|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
38-1179 |
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: 1086.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFE 431
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIK 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 432 YLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLM 511
Cdd:cd00653 294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 512 NHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkslalsprlq 591
Cdd:cd00653 372 KNLALMARIS---------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 592 csgvilahcslrlpcssnspasvsqvagitgahhhawvlrekrippwmevvlipmtgkpslypglflfttpcrlvrpvqn 671
Cdd:cd00653 --------------------------------------------------------------------------------
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 672 lalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQD 751
Cdd:cd00653 382 ---------GRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQY 444
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 752 RSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKI 831
Cdd:cd00653 445 RMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK 524
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 832 KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDN 897
Cdd:cd00653 525 NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDD 604
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 898 IKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE 977
Cdd:cd00653 605 VKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLE 684
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 978 SMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQ 1057
Cdd:cd00653 685 SLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIH 760
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1058 VRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsam 1137
Cdd:cd00653 761 ARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA------------ 828
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|..
gi 1713222114 1138 rnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1179
Cdd:cd00653 829 ----NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
563-667 |
9.24e-16 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
:
Pssm-ID: 462028 Cd Length: 58 Bit Score: 72.52 E-value: 9.24e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 563 VGWVDKDLAPGIADSLRHFKslalsprlqcsgvilahcslrlpcssnspasvsqvagitgahhhawVLREKRIPPWMEVV 642
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLK----------------------------------------------VEGEHGVPLTLEIG 34
|
90 100
....*....|....*....|....*
gi 1713222114 643 LIPMTgKPSLYPGLFLFTTPCRLVR 667
Cdd:pfam06883 35 YVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 super family |
cl37712 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
6.91e-11 |
|
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).
The actual alignment was detected with superfamily member pfam04561:
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 62.36 E-value: 6.91e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 264 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 335
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1713222114 336 LKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 375
Cdd:pfam04561 146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
38-1179 |
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: 1086.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFE 431
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIK 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 432 YLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLM 511
Cdd:cd00653 294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 512 NHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkslalsprlq 591
Cdd:cd00653 372 KNLALMARIS---------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 592 csgvilahcslrlpcssnspasvsqvagitgahhhawvlrekrippwmevvlipmtgkpslypglflfttpcrlvrpvqn 671
Cdd:cd00653 --------------------------------------------------------------------------------
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 672 lalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQD 751
Cdd:cd00653 382 ---------GRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQY 444
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 752 RSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKI 831
Cdd:cd00653 445 RMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK 524
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 832 KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDN 897
Cdd:cd00653 525 NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDD 604
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 898 IKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE 977
Cdd:cd00653 605 VKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLE 684
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 978 SMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQ 1057
Cdd:cd00653 685 SLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIH 760
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1058 VRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsam 1137
Cdd:cd00653 761 ARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA------------ 828
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|..
gi 1713222114 1138 rnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1179
Cdd:cd00653 829 ----NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
38-1180 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 596.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQA-------IPPFEFAFKDERI---SFTILDAVISPptvpkgtickeanVYPAECRGRR 107
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVgepEIKEADGSERP-------------ITPMEARLRN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 108 STYRGKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMP 185
Cdd:PRK08565 81 LTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 186 RRnfpiamIRPKWKTRGPGYTqygvsmhcvreeHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFAL 253
Cdd:PRK08565 161 NR------VLVDKGEAGSSIT------------HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILM 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 254 KAL-----------VSfSDYQIFQELIKGKEDdsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQ 322
Cdd:PRK08565 219 RALgletdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIER 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 323 AAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKI 398
Cdd:PRK08565 281 AEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 399 AFDKKAQKTSvSMNTDNLMRiftMGIdLTKPFEYLFATGN-LRSKTGLG-LLqdsglcvvaDKLNFIRYLSHFRCV---- 472
Cdd:PRK08565 360 QLEKSYARGR-KLDLRAIVR---PDI-ITERIRHALATGNwVGGRTGVSqLL---------DRTNYLSTLSHLRRVvspl 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 473 HRG-ADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVvTQFVYTASIPALLCNLGVTPIDGAPHRSYS 551
Cdd:PRK08565 426 SRGqPHFE------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI-SVGVDEEEVEEILYELGVVPVEEAREEEYI 498
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 552 ECYPVLLDGVMVGWVD--KDLAPGIADSLRhfkslalsprlqcSGVIlahcslrlpcssnspasvSQVAGItgAHHHAWV 629
Cdd:PRK08565 499 SWSRVYLNGRLIGYHPdgEELAEKIRELRR-------------SGKI------------------SDEVNV--AYIETGE 545
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 630 LRE-------KRIppwMEVVLIPMTGKPSLYP--------GLFLFTTpcrLVRpvqnlaLGKEELIGTMEQIFMNVAIFE 694
Cdd:PRK08565 546 INEvyvncdsGRV---RRPLIVVENGKPKLTRehveklkkGELTFDD---LVK------MGVIEYLDAEEEENAYVALDP 613
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 695 DEVFAGvTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYD 774
Cdd:PRK08565 614 EDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALE 692
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 775 YYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK----QGD-----SSLVFGIK 843
Cdd:PRK08565 693 IIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypggQEDkieipEPNVRGYR 767
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 844 PgdPRVLQKLDDDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKENCVVDNIKVCSNDTGS 907
Cdd:PRK08565 768 G--EEYYRKLDEDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGEKGIVDTVLITESPEGN 843
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 908 gkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALH 987
Cdd:PRK08565 844 ---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALE 920
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 988 GLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRV 1067
Cdd:PRK08565 921 GRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQIL 996
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1068 TNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekppPSWSAMRNRKYNCTLC 1147
Cdd:PRK08565 997 TRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH----------IAWYDRRKNKYVCPIH 1066
|
1210 1220 1230
....*....|....*....|....*....|...
