|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
1-1072 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 2461.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 1 MLGDEKEGTSAIPGFNQIQFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVEPLIKERDAVYESLTYSSEL 80
Cdd:CHL00001 1 MLRDGNEGMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 81 YVSAGLIWKTSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDHNGISVYTGTIISDWGGRLEL 160
Cdd:CHL00001 81 YVPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLEL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 161 EIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFS 240
Cdd:CHL00001 161 EIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 241 ESLCKELQKKFFHQRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADL 320
Cdd:CHL00001 241 ESLCKELQKKFFQQRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 321 LQDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGG 400
Cdd:CHL00001 321 LQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGG 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 401 LTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYELFEKSKkaRIRMLFLSPSQDEYYM 480
Cdd:CHL00001 401 LTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSK--EERMVYLSPSEDEYYM 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 481 IAAGNSLALNRGIQEEQAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRS 560
Cdd:CHL00001 479 IAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRS 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 561 EKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQIL 640
Cdd:CHL00001 559 EKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQIL 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 641 ADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLR 720
Cdd:CHL00001 639 ADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLR 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 721 NLDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSS 800
Cdd:CHL00001 719 NLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSS 798
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 801 YNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLL 880
Cdd:CHL00001 799 YNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLL 878
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 881 DRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKI 960
Cdd:CHL00001 879 NRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKI 958
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 961 HGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPES 1040
Cdd:CHL00001 959 HARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPEDAPES 1038
|
1050 1060 1070
....*....|....*....|....*....|..
gi 7525025 1041 FRLLVRELRSLALELNHFLVSEKNFQINRKEV 1072
Cdd:CHL00001 1039 FRLLVRELRSLALELNHFLVSEKNFQINRKEV 1070
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
12-1056 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 1099.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 12 IPGFNQIQFEGFYRFI----------DQGLIEELAKFPKIEDI--DHEIEFQlfveTYQLVEPLIKERDAVYESLTYSSE 79
Cdd:TIGR02013 17 VPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYtgNIELEYL----SYRLGEPKYSVEECKERGLTYSAP 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 80 LYVSAGLIWK---TSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDH--NGISVYTGTIISDW 154
Cdd:TIGR02013 93 LKVKLRLINKeedGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDTtkSGKVLFSARIIPYR 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 155 GGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVC--YPEIFLSFLTDKEKkkigSKENAILEFYQQFSc 232
Cdd:TIGR02013 173 GSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLgsGEYIRNTLRKDPTN----SEEEALVEIYRKLR- 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 233 vGGDPIFSESLCKELQKKFFH-QRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKN 311
Cdd:TIGR02013 248 -PGEPPTVEAARSLLENLFFDpKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGN 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 312 KRIRSVADLLQDQLGLALARLENVVKGTISGAIRHKLipTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGR 391
Cdd:TIGR02013 327 RRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTL--TPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 392 KLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYELFEKSKKARIRMLFL 471
Cdd:TIGR02013 405 RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTDEIDYL 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 472 SPSQDEYYMIAAGNS-LALNRGIQEEqAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNM 550
Cdd:TIGR02013 485 TADEEDNYVIAQANApLDENGRFVED-LVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNM 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 551 QRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDTLSI-------PLIMYQRSNKNTCMH 623
Cdd:TIGR02013 564 QRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPdggidiyRLLKYQRSNQDTCIN 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 624 QKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQG 703
Cdd:TIGR02013 644 QRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG 723
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 704 PERITKEIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQvaKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGG 783
Cdd:TIGR02013 724 PEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPK--GETELTPEEKLLRAIFGEKARDVRDTSLRVPPGV 801
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 784 RGRVIDVRWVQKKGGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVP 860
Cdd:TIGR02013 802 EGTVIDVKVFSREQGDELPPgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVP 881
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 861 SRMNVGQIFECSLGLAGSLLDRHyriapfderyEQEASRKLVFSELYEASKQTANPWVFEPEypGKSRIFDGRTGDPFEQ 940
Cdd:TIGR02013 882 SRMNIGQILETHLGWAGKRLGRK----------GVPIATPVFDGASEEEIKEYLEKAGLPRD--GKVRLYDGRTGEQFDR 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 941 PVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQE 1020
Cdd:TIGR02013 950 PVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTK 1029
|
1050 1060 1070
....*....|....*....|....*....|....*.
gi 7525025 1021 VLGTTIIGGTIPKPeDAPESFRLLVRELRSLALELN 1056
Cdd:TIGR02013 1030 AYEAIVKGENVPEP-GIPESFNVLIKELQSLGLDIE 1064
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1053 |
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: 1052.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 12 IPGFNQIQFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQlFVEtYQLVEPLI-----KERDavyesLTYSSELYVSAGL 86
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLE-FGD-YRLGEPKYtpeecKERD-----LTYAAPLYVKVRL 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 87 IWKTSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDHNGISVYTGTIISDWGGRLELEIDKKA 166
Cdd:COG0085 86 VNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDG 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 167 RIWARVSRKQKISILVLSSAMGL-NLREILENVCYPEIFLSFLTDKEKKKIGSKENAILEFYQQFscVGGDPIFSESLCK 245
Cdd:COG0085 166 TIYVRIDRKRKIPVTVLLRALGLeTDEEILEAFGDDPIQEYILATLEKDNTKTQEEALLEIYRKL--RPGEPPTIERAEQ 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 246 ELQKKFF-HQRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 324
Cdd:COG0085 244 LLDNLFFdPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQ 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 325 LGLALARLENVVKG--TISGAIRhkliPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLT 402
Cdd:COG0085 324 FRVGLSRMERVVRErmTTQDVEA----ITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 403 GRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYelfeKSKKARIR--MLFLSPSQDEYYM 480
Cdd:COG0085 400 RERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYR----KVENGKVTdeIEYLTADEEENYY 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 481 IAAGNSLALNRGIQEEQAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRS 560
Cdd:COG0085 476 IAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRP 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 561 EkcivgtglerqvaldsgVPaiaehegkilytdtekivfsgngdTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQIL 640
Cdd:COG0085 556 E-----------------AP------------------------LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVL 594
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 641 ADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLR 720
Cdd:COG0085 595 ADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALR 674
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 721 NLDKNGIVMLGSWVETGDILVGKLTPQvaKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSS 800
Cdd:COG0085 675 NLDEDGIIRIGAEVKGGDILVGKVTPK--GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDE 752
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 801 YNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 877
Cdd:COG0085 753 LPPgvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAA 832
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 878 SLLDRHYRIAPFDERYEQEasrklVFSELYEASkqtanpwvfePEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVD 957
Cdd:COG0085 833 ALLGRRVATPVFDGAPEEE-----IRELLEKAG----------LPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVD 897
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 958 DKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEdA 1037
Cdd:COG0085 898 DKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPG-I 976
|
1050
....*....|....*.
