQEFKT-------------VNPSKVDFIA--- 511
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 666 kdidqavthleIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAI---------AYNQFKRIDTLL--------- 727
Cdd:CHL00207 512 -----------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisltegi 580
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 728 ---------------------YLMIYP---------QQPMV----KTKTIEL------IDYDKLPAGQNATVAVMSYSGY 767
Cdd:CHL00207 581 vvsvsaykiiiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMPWEGY 660
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 768 DIEDALVLNK----------ASLDR-GFGRCETRRKTTTVLKRYPNHTQDIIggmrvdekgepiwqhKALGPDGLGEVGM 836
Cdd:CHL00207 661 NFEDAILINKrlvyedlftsIHIEKyEIELRQTKLGSEEITRNIPNVSEYSL---------------KNLDENGIISIGS 725
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 837 KLDSGQIYINKSVPTNSTD---------AFNGAAQASYRETPviYRAPEPSH---IDQVMMSVSDNDQ------ALIKVL 898
Cdd:CHL00207 726 KVLAGDILVGKITPKGESDqlpegkllrAIFGEKAKDVKDTS--LRMPNGGYgrvIKVEIFSRSKGDElkfgyyLKIRVF 803
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 899 LRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAG--------VLNG 970
Cdd:CHL00207 804 IAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdnlnkrfkILPF 883
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 971 SLEYGTcfggskleDMSKILVEKGFN---------------YSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMH 1035
Cdd:CHL00207 884 DEMYGS--------EYSRILINNKLNqasiknneywlfnsyHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIH 955
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1036 ARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDafevDVCAKCGLMGYsgwcttCKSAENV 1115
Cdd:CHL00207 956 ARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD----DMQGRNETLNA------IVKGQPI 1025
|
1210 1220
....*....|....*....|.
gi 372464957 1116 IKMTIPYAAKLLFQELLSMNI 1136
Cdd:CHL00207 1026 PKPGTPESFKVLMRELQSLGL 1046
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
203-380 |
3.10e-47 |
|
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: 167.14 E-value: 3.10e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 203 SKNRIIVEADEKKGIVQASVTSSTHERKSKTYVVTKNDKIYLKHN-SISEEIPIVIVLKACGVVSELEIMQLVCGNDSSY 281
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 282 QDIFAVNIEEASKFNIYTQQQALEYIGaKVKTMRRQKLTVLQEGIEAIATT-----VIAHLTVEAL--NFREKALYMAMM 354
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSRdpkynLNKHLGLNEPfeNERLKAQDILYM 159
|
170 180
....*....|....*....|....*.
gi 372464957 355 TRRVVMAMHNPKMVDDRDYVGNKRLE 380
Cdd:pfam04561 160 IDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1057-1143 |
4.88e-42 |
|
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: 148.51 E-value: 4.88e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1057 GGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCAKCGLMGYSGWCTTCKSAENVIKMTIPYAAKLLFQELLSMNI 1136
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 372464957 1137 APRLRLE 1143
Cdd:pfam04560 81 DPRLLLE 87
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
894-1087 |
5.76e-42 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 167.59 E-value: 5.76e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 894 LIKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGVLNGsLE 973
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLG-IK 947
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 974 YGT-CFGGSKLEDMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 1052
Cdd:PRK00405 948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
170 180 190
....*....|....*....|....*....|....*...
gi 372464957 1053 RSRDGGLRLGEMErdcVIA---YGASQLLLERLMISSD 1087
Cdd:PRK00405 1028 KAQFGGQRFGEME---VWAleaYGAAYTLQEMLTVKSD 1062
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
888-1087 |
8.96e-32 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 134.64 E-value: 8.96e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 888 SDNDQALIKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKAGv 967
Cdd:CHL00001 797 SSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAG- 875
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 968 lnGSLE-----------YGT------CFggSKLEDMSKI-----LVEKgfNYSGKDMLYSGITGECLQAYIFFGPIYYQK 1025
Cdd:CHL00001 876 --DLLNrhyriapfderYEQeasrklVF--SELYEASKQtanpwVFEP--EYPGKSRLFDGRTGDPFEQPVTIGKAYILK 949
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 372464957 1026 LKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMErdcVIA---YGASQLLLERLMISSD 1087
Cdd:CHL00001 950 LIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEME---VWAlegFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
368-1134 |
1.99e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 124.65 E-value: 1.99e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 368 VDDRDYVGNKRLELAGQLISllfEDLFKKFNSDFKASIDKvLKKPNRAmeYDALLSIN-VHSNNITSGLNRAISTGNwsL 446
Cdd:PRK09603 454 IDDRDHLGNRRIRAVGELLA---NELHSGLVKMQKTIKDK-LTTMSGA--FDSLMPHDlVNSKMITSTIMEFFMGGQ--L 525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 447 KRFkMERagvTHVLSRLSY---ISALGmmtriSSQFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHit 523
Cdd:PRK09603 526 SQF-MDQ---TNPLSEVTHkrrLSALG-----EGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTR-- 594
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 524 tddeeepikklcyvlgVEDINLIDSAslhlnYSVFLNGtligsarfprkfvshfralrrscKVSAFISIHTNSEQKAVHI 603
Cdd:PRK09603 595 ----------------VNDLGFIEAP-----YKKVVDG-----------------------KVVGETIYLTAIQEDSHII 630