gi 1713222114 1148 SRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1180
Cdd:PRK08565 1067 GDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
716-1075 |
2.55e-179 |
|
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: 530.56 E-value: 2.55e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 716 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 795
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 796 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 874
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 875 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 939
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 940 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 1019
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1713222114 1020 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 1075
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
631-1180 |
2.83e-142 |
|
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: 442.93 E-value: 2.83e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 631 REKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGKEELigtmEQIFMNVAIFEDEVFAGVT--- 702
Cdd:TIGR03670 26 RSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTREHV----EKLKEGELTWDDLVKQGVIeyl 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 703 ---------------------THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ 761
Cdd:TIGR03670 96 daeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLH 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 762 TPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGS---VYKSEFID----LSEKIKQG 834
Cdd:TIGR03670 176 YPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTffrTYEAEERRypggQEDRFEIP 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 835 DSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYLNLNTGE------SFVMyyKSKENCVVDNI 898
Cdd:TIGR03670 256 EPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELREFGLVTerrrdtSVTV--RHGEKGIVDKV 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 899 KVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES 978
Cdd:TIGR03670 331 IITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 979 MAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQV 1058
Cdd:TIGR03670 408 IAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHA 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1059 RTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLlspllekpppSWSAMR 1138
Cdd:TIGR03670 484 RSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHI----------AWEDKR 553
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 1713222114 1139 NRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1180
Cdd:TIGR03670 554 KGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
38-1178 |
8.22e-106 |
|
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: 356.73 E-value: 8.22e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFtiLDAVISPPTVpkgtickeanvYPAECRGRRSTYRGKLTAD 117
Cdd:COG0085 16 LLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKY-----------TPEECKERDLTYAAPLYVK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 118 INWAVNGIskGIIKQ---FLGYVPIMVKSklcnlrnlppqaliehheeaeemgGYFIINGIEKVIRMLImprrnfpiami 194
Cdd:COG0085 83 VRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQL----------- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 195 rpkwkTRGPG--YTQYGVSMHcvREEHSA--VNMNLHYLE-----NGTVMLNFIYRKELFFLPLgfaLKALVSFSDYQIF 265
Cdd:COG0085 126 -----VRSPGvyFVEEEDKSG--KDLYSAkvIPSRGAWLEfetdkDGTIYVRIDRKRKIPVTVL---LRALGLETDEEIL 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 266 qELIKGKEDDSFLRNSVsqmlrivMEEGCSTQKQVLNYLGEcfRVKLNVPdwyPNEQAAE-----FLFNQC--------- 331
Cdd:COG0085 196 -EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYR--KLRPGEP---PTIERAEqlldnLFFDPKrydlahvgr 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 332 --------ICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLM-F----------LKEKLEgw 392
Cdd:COG0085 263 ykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNqFrvglsrmervVRERMT-- 340
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 393 lVSikiafDKKAQKTSVSMNTdnlmRIFTMGIdltKPFeylFATgnlrsktglgllqdSGLCVVADKLNFIRYLSHFRCV 472
Cdd:COG0085 341 -TQ-----DVEAITPQSLINI----RPVVAAI---KEF---FGS--------------SQLSQFMDQTNPLSELTHKRRL 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 473 ----------HRgADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLtavcevvtqfvytasipALLCNLGV--- 539
Cdd:COG0085 391 salgpgglsrER-AGFE------VRDVHPSHYGRMCPIETPEGPNIGLIGSL-----------------ALYARVNEygf 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 540 --TPidgaphrsysecYPVLLDGVM---VGWVDKDlapgiaDSLRHFKSLALSPrLQCSGVILahcslrlpcssnspasv 614
Cdd:COG0085 447 ieTP------------YRKVENGKVtdeIEYLTAD------EEENYYIAQANAP-LDEDGNFL----------------- 490