gi 7525025 1038 PESFRLLVRELRSLAL 1053
Cdd:COG0085 977 PESFKVLLKELQSLGL 992
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
17-1058 |
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: 855.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 17 QIQFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVEPLIKE---------RDAVYESLTYSSELYVSAGLI 87
Cdd:cd00653 3 KQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIRLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 88 WKTSRNMQEQRIFIGNIPLMNSL------------------------GTSIVNGIYRIVINQILQSPGIYYQSelDHNGI 143
Cdd:cd00653 83 VNDKGKIKEQEVFIGEIPIMLRSklcnlngltpeeliklgecpldpgGYFIINGTEKVIINQEQRSPNVIIVE--DSKGK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 144 SVYTGTIISD----WGGRLELEID-KKARIWARVSRKQKisilvlssamglnlreilenvcypeiflsfltdkekkkigs 218
Cdd:cd00653 161 RIYTKTSIPSyspyRGSWLEVKSDkKKDRIYVRIDLKRQ----------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 219 kENAILEFYQQFscvggdpifseslckelqkkffhqrcelgrigrrninwrlnlnipqnnifllpRDVLAAADHLIGMKF 298
Cdd:cd00653 200 -EEALKYIGKRF-----------------------------------------------------EDLIYMIRKLILLVL 225
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 299 GMGTLDDMNHLKNKRIRSVADLLQDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP----- 373
Cdd:cd00653 226 GKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskr 305
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 374 -------LSQVLDRTNPLTQIVHGRKLSylgPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGd 446
Cdd:cd00653 306 flmqrsgLSQVLDRLNPLSELSHKRRIS---SLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 447 wGSLESPFYELFEkskkarirmlflspsqdeyymiaagnslalnrgiqeeqavparyrqefltiaweEVHLRSIFPFQYF 526
Cdd:cd00653 382 -GRIERPYRIVEK------------------------------------------------------EVTHIEISPSQIL 406
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 527 SIGASLIPFIEHNDANRALMSSNMQRQAVP----------------LSRSEKCIVGTGLERQVALDsgvpaiaehegkil 590
Cdd:cd00653 407 SVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG-------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 591 ytdtekivfsgngdtlsiplimyqrsnkntcmhqkpqvrrgkcikkgqiladgaatvggELALGKNILVAYMPWEGYNFE 670
Cdd:cd00653 473 -----------------------------------------------------------ELPLGQNAIVAVMSYSGYNFE 493
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 671 DAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITK-EIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQVA 749
Cdd:cd00653 494 DAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGE 573
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 750 KESSYapedrllraILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSSYNpEIIRVYISQKREIKVGDKVAGRHGNK 829
Cdd:cd00653 574 TESTP---------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGN-KLVKVYIRQKRKPQIGDKFASRHGQK 643
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 830 GIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELyea 909
Cdd:cd00653 644 GVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGL--- 720
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 910 skqtanpwvfepEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGE 989
Cdd:cd00653 721 ------------NYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 7525025 990 MEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTII---------GGTIPKPEDAPESFRLLVRELRSLALELNHF 1058
Cdd:cd00653 789 MERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
530-981 |
1.03e-128 |
|
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: 396.13 E-value: 1.03e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 530 ASLIPFIEHNDANRALMSSNMQRQAVPLsrsekcivgtglerqvaldsgvpaiaehegkilytdtekivfsgngdtlsIP 609
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGI--------------------------------------------------YT 31
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 610 LIMYQRSNKNT---CMHQKPQVRRGKcIKKGQIladgaatvgGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYT 686
Cdd:pfam00562 32 LNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFT 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 687 SFHIRKYEIQThvTTQGP-ERITKEIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQvakessyaPEDRLLRAIL 765
Cdd:pfam00562 102 SIHIKEIEARK--TKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGPT--------ELTKLLRAIF 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 766 GIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSSynpEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQ 845
Cdd:pfam00562 172 GEKARDVKDTSLKVPPGEEGVVDDVIVFELPPGGI---KMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTE 248
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 846 DGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDeryEQEASRKLVFSELYEASkqtanpwvfePEYPG 925
Cdd:pfam00562 249 DGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAG----------YNYYG 315
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 7525025 926 KSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSK 981
Cdd:pfam00562 316 KEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
1-1072 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 2461.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 1 MLGDEKEGTSAIPGFNQIQFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVEPLIKERDAVYESLTYSSEL 80
Cdd:CHL00001 1 MLRDGNEGMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 81 YVSAGLIWKTSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDHNGISVYTGTIISDWGGRLEL 160
Cdd:CHL00001 81 YVPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLEL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 161 EIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFS 240
Cdd:CHL00001 161 EIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFACVGGDPVFS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 241 ESLCKELQKKFFHQRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADL 320
Cdd:CHL00001 241 ESLCKELQKKFFQQRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 321 LQDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGG 400
Cdd:CHL00001 321 LQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGG 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 401 LTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYELFEKSKkaRIRMLFLSPSQDEYYM 480
Cdd:CHL00001 401 LTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSK--EERMVYLSPSEDEYYM 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 481 IAAGNSLALNRGIQEEQAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRS 560
Cdd:CHL00001 479 IAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRS 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 561 EKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQIL 640
Cdd:CHL00001 559 EKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQIL 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 641 ADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLR 720
Cdd:CHL00001 639 ADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLR 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 721 NLDKNGIVMLGSWVETGDILVGKLTPQVAKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSS 800
Cdd:CHL00001 719 NLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSS 798
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 801 YNPEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLL 880
Cdd:CHL00001 799 YNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLL 878
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 881 DRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKI 960
Cdd:CHL00001 879 NRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKI 958
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 961 HGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEDAPES 1040
Cdd:CHL00001 959 HARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPEDAPES 1038
|
1050 1060 1070
....*....|....*....|....*....|..