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 604 AtdggricrPLIIVTNGESHVKAHHLKRLLEGELVfddflklglveyldvneendsfiaLYEKDidqAVTHLEIEPFTVL 683
Cdd:PRK09603 631 A--------PASTPIDEEGNILGDLIETRVEGEIV------------------------LNEKS---KVTLMDLSSSMLV 675
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 684 GAVAGLIPYPHHNQSPRNTYQCAMGKQAI-----------------------GAIAYNQ---FKRIDT----LL------ 727
Cdd:PRK09603 676 GVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswGAIKANRagvVEKIDSkniyILgegkee 755
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 728 -YLMIYP--------------QQPMVKT-KTIEL---------IDYDKLPAGQNATVAVMSYSGYDIEDALVLNKasldr 782
Cdd:PRK09603 756 aYIDAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiiadgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSE----- 830
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 783 gfgrCETRRKTTTVLKRYPNH-------------TQDIiGGMRVDEKGEpiwqhkaLGPDGLGEVGMKLDSGQIYINKSV 849
Cdd:PRK09603 831 ----RITKDDIFTSTHIYEKEvdarelkhgveefTADI-PDVKEEALAH-------LDESGIVKVGTYVSAGMILVGKTS 898
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 850 P---------------------------------------------TNSTDAFNGAAQASYRETPviyRAPEPSHIDQVM 884
Cdd:PRK09603 899 PkgeikstpeerllraifgdkaghvvnkslycppslegtvidvkvfTKKGYEKDARVLSAYEEEK---AKLDMEHFDRLT 975
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 885 M------------------------------------------------------------------------------- 885
Cdd:PRK09603 976 Mlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlaslvkkyskevqnhyeitknnfleqkkvlge 1055
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 886 ------SVSDNDQAL-------IKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRM 952
Cdd:PRK09603 1056 eheeklSILEKDDILpngvikkVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRM 1135
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 953 TVGKMIE----LVSGKAG---------------------------VLNGS----------------LEYGT--------- 976
Cdd:PRK09603 1136 NIGQILEmhlgLVGKEFGkqiasmledktkdfakelrakmleianAINEKdpltihalencsdeelLEYAKdwskgvkma 1215
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 977 --CFGGSKLEDMSKILVEKGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRS 1054
Cdd:PRK09603 1216 ipVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKA 1295
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1055 RDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEvdvcakcglmGYSGWCTTCKSAENVIKMTIPYAAKLLFQELLSM 1134
Cdd:PRK09603 1296 LFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR----------GRENAYRAIAKGEQVGESEIPETFYVLTKELQSL 1365
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
557-617 |
5.98e-28 |
|
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: 107.07 E-value: 5.98e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 372464957 557 VFLNGTLIGSARFPRKFVSHFRALRRSCKVSAFISIHTNSEQKAVHIATDGGRICRPLIIV 617
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIV 61
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
895-1148 |
3.74e-22 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 103.93 E-value: 3.74e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 895 IKVLLRQHRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKMIELVSGKA--------- 965
Cdd:PRK14844 1071 VKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWAckklgekvg 1150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 966 --------------------------------------------------------GVLNGSLE------YGTC------ 977
Cdd:PRK14844 1151 nildeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpnkNALNDELNelvenyLNSCksaysn 1230
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 978 ----------------------------------------------FGGSKLEDMSKILVEKGFNYSGKDMLYSGITGEC 1011
Cdd:PRK14844 1231 lrnflievyscgsnvsicnnirdisdnnliefarklrdgipvaapvFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEK 1310
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 1012 LQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDafev 1091
Cdd:PRK14844 1311 FDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD---- 1386
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 372464957 1092 DVCAKcglmgysgwcttCKSAENVIK------MTIPYAAKLLFQELLSMNIAPRLRLEDIFQE 1148
Cdd:PRK14844 1387 DINGR------------VKIYESIIKgdsnfeCGIPESFNVMIKELRSLCLNVDLKQNDVVIE 1437
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
459-521 |
1.38e-17 |
|
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: 77.95 E-value: 1.38e-17
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 372464957 459 VLSRLSYISALGMMTRISS---QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTH 521
Cdd:pfam04565 2 VLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
639-679 |
2.47e-11 |
|
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: 59.86 E-value: 2.47e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 372464957 639 FDDFLKLGLVEYLDVNEENDSFIALYEKDIDQAV------------THLEIEP 679
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSreeregpyahtyTHCEIHP 53
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
64-199 |
3.19e-10 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 64.74 E-value: 3.19e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 372464957 64 LDSFNYFVDIDLKKIIKANQTILSDVDP------EFYLKYVDIRIGKkstsstkdyltPPH---ECRLRDMTYSAPIYVD 134
Cdd:PRK00405 32 LDSFDWFLQLDVPPEDEGLEEVFRSIFPiedfngNLSLEFVSYELGE-----------PKYdveECKERGLTYSAPLRVK 100
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 372464957 135 IEYTRgRNI--IMHKDVEIGRMPIMlrsnkcTlygcdeaemaklnecpldPGGYFIVNGTEKVILVQ 199
Cdd:PRK00405 101 LRLIN-KETgeIKEQEVYMGDIPLM------T------------------ENGTFIINGTERVIVSQ 142
|
|
| |