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 615 sqvagitgahhhawvlrEKRIPpwmevvlipmtgkpSLYPGLFLFTTPcrlvrpvqnlalgkeeligtmeqifmnvaife 694
Cdd:COG0085 491 -----------------EERVL--------------VRYRGEEVLVPP-------------------------------- 507
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 695 DEVfagvtTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLTY---------QDRSDNklyrl 760
Cdd:COG0085 508 EEV-----DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN----- 577
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 761 qtpQSPLVR--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFID 826
Cdd:COG0085 578 ---QRPIVRvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIE 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 827 LSE----KIKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD---------------PYYSYLNLNTGEsfvmy 886
Cdd:COG0085 646 EYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE----- 719
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 887 yKSK------------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPF 950
Cdd:COG0085 720 -KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 951 TESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGI 1029
Cdd:COG0085 799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGR 873
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1030 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1109
Cdd:COG0085 874 TGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
|
1210 1220 1230 1240 1250 1260
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1713222114 1110 RSVAHVCVkcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAELAAMNIKVKL 1178
Cdd:COG0085 954 DVCGRVKV---------YE---------AIVK--------GENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
563-667 |
9.24e-16 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 72.52 E-value: 9.24e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 563 VGWVDKDLAPGIADSLRHFKslalsprlqcsgvilahcslrlpcssnspasvsqvagitgahhhawVLREKRIPPWMEVV 642
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLK----------------------------------------------VEGEHGVPLTLEIG 34
|
90 100
....*....|....*....|....*
gi 1713222114 643 LIPMTgKPSLYPGLFLFTTPCRLVR 667
Cdd:pfam06883 35 YVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
6.91e-11 |
|
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: 62.36 E-value: 6.91e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 264 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 335
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1713222114 336 LKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 375
Cdd:pfam04561 146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
38-1179 |
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: 1086.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFE 431
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIK 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 432 YLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLM 511
Cdd:cd00653 294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 512 NHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkslalsprlq 591
Cdd:cd00653 372 KNLALMARIS---------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 592 csgvilahcslrlpcssnspasvsqvagitgahhhawvlrekrippwmevvlipmtgkpslypglflfttpcrlvrpvqn 671
Cdd:cd00653 --------------------------------------------------------------------------------
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 672 lalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQD 751
Cdd:cd00653 382 ---------GRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQY 444
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 752 RSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKI 831
Cdd:cd00653 445 RMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK 524
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 832 KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MYYKSKENCVVDN 897
Cdd:cd00653 525 NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLKYPGGEKGIVDD 604
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 898 IKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE 977
Cdd:cd00653 605 VKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLE 684
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 978 SMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQ 1057
Cdd:cd00653 685 SLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIH 760
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1058 VRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPllekpppswsam 1137
Cdd:cd00653 761 ARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA------------ 828
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|..