gi 7525025 1041 FRLLVRELRSLALELNHFLVSEKNFQINRKEV 1072
Cdd:CHL00001 1039 FRLLVRELRSLALELNHFLVSEKNFQINRKEV 1070
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
12-1055 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1124.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 12 IPGFNQIQFEGFYRFI-------DQGLIEELAK-FPkIEDIDHEIEFQlFVEtYQLVEPLIKERDAVYESLTYSSELYVS 83
Cdd:PRK00405 24 LPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSiFP-IEDFNGNLSLE-FVS-YELGEPKYDVEECKERGLTYSAPLRVK 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 84 AGLIWKTSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDH--NGISVYTGTIISDWGGRLELE 161
Cdd:PRK00405 101 LRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKLLYSARIIPYRGSWLEFE 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 162 IDKKARIWARVSRKQKISILVLSSAMGLNLREILEN-------VCYPEIFLSFLTDK----------------------- 211
Cdd:PRK00405 181 FDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLfyekeefGKEIEVPVEYLLGKvlaedivdeetgevlaeandeit 260
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 212 ------------EKKKIGSKENAILEFYQQFScvGGDPIFSESLCKELQKKFF-HQRCELGRIGRRNINWRLNLNIPQNN 278
Cdd:PRK00405 261 eeldgpyirntlEKDPTSSREEALVEIYRRLR--PGEPPTVEAARSLLENLFFdPKRYDLSKVGRYKLNKKLGLDEDEDV 338
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 279 IFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQLGLALARLENVVKGTISGAIRHKLipTPQNLVTS 358
Cdd:PRK00405 339 RVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTL--TPQDLINA 416
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 359 TPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSL 438
Cdd:PRK00405 417 KPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSL 496
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 439 SIHARIGDWGSLESPFYelfeKSKKARI--RMLFLSPSQDEYYMIAAGNS-LALNRGIQEEQaVPARYRQEFLTIAWEEV 515
Cdd:PRK00405 497 ATYARVNEYGFIETPYR----KVVDGKVtdEIVYLTADEEDNYVIAQANApLDEDGRFVDEL-VTARYKGEFVLVPPEEV 571
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 516 HLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTE 595
Cdd:PRK00405 572 DYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDAS 651
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 596 KIV------FSGNGDTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNF 669
Cdd:PRK00405 652 RIVvrveelDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNF 731
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 670 EDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQva 749
Cdd:PRK00405 732 EDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPK-- 809
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 750 KESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVR-WVQKKGGSSYNP---EIIRVYISQKREIKVGDKVAGR 825
Cdd:PRK00405 810 GETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKvFTRIEQGDELPPgvnKLVKVYIAQKRKIQVGDKMAGR 889
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 826 HGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEasrklVFSE 905
Cdd:PRK00405 890 HGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEE-----IKEL 964
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 906 LYEASKQTanpwvfepeyPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQ 985
Cdd:PRK00405 965 LEEAGLPE----------DGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQ 1034
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 986 RVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPeDAPESFRLLVRELRSLALEL 1055
Cdd:PRK00405 1035 RFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEP-GIPESFNVLVKELQSLGLDV 1103
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
12-1056 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 1099.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 12 IPGFNQIQFEGFYRFI----------DQGLIEELAKFPKIEDI--DHEIEFQlfveTYQLVEPLIKERDAVYESLTYSSE 79
Cdd:TIGR02013 17 VPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYtgNIELEYL----SYRLGEPKYSVEECKERGLTYSAP 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 80 LYVSAGLIWK---TSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDH--NGISVYTGTIISDW 154
Cdd:TIGR02013 93 LKVKLRLINKeedGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDTtkSGKVLFSARIIPYR 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 155 GGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREILENVC--YPEIFLSFLTDKEKkkigSKENAILEFYQQFSc 232
Cdd:TIGR02013 173 GSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLgsGEYIRNTLRKDPTN----SEEEALVEIYRKLR- 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 233 vGGDPIFSESLCKELQKKFFH-QRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKN 311
Cdd:TIGR02013 248 -PGEPPTVEAARSLLENLFFDpKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGN 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 312 KRIRSVADLLQDQLGLALARLENVVKGTISGAIRHKLipTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGR 391
Cdd:TIGR02013 327 RRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTL--TPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 392 KLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYELFEKSKKARIRMLFL 471
Cdd:TIGR02013 405 RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTDEIDYL 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 472 SPSQDEYYMIAAGNS-LALNRGIQEEqAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNM 550
Cdd:TIGR02013 485 TADEEDNYVIAQANApLDENGRFVED-LVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNM 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 551 QRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDTLSI-------PLIMYQRSNKNTCMH 623
Cdd:TIGR02013 564 QRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPdggidiyRLLKYQRSNQDTCIN 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 624 QKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQG 703
Cdd:TIGR02013 644 QRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG 723
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 704 PERITKEIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQvaKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGG 783
Cdd:TIGR02013 724 PEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPK--GETELTPEEKLLRAIFGEKARDVRDTSLRVPPGV 801
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 784 RGRVIDVRWVQKKGGSSYNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVP 860
Cdd:TIGR02013 802 EGTVIDVKVFSREQGDELPPgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVP 881
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 861 SRMNVGQIFECSLGLAGSLLDRHyriapfderyEQEASRKLVFSELYEASKQTANPWVFEPEypGKSRIFDGRTGDPFEQ 940
Cdd:TIGR02013 882 SRMNIGQILETHLGWAGKRLGRK----------GVPIATPVFDGASEEEIKEYLEKAGLPRD--GKVRLYDGRTGEQFDR 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 941 PVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQE 1020
Cdd:TIGR02013 950 PVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTK 1029
|
1050 1060 1070
....*....|....*....|....*....|....*.