gi 1713222114 1138 rnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1179
Cdd:cd00653 829 ----NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
38-1180 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 596.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQA-------IPPFEFAFKDERI---SFTILDAVISPptvpkgtickeanVYPAECRGRR 107
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVgepEIKEADGSERP-------------ITPMEARLRN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 108 STYRGKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMP 185
Cdd:PRK08565 81 LTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 186 RRnfpiamIRPKWKTRGPGYTqygvsmhcvreeHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFAL 253
Cdd:PRK08565 161 NR------VLVDKGEAGSSIT------------HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILM 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 254 KAL-----------VSfSDYQIFQELIKGKEDdsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQ 322
Cdd:PRK08565 219 RALgletdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIER 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 323 AAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKI 398
Cdd:PRK08565 281 AEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 399 AFDKKAQKTSvSMNTDNLMRiftMGIdLTKPFEYLFATGN-LRSKTGLG-LLqdsglcvvaDKLNFIRYLSHFRCV---- 472
Cdd:PRK08565 360 QLEKSYARGR-KLDLRAIVR---PDI-ITERIRHALATGNwVGGRTGVSqLL---------DRTNYLSTLSHLRRVvspl 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 473 HRG-ADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVvTQFVYTASIPALLCNLGVTPIDGAPHRSYS 551
Cdd:PRK08565 426 SRGqPHFE------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI-SVGVDEEEVEEILYELGVVPVEEAREEEYI 498
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 552 ECYPVLLDGVMVGWVD--KDLAPGIADSLRhfkslalsprlqcSGVIlahcslrlpcssnspasvSQVAGItgAHHHAWV 629
Cdd:PRK08565 499 SWSRVYLNGRLIGYHPdgEELAEKIRELRR-------------SGKI------------------SDEVNV--AYIETGE 545
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 630 LRE-------KRIppwMEVVLIPMTGKPSLYP--------GLFLFTTpcrLVRpvqnlaLGKEELIGTMEQIFMNVAIFE 694
Cdd:PRK08565 546 INEvyvncdsGRV---RRPLIVVENGKPKLTRehveklkkGELTFDD---LVK------MGVIEYLDAEEEENAYVALDP 613
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 695 DEVFAGvTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYD 774
Cdd:PRK08565 614 EDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALE 692
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 775 YYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK----QGD-----SSLVFGIK 843
Cdd:PRK08565 693 IIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypggQEDkieipEPNVRGYR 767
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 844 PgdPRVLQKLDDDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKENCVVDNIKVCSNDTGS 907
Cdd:PRK08565 768 G--EEYYRKLDEDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGEKGIVDTVLITESPEGN 843
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 908 gkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALH 987
Cdd:PRK08565 844 ---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALE 920
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 988 GLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRV 1067
Cdd:PRK08565 921 GRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQIL 996
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1068 TNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekppPSWSAMRNRKYNCTLC 1147
Cdd:PRK08565 997 TRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH----------IAWYDRRKNKYVCPIH 1066
|
1210 1220 1230
....*....|....*....|....*....|...
gi 1713222114 1148 SRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1180
Cdd:PRK08565 1067 GDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
716-1075 |
2.55e-179 |
|
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: 530.56 E-value: 2.55e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 716 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 795
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 796 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 874
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 875 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 939
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 940 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 1019
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1713222114 1020 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 1075
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
631-1180 |
2.83e-142 |
|
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: 442.93 E-value: 2.83e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 631 REKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGKEELigtmEQIFMNVAIFEDEVFAGVT--- 702
Cdd:TIGR03670 26 RSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTREHV----EKLKEGELTWDDLVKQGVIeyl 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 703 ---------------------THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQ 761
Cdd:TIGR03670 96 daeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLH 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 762 TPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGS---VYKSEFID----LSEKIKQG 834
Cdd:TIGR03670 176 YPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTffrTYEAEERRypggQEDRFEIP 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 835 DSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYLNLNTGE------SFVMyyKSKENCVVDNI 898
Cdd:TIGR03670 256 EPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELREFGLVTerrrdtSVTV--RHGEKGIVDKV 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 899 KVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES 978
Cdd:TIGR03670 331 IITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 979 MAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQV 1058
Cdd:TIGR03670 408 IAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHA 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1059 RTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLlspllekpppSWSAMR 1138
Cdd:TIGR03670 484 RSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHI----------AWEDKR 553
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 1713222114 1139 NRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1180
Cdd:TIGR03670 554 KGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
630-1180 |