gi 7525025 1021 VLGTTIIGGTIPKPeDAPESFRLLVRELRSLALELN 1056
Cdd:TIGR02013 1030 AYEAIVKGENVPEP-GIPESFNVLIKELQSLGLDIE 1064
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
9-1059 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1054.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 9 TSAIPGFNQIQFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVSAGLIW 88
Cdd:CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFIN 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 89 KTSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDHNGISVYTGTIISDWGGRLELEIDKKARI 168
Cdd:CHL00207 84 LKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 169 WARVSRKQKISILVLSSAMGLNLREILENVCYPEIFLSFLTDKEKKKIGSKENAILEFYQQFScvGGDPIFSESLCKELQ 248
Cdd:CHL00207 164 WIRIDKNRKKPLIIFLKALGLTDQDIYSRLTKSEFLKKLKPILLNSNSYTNEEILLEIYKNLS--PIEPATVNDANQNLF 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 249 KKFFH-QRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQLGL 327
Cdd:CHL00207 242 SRFFDpKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRI 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 328 ALARLENVVKGTISGAIRHKLipTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTAN 407
Cdd:CHL00207 322 GLKRLERILRNRMTICDIDSL--SKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRIS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 408 FRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYELFEKSKKARIRMLFLSPSQDEYYMIAAGN-S 486
Cdd:CHL00207 400 FAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFGNPIYLTADSEDLYRIAPNDiN 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 487 LALNRGIQEEQaVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVG 566
Cdd:CHL00207 480 LNKNNYFKKNI-IPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVG 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 567 TGLERQVALDSGVPAIAEHEGKILYTDTEKI-VFSGNGDTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAA 645
Cdd:CHL00207 559 TGYEKQIALDSGMTIISLTEGIVVSVSAYKIiIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSD 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 646 TVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKN 725
Cdd:CHL00207 639 IDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDEN 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 726 GIVMLGSWVETGDILVGKLTPQvaKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSSYNP-- 803
Cdd:CHL00207 719 GIISIGSKVLAGDILVGKITPK--GESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFgy 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 804 -EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDR 882
Cdd:CHL00207 797 yLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNK 876
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 883 HYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHG 962
Cdd:CHL00207 877 RFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHA 956
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 963 RSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPeDAPESFR 1042
Cdd:CHL00207 957 RTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKP-GTPESFK 1035
|
1050
....*....|....*..
gi 7525025 1043 LLVRELRSLALELNHFL 1059
Cdd:CHL00207 1036 VLMRELQSLGLDIEAYK 1052
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1053 |
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: 1052.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 12 IPGFNQIQFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQlFVEtYQLVEPLI-----KERDavyesLTYSSELYVSAGL 86
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLE-FGD-YRLGEPKYtpeecKERD-----LTYAAPLYVKVRL 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 87 IWKTSRNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELDHNGISVYTGTIISDWGGRLELEIDKKA 166
Cdd:COG0085 86 VNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDG 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 167 RIWARVSRKQKISILVLSSAMGL-NLREILENVCYPEIFLSFLTDKEKKKIGSKENAILEFYQQFscVGGDPIFSESLCK 245
Cdd:COG0085 166 TIYVRIDRKRKIPVTVLLRALGLeTDEEILEAFGDDPIQEYILATLEKDNTKTQEEALLEIYRKL--RPGEPPTIERAEQ 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 246 ELQKKFF-HQRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQ 324
Cdd:COG0085 244 LLDNLFFdPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQ 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 325 LGLALARLENVVKG--TISGAIRhkliPTPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLT 402
Cdd:COG0085 324 FRVGLSRMERVVRErmTTQDVEA----ITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 403 GRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYelfeKSKKARIR--MLFLSPSQDEYYM 480
Cdd:COG0085 400 RERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYR----KVENGKVTdeIEYLTADEEENYY 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 481 IAAGNSLALNRGIQEEQAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRS 560
Cdd:COG0085 476 IAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRP 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 561 EkcivgtglerqvaldsgVPaiaehegkilytdtekivfsgngdTLSIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQIL 640
Cdd:COG0085 556 E-----------------AP------------------------LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVL 594
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 641 ADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLR 720
Cdd:COG0085 595 ADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALR 674
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 721 NLDKNGIVMLGSWVETGDILVGKLTPQvaKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSS 800
Cdd:COG0085 675 NLDEDGIIRIGAEVKGGDILVGKVTPK--GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDE 752
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 801 YNP---EIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG 877
Cdd:COG0085 753 LPPgvnKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAA 832
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 878 SLLDRHYRIAPFDERYEQEasrklVFSELYEASkqtanpwvfePEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVD 957
Cdd:COG0085 833 ALLGRRVATPVFDGAPEEE-----IRELLEKAG----------LPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVD 897
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 958 DKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTIIGGTIPKPEdA 1037
Cdd:COG0085 898 DKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPG-I 976
|
1050
....*....|....*.
gi 7525025 1038 PESFRLLVRELRSLAL 1053
Cdd:COG0085 977 PESFKVLLKELQSLGL 992
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
17-1058 |
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: 855.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 17 QIQFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQLFVETYQLVEPLIKE---------RDAVYESLTYSSELYVSAGLI 87
Cdd:cd00653 3 KQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIRLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 88 WKTSRNMQEQRIFIGNIPLMNSL------------------------GTSIVNGIYRIVINQILQSPGIYYQSelDHNGI 143
Cdd:cd00653 83 VNDKGKIKEQEVFIGEIPIMLRSklcnlngltpeeliklgecpldpgGYFIINGTEKVIINQEQRSPNVIIVE--DSKGK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 144 SVYTGTIISD----WGGRLELEID-KKARIWARVSRKQKisilvlssamglnlreilenvcypeiflsfltdkekkkigs 218
Cdd:cd00653 161 RIYTKTSIPSyspyRGSWLEVKSDkKKDRIYVRIDLKRQ----------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 219 kENAILEFYQQFscvggdpifseslckelqkkffhqrcelgrigrrninwrlnlnipqnnifllpRDVLAAADHLIGMKF 298
Cdd:cd00653 200 -EEALKYIGKRF-----------------------------------------------------EDLIYMIRKLILLVL 225
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 299 GMGTLDDMNHLKNKRIRSVADLLQDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYESFFGLHP----- 373
Cdd:cd00653 226 GKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskr 305
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 374 -------LSQVLDRTNPLTQIVHGRKLSylgPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGd 446
Cdd:cd00653 306 flmqrsgLSQVLDRLNPLSELSHKRRIS---SLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 447 wGSLESPFYELFEkskkarirmlflspsqdeyymiaagnslalnrgiqeeqavparyrqefltiaweEVHLRSIFPFQYF 526
Cdd:cd00653 382 -GRIERPYRIVEK------------------------------------------------------EVTHIEISPSQIL 406
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 527 SIGASLIPFIEHNDANRALMSSNMQRQAVP----------------LSRSEKCIVGTGLERQVALDsgvpaiaehegkil 590
Cdd:cd00653 407 SVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG-------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 591 ytdtekivfsgngdtlsiplimyqrsnkntcmhqkpqvrrgkcikkgqiladgaatvggELALGKNILVAYMPWEGYNFE 670
Cdd:cd00653 473 -----------------------------------------------------------ELPLGQNAIVAVMSYSGYNFE 493
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 671 DAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITK-EIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQVA 749
Cdd:cd00653 494 DAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGE 573
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 750 KESSYapedrllraILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSSYNpEIIRVYISQKREIKVGDKVAGRHGNK 829
Cdd:cd00653 574 TESTP---------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGN-KLVKVYIRQKRKPQIGDKFASRHGQK 643
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 830 GIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEASRKLVFSELyea 909
Cdd:cd00653 644 GVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGL--- 720
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 910 skqtanpwvfepEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGE 989
Cdd:cd00653 721 ------------NYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 7525025 990 MEVWALEGFGVAHILQEMLTYKSDHIRARQEVLGTTII---------GGTIPKPEDAPESFRLLVRELRSLALELNHF 1058
Cdd:cd00653 789 MERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
67-1058 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 687.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 67 RDAVYESLTYSSELYVSAGLI-W----KTS-----RNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQS 136
Cdd:PRK09603 83 REAMERGITYSIPLKIKVRLIlWekdtKSGekngiKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKE 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 137 ELDHNGIS--VYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGLNLREI-------------------- 194
Cdd:PRK09603 163 EESSTSLNklIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIikmfyplvkvryendkylip 242
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 195 -----------------------------------------LENVCYP-----------------EIFLSFLT--DKEK- 213
Cdd:PRK09603 243 fasldanqrmefdlkdpqgkiillagkkltsrkikelkenhLEWVEYPmdillnrhlaepvmvgkEVLLDMLTqlDKNKl 322
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 214 KKI---GSKENAI----------------------LEFYQQFSCVG----------------GDPIFSESLCKELQKKFF 252
Cdd:PRK09603 323 EKIhdlGVQEFVIindlalghdasiihsfsadsesLKLLKQTEKIDdenalaairihkvmkpGDPVTTEVAKQFVKKLFF 402
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 253 H-QRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQLGLALAR 331
Cdd:PRK09603 403 DpERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVK 482
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 332 LENVVKG---TISGAIRHKLiptPQNLVTSTPLTTTYESFFGLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTANF 408
Cdd:PRK09603 483 MQKTIKDkltTMSGAFDSLM---PHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGF 559
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 409 RIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPFYELFEKskKARIRMLFLSPSQDEYYMIAAGNSLA 488
Cdd:PRK09603 560 EARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDG--KVVGETIYLTAIQEDSHIIAPASTPI 637
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 489 LNRGIQEEQAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTG 568
Cdd:PRK09603 638 DEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 569 LERQVALDSGVPAIAEHEGKILYTDTEKIVFSGNGDTL----SIPLIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGA 644
Cdd:PRK09603 718 IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEayidAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGP 797
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 645 ATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDK 724
Cdd:PRK09603 798 SMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDE 877
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 725 NGIVMLGSWVETGDILVGKLTPQvaKESSYAPEDRLLRAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGG------ 798
Cdd:PRK09603 878 SGIVKVGTYVSAGMILVGKTSPK--GEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYekdarv 955
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 799 -SSYNPE------------------------------------------------------------------------- 804
Cdd:PRK09603 956 lSAYEEEkakldmehfdrltmlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlaslvkkyskev 1035
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 805 -----------------------------------------IIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPY 843
Cdd:PRK09603 1036 qnhyeitknnfleqkkvlgeeheeklsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPY 1115
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 844 LQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAG--------------------SLLDRHYRIAPF-------------- 889
Cdd:PRK09603 1116 TADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGkefgkqiasmledktkdfakELRAKMLEIANAinekdpltihalen 1195
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 890 --DER---YEQEASRKLVFS-ELYEASKQTANPWVFE---PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKI 960
Cdd:PRK09603 1196 csDEElleYAKDWSKGVKMAiPVFEGISQEKFYKLFElakIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKV 1275
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 961 HGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLgTTIIGGTIPKPEDAPES 1040
Cdd:PRK09603 1276 HARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAY-RAIAKGEQVGESEIPET 1354
|
1290
....*....|....*...
gi 7525025 1041 FRLLVRELRSLALELNHF 1058
Cdd:PRK09603 1355 FYVLTKELQSLALDINIF 1372
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
92-1056 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 615.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 92 RNMQEQRIFIGNIPLMNSLGTSIVNGIYRIVINQILQSPGIYYQSELD---HNGISVYTGTIISDWGGRLELEIDKKARI 168
Cdd:PRK14844 135 KSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGktyNSGKLIYSARVIPYRGSWLDIEFDVKDHL 214
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 169 WARVSRKQKISILVLSSAMGLNLREIL----ENVCY------------PEIF----LSF-LTD-------KEKKKIGSK- 219
Cdd:PRK14844 215 YFRIDRKRKLPISVLLKALGLSNNDILdrfyEKIKYikhkdgwkvpfvPDKFkgvrLPFdLMDvegnvllKANVRITSRl 294
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 220 -----ENAILEFYQQFSCVGG-----DPIFSESLCK-------------------------------------------- 245
Cdd:PRK14844 295 akklyDNELKEYLVPFDSICGlflaeDLIDSASSTKilsagesikledikklellsideisvlnidnlsvgpyilntlfl 374
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 246 -------------------------ELQKKFFH------QRCELGRIGRRNINWRLNLNIPQNNIFLLPRDVLAAADHLI 294
Cdd:PRK14844 375 denmsyqdalyeiykvlrpgevpvlEIVEEFFRnlffspEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIV 454
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 295 GMKFGMGTLDDMNHLKNKRIRSVADLLQDQLGLALARLENVVKGTISGAIRHKLipTPQNLVTSTPLTTTYESFFGLHPL 374
Cdd:PRK14844 455 LLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKV--SPSDFINPKVLTNVLRDFFNSSQL 532
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 375 SQVLDRTNPLTQIVHGRKLSYLGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHARIGDWGSLESPF 454
Cdd:PRK14844 533 SQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPY 612
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 455 YELFEKSKKARIRmlFLSPSQDEYYMIAAGNSLALNRGIQEEQAVPARYRQEFLTIAWEEVHLRSIFPFQYFSIGASLIP 534
Cdd:PRK14844 613 RKVVNRVVTDQIE--YLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIP 690
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 535 FIEHNDANRALMSSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVPAIAEHEGKILYTDTEKIVF----SGNGDTLSIP- 609
Cdd:PRK14844 691 FLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIrafdKERVNYLDVDi 770
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 610 --LIMYQRSNKNTCMHQKPQVRRGKCIKKGQILADGAATVGGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYTS 687
Cdd:PRK14844 771 yhLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTS 850
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 688 FHIRKYEIQTHVTTQGPERITKEIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQvaKESSYAPEDRLLRAILGI 767
Cdd:PRK14844 851 IHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPK--PSLSLPPETKLLMTIFGE 928
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 768 QVSTSKETCLKLPIGGRGRVIDVRWVQKKG----------------------------GSSY------------------ 801
Cdd:PRK14844 929 KSFDCADSSLYTSPDVEGTVIDVQVFTRRGveenerallikqkeindfekerdyiinvTSEYfydelkkllinsgsqdre 1008
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 802 ----------------NPEI------------------------------------------IRVYISQKREIKVGDKVA 823
Cdd:PRK14844 1009 kfdsiereqwwgiglkNQSIseqvkslkkdfdekvshaiaqfkrkveklhegydlpqgvsmsVKVFIAVKHSLQPGDKMA 1088
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 824 GRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLA--------GSLLDRHYRI-APF----- 889
Cdd:PRK14844 1089 GRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWAckklgekvGNILDEINKIkSAFckgir 1168
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 890 ---DERYEQ----------------------------------------------------------------------- 895
Cdd:PRK14844 1169 slnDDNFTKfaaayldnkkienidddeitasvlntpnknalndelnelvenylnscksaysnlrnflievyscgsnvsic 1248
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 896 ------------EASRKL-----VFSELYEASKQTANPWVFE---PEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQ 955
Cdd:PRK14844 1249 nnirdisdnnliEFARKLrdgipVAAPVFEGPKDEQIAKLFElagLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHL 1328
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 956 VDDKIHGRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSDHIRARQEVLgTTIIGGTIPKPE 1035
Cdd:PRK14844 1329 VDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIY-ESIIKGDSNFEC 1407
|
1290 1300
....*....|....*....|.
gi 7525025 1036 DAPESFRLLVRELRSLALELN 1056
Cdd:PRK14844 1408 GIPESFNVMIKELRSLCLNVD 1428
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
530-981 |
1.03e-128 |
|
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: 396.13 E-value: 1.03e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 530 ASLIPFIEHNDANRALMSSNMQRQAVPLsrsekcivgtglerqvaldsgvpaiaehegkilytdtekivfsgngdtlsIP 609
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGI--------------------------------------------------YT 31
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 610 LIMYQRSNKNT---CMHQKPQVRRGKcIKKGQIladgaatvgGELALGKNILVAYMPWEGYNFEDAVLISECLVYGDIYT 686
Cdd:pfam00562 32 LNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFT 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 687 SFHIRKYEIQThvTTQGP-ERITKEIPHLEGRLLRNLDKNGIVMLGSWVETGDILVGKLTPQvakessyaPEDRLLRAIL 765
Cdd:pfam00562 102 SIHIKEIEARK--TKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGPT--------ELTKLLRAIF 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 766 GIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSSynpEIIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQ 845
Cdd:pfam00562 172 GEKARDVKDTSLKVPPGEEGVVDDVIVFELPPGGI---KMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTE 248
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 846 DGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDeryEQEASRKLVFSELYEASkqtanpwvfePEYPG 925
Cdd:pfam00562 249 DGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAG----------YNYYG 315
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 7525025 926 KSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSK 981
Cdd:pfam00562 316 KEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
19-1051 |
4.55e-78 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 278.38 E-value: 4.55e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 19 QFEGFYRFIDQGLIEELAKFPKIEDIDHEIEFQLfvETYQLVEPLIKERD----------AVYESLTYSSELYVSAGLIw 88
Cdd:PRK08565 18 HLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVL--GKIRVGEPEIKEADgserpitpmeARLRNLTYAAPLYLTMIPV- 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 89 ktSRNMQ--EQRIFIGNIPLM----------NSL--------------GTSIVNGIYRIVINQILQSPG--IYYQSELDH 140
Cdd:PRK08565 95 --ENGIEyePEEVKIGDLPIMvkskicplsgLSPdelieigedpkdpgGYFIINGSERVIVSQEDLAPNrvLVDKGEAGS 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 141 NgiSVYTGTIISDWGG---RLELEIDKKARIWARVSR-KQKISILVLSSAMGLNL-REILENVCY-PEI---FLSFLTDK 211
Cdd:PRK08565 173 S--ITHTAKVISSRAGyraQVTVERRKDGTIYVSFPAvPGKIPFVILMRALGLETdRDIVYAVSLdPEIqqeLLPSLEQA 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 212 EKKKIgSKENAiLEFYQQFSCVGGDPIFSESLCKELQKKFFhqrceLGRIGRRninwrlnlniPQNNI---FLLPRdvla 288
Cdd:PRK08565 251 SSIAA-TVEDA-LDYIGKRVAIGQPREYRIERAEQILDKYL-----LPHLGTS----------PEDRIkkaYFLGQ---- 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 289 AADHLIGMKFGMGTLDDMNHLKNKRIRSVADLLQDQLGLALARLENVVKGTISGAIRHKLIPTPQNLVTSTPLTTTYEsf 368
Cdd:PRK08565 310 MASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIR-- 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 369 fglHPL------------SQVLDRTNPLTQIVHGRKLsyLGPggLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIG 436
Cdd:PRK08565 388 ---HALatgnwvggrtgvSQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVK 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 437 SLSIHARIG-------------DWGSLE------------SPFY-------------ELFEKSKKARiRMLFLSP----- 473
Cdd:PRK08565 461 NLALMAQISvgvdeeeveeilyELGVVPveeareeeyiswSRVYlngrligyhpdgeELAEKIRELR-RSGKISDevnva 539
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 474 -----SQDEYYM------------IAAGNSLALNR-------------------GI-------QEEQAVPARYRQEFLTi 510
Cdd:PRK08565 540 yietgEINEVYVncdsgrvrrpliVVENGKPKLTRehveklkkgeltfddlvkmGVieyldaeEEENAYVALDPEDLTP- 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 511 awEEVHLrSIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSRSEkcivgtgleRQVALDSgvpaiaehEGKIL 590
Cdd:PRK08565 619 --EHTHL-EIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAAN---------FRIRTDT--------RGHLL 678
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 591 YTDTEKIVfsgngDTLSIPLIMYQRsnkntcmhqKPQvrrgkcikkgqiladgaatvggelalGKNILVAYMPWEGYNFE 670
Cdd:PRK08565 679 HYPQRPLV-----QTRALEIIGYND---------RPA--------------------------GQNAVVAVLSYTGYNIE 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 671 DAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPE-RITKEIPHLEG----RLLRNLDKNGIVMLGSWVETGDILVGKLT 745
Cdd:PRK08565 719 DAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVRGyrgeEYYRKLDEDGIVSPEVEVKGGDVLIGKTS 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 746 PqvakeSSYAPEDRLLRAILGiqvsTSKETCLKLPIGGRGRVIDVRWVQKKGGSsynpEIIRVYISQKREIKVGDKVAGR 825
Cdd:PRK08565 799 P-----PRFLEELEELSLGLQ----ERRDTSVTVRHGEKGIVDTVLITESPEGN----KLVKVRVRDLRIPELGDKFASR 865
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 826 HGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRIAPFDERYEQEAsRKLVFSE 905
Cdd:PRK08565 866 HGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEEL-RKELLKL 944
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 906 LYEaskqtanpwvfepeYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSGHYALVTQQPLRGRSKQGGQ 985
Cdd:PRK08565 945 GYK--------------PDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGL 1010
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 986 RVGEMEVWALEGFGVAHILQEMLTYKSD-----------HI---RARQEVLGTTIIG--GTIpKPEDAPESFRLLVRELR 1049
Cdd:PRK08565 1011 RFGEMERDCLIGHGAAMLLKERLLDSSDkttiyvcelcgHIawyDRRKNKYVCPIHGdkGNI-SPVEVSYAFKLLLQELM 1089
|
..
gi 7525025 1050 SL 1051
Cdd:PRK08565 1090 SM 1091
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
494-1051 |
2.60e-62 |
|
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: 223.37 E-value: 2.60e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 494 QEEQAVPARYRQEFLTiawEEVHLRsIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVplsrsekcivgtglerqv 573
Cdd:TIGR03670 99 EEENAYIALDPEELTP---EHTHLE-IDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSL------------------ 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 574 aldsGVPAIAEhegkilytdteKIVFSGNGDTLSIPlimyqrsnkntcmhQKPQVrrgKCIKKGQILADgaatvggELAL 653
Cdd:TIGR03670 157 ----GLYAANY-----------RIRLDTRGHLLHYP--------------QKPLV---KTRVLELIGYD-------DRPA 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 654 GKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPE-RITKEIPHLEG----RLLRNLDKNGIV 728
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVRGyrgeEAYKHLDEDGIV 277
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 729 MLGSWVETGDILVGKLTPqvakessyaPedRLL--RAILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSsynpEII 806
Cdd:TIGR03670 278 YPEVEVKGGDVLIGKTSP---------P--RFLeeLREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGN----KLV 342
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 807 RVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHYRI 886
Cdd:TIGR03670 343 KVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDG 422
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 887 APFDERYEQEAsRKLVFSELYEASkqtanpwvfepeypGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIHGRSSG 966
Cdd:TIGR03670 423 TPFEGEPEEEL-RKELLKLGFKPD--------------GKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRG 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 967 HYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSD-----------HI---RARQEVLGTTIIG--GT 1030
Cdd:TIGR03670 488 PVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDkyvvyvcencgHIaweDKRKGTAYCPVCGetGD 567
|
570 580
....*....|....*....|.
gi 7525025 1031 IPKPEdAPESFRLLVRELRSL 1051
Cdd:TIGR03670 568 ISPVE-MSYAFKLLLDELKSL 587
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
494-1013 |
7.19e-58 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 210.97 E-value: 7.19e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 494 QEEQAVPARYRQEFLTiawEEVHLRsIFPFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVplsrsekcivgtglerqv 573
Cdd:PRK07225 105 EEENAYIAVYEEDLTE---EHTHLE-IDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSL------------------ 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 574 aldsGVPAIAEHegkiLYTDTEkivfsgnGDTLSIPlimyqrsnkntcmhQKPQVrrgKCIKKGQILADgaatvggELAL 653
Cdd:PRK07225 163 ----GLPAANYK----LRPDTR-------GHLLHYP--------------QVPLV---KTQTQEIIGFD-------ERPA 203
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 654 GKNILVAYMPWEGYNFEDAVLISECLVYGDIYTSFHIRKYEIQTHVTTQGPE-RItkEIPHLEGR------LLRNLDKNG 726
Cdd:PRK07225 204 GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEdRF--EIPDKDVRgyrgeeAYRHLDEDG 281
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 727 IVMLGSWVETGDILVGKLTPqvakessyaPedRLLR--AILGIQVSTSKETCLKLPIGGRGRVIDVRWVQKKGGSsynpE 804
Cdd:PRK07225 282 LVNPETEVKEGDVLIGKTSP---------P--RFLEepDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGS----R 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 805 IIRVYISQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFECSLGLAGSLLDRHY 884
Cdd:PRK07225 347 LVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRV 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 885 RIAPF-DERYE--QEASRKLVFselyeaskqtanpwvfepEYPGKSRIFDGRTGDPFEQPVIIGKPYILKLIHQVDDKIH 961
Cdd:PRK07225 427 DGTAFsGEDEEdlREALEKLGF------------------EHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLH 488
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|..
gi 7525025 962 GRSSGHYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAHILQEMLTYKSD 1013
Cdd:PRK07225 489 ARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 540
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
128-315 |
3.06e-52 |
|
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: 181.39 E-value: 3.06e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 128 QSPGIYYQSELDHNGIS-VYTGTIISDWGGRLELEIDKKARIWARVSRKQKISILVLSSAMGL-NLREILENVCY----- 200
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIaTYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLvSDREILDRLCYdfndp 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 201 PEIFLSFLTDKEKKKIGSKENAILEFYQQFSCVGGDPIFSESLCKELQKKFfhqrcelgriGRRNINWRLNLNIPQNNIF 280
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREILYSRD----------PKYNLNKHLGLNEPFENER 150
|
170 180 190
....*....|....*....|....*....|....*
gi 7525025 281 LLPRDVLAAADHLIGMKFGMGTLDDMNHLKNKRIR 315
Cdd:pfam04561 151 LKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
376-443 |
1.20e-27 |
|
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: 106.46 E-value: 1.20e-27
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 7525025 376 QVLDRTNPLTQIVHGRKLSYlGPGGLTGRTANFRIRDIHPSHYGRICPIDTSEGINVGLIGSLSIHAR 443
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
983-1060 |
7.31e-27 |
|
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: 104.98 E-value: 7.31e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 983 GGQRVGEMEVWALEGFGVAHILQEMLTYKSD----HIRARQEVLG-----TTIIGGTIPKPEDAPESFRLLVRELRSLAL 1053
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAaynkcPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 7525025 1054 ELNHFLV 1060
Cdd:pfam04560 81 DPRLLLE 87
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
19-444 |
1.27e-21 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 99.64 E-value: 1.27e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 19 QFEGFYRFIDQGL---IEElakfpkIEDIDHEIEFQLFVET--YQLVEPLIKERD----------AVYESLTYSSELYVS 83
Cdd:PRK09606 22 HIDSYNDFVDNGLqkiIDE------QGPIETEIEDGVYVELgkIRVGKPVVKEADgsereiypmeARLRNLTYSAPLYLE 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 84 AGLIWKTSRNMQEQrIFIGNIPLM------NSLGTS------------------IVNGIYRIVINQILQSPGIYYQSELD 139
Cdd:PRK09606 96 MSPVEGGEEEEPEE-VYIGELPVMvgskicNLYGLSeeelievgedpldpggyfIVNGSERVLMTLEDLAPNKILVEKDE 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 140 HNGISVYTGTIISDWGG---RLELEIDKKARIWA---RVSRKqkISILVLSSAMGL-NLREILENVC-YPEIFLSFLTDK 211
Cdd:PRK09606 175 RYGDRIEVAKVFSQRRGyraLVTVERNRDGLLEVsfpSVPGS--IPFVILMRALGLeTDEEIVEAVSdDPEIVKFMLENL 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 212 EKKKIGSKENAIlEFYQQFSCVGgdpifsESlcKELQKKffhqrcelgrigrrninwRLNLNIPQnniFLLP------RD 285
Cdd:PRK09606 253 EEAEVDTQEEAL-EYIGKRVAPG------QT--KEYRIK------------------RAEYVIDR---YLLPhlgvepEV 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 286 VLAAADHLIGM-------KFGMGTLDDMNHLKNKRIRSVADLLQDQLGLALARLENVVKGTISGA-IRHKlIPTPQNLVT 357
Cdd:PRK09606 303 RRAKAHYLGRMaeacfelALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERAnMRNR-ELSIKTAVR 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 358 STPLTTTYEsffglHPL------------SQVLDRTNPLTQIVHGRKLsyLGPggLTGRTANFRIRDIHPSHYGRICPID 425
Cdd:PRK09606 382 SDVLTERLE-----HAMatgnwvggrtgvSQLLDRTDYMATLSHLRRV--VSP--LSRSQPHFEARDLHPTQWGRICPSE 452
|
490
....*....|....*....
gi 7525025 426 TSEGINVGLIGSLSIHARI 444
Cdd:PRK09606 453 TPEGPNCGLVKNFAQMVEI 471
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
17-362 |
1.55e-14 |
|
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: 77.03 E-value: 1.55e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 17 QIQFEGFYRFID---QGLIEELAKFPKIEDIDHEIE----FQLFVETYQLVEPLIKERDAVYES----------LTYSSE 79
Cdd:pfam04563 4 RQQLDSFNEFVDndlQKIIDENALIESEFEIQHPGEngdkLSLKFGQIRLGKPMFDETDGSTREiypqecrlrnLTYSAP 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 80 LYVSAGLIWKTSRNMQEQRIFIGNIPLM------------------------NSLGTSIVNGIYRIVINQILQS---PGI 132
Cdd:pfam04563 84 LYVDLELSVYNGEDIKPIEVFIGRLPIMlrsnacilsgateselvklgecplDPGGYFIINGSEKVIVAQEHRSrnhPIV 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 133 YYQSElDHNGISVYTGTIISDWGGRLE-------LEIDKKARIWARVS-RKQKISILVLSSAMGLNL-REILENVCYP-- 201
Cdd:pfam04563 164 FKKAD-PKKRGSVASVRSSAEISVRPDstswvnvLEYLSNGTIYFKFPyIKKEIPIVIILRALGFTSdREIFELICYDvn 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 202 -----EIFLSFLTDKEKKKIGSKENAiLEFyqqfscVG--GDPIFSESLCKE---------LQKKFF-----HQRCELGR 260
Cdd:pfam04563 243 dqqlqEELLPSLEEGFKIRIQTQEQA-LDY------IGgrGRAIFRMGRPREprikyaeeiLQKEVLphlgtYELDETKK 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7525025 261 ---IGrrninwrlnlnipqnniFLLPRDVLAAAdhligmkfGMGTLDDMNHLKNKRIRSVADLLQDQLGLALARLENVVK 337
Cdd:pfam04563 316 ayfIG-----------------YMIRRLLLLAL--------GRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVR 370
|
410 420
....*....|....*....|....*
gi 7525025 338 GTISGAIRHKLIPTPQNLVTSTPLT 362
Cdd:pfam04563 371 ERLQKVLGSPDDLMLQLLVNAKPIT 395
|
|
| |