9.26e-128 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 404.73 E-value: 9.26e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 630 LREKR----IPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN-----------------------LALGKEEL 679
Cdd:PRK07225 27 IREARrsgeISEEVNVSYKEETNE------VIINTDAGRARRPlivVENgepllteehieklkngeltfddlVKQGVIEY 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 680 IGTMEQIFMNVAIFEDEVFAGvTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYR 759
Cdd:PRK07225 101 LDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHL 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 760 LQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSefIDLSEKIKQGDSSLV 839
Cdd:PRK07225 180 LHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRT--YEGEERRYPGGQEDR 257
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 840 FGIKPGDPR------VLQKLDDDGLPFIGAKLQYGD--------PyySYLNLNTGE----------SFVMyyKSKENCVV 895
Cdd:PRK07225 258 FEIPDKDVRgyrgeeAYRHLDEDGLVNPETEVKEGDvligktspP--RFLEEPDDFgispekrretSVTM--RSGEEGIV 333
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 896 DNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGML 975
Cdd:PRK07225 334 DTVILTETEEGS---RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHV 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 976 IESMAGKSAALHGLCHDATPFifSEENSalEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDK 1055
Cdd:PRK07225 411 LEMIGGKVGSLEGRRVDGTAF--SGEDE--EDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANK 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1056 FQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLlspllekpppsws 1135
Cdd:PRK07225 487 LHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMI------------- 553
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 1713222114 1136 AMRNRKYN---CTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1180
Cdd:PRK07225 554 AIYDKKRNrkyCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
38-1178 |
8.22e-106 |
|
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: 356.73 E-value: 8.22e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFtiLDAVISPPTVpkgtickeanvYPAECRGRRSTYRGKLTAD 117
Cdd:COG0085 16 LLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKY-----------TPEECKERDLTYAAPLYVK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 118 INWAVNGIskGIIKQ---FLGYVPIMVKSklcnlrnlppqaliehheeaeemgGYFIINGIEKVIRMLImprrnfpiami 194
Cdd:COG0085 83 VRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQL----------- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 195 rpkwkTRGPG--YTQYGVSMHcvREEHSA--VNMNLHYLE-----NGTVMLNFIYRKELFFLPLgfaLKALVSFSDYQIF 265
Cdd:COG0085 126 -----VRSPGvyFVEEEDKSG--KDLYSAkvIPSRGAWLEfetdkDGTIYVRIDRKRKIPVTVL---LRALGLETDEEIL 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 266 qELIKGKEDDSFLRNSVsqmlrivMEEGCSTQKQVLNYLGEcfRVKLNVPdwyPNEQAAE-----FLFNQC--------- 331
Cdd:COG0085 196 -EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYR--KLRPGEP---PTIERAEqlldnLFFDPKrydlahvgr 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 332 --------ICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLM-F----------LKEKLEgw 392
Cdd:COG0085 263 ykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNqFrvglsrmervVRERMT-- 340
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 393 lVSikiafDKKAQKTSVSMNTdnlmRIFTMGIdltKPFeylFATgnlrsktglgllqdSGLCVVADKLNFIRYLSHFRCV 472
Cdd:COG0085 341 -TQ-----DVEAITPQSLINI----RPVVAAI---KEF---FGS--------------SQLSQFMDQTNPLSELTHKRRL 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 473 ----------HRgADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLtavcevvtqfvytasipALLCNLGV--- 539
Cdd:COG0085 391 salgpgglsrER-AGFE------VRDVHPSHYGRMCPIETPEGPNIGLIGSL-----------------ALYARVNEygf 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 540 --TPidgaphrsysecYPVLLDGVM---VGWVDKDlapgiaDSLRHFKSLALSPrLQCSGVILahcslrlpcssnspasv 614
Cdd:COG0085 447 ieTP------------YRKVENGKVtdeIEYLTAD------EEENYYIAQANAP-LDEDGNFL----------------- 490
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 615 sqvagitgahhhawvlrEKRIPpwmevvlipmtgkpSLYPGLFLFTTPcrlvrpvqnlalgkeeligtmeqifmnvaife 694
Cdd:COG0085 491 -----------------EERVL--------------VRYRGEEVLVPP-------------------------------- 507
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 695 DEVfagvtTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLTY---------QDRSDNklyrl 760
Cdd:COG0085 508 EEV-----DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN----- 577
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 761 qtpQSPLVR--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFID 826
Cdd:COG0085 578 ---QRPIVRvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIE 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 827 LSE----KIKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD---------------PYYSYLNLNTGEsfvmy 886
Cdd:COG0085 646 EYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE----- 719
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 887 yKSK------------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPF 950
Cdd:COG0085 720 -KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 951 TESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGI 1029
Cdd:COG0085 799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGR 873
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1030 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1109
Cdd:COG0085 874 TGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
|
1210 1220 1230 1240 1250 1260
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1713222114 1110 RSVAHVCVkcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAELAAMNIKVKL 1178
Cdd:COG0085 954 DVCGRVKV---------YE---------AIVK--------GENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
37-416 |
5.25e-68 |
|
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: 234.20 E-value: 5.25e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 37 ELTRAHVESFNYAVHEGLGLAVQAIPPFEFAFK-------DERISFTILDAVISPPTVPKGTIcKEANVYPAECRGRRST 109
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEiqhpgenGDKLSLKFGQIRLGKPMFDETDG-STREIYPQECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 110 YRGKLTADINWAVNGISKGI-IKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRN 188
Cdd:pfam04563 80 YSAPLYVDLELSVYNGEDIKpIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRN 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 189 FPIAMIRPKWKTRGPGYTQYGVSMHCVRE-EHSAVNMnLHYLENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqE 267
Cdd:pfam04563 160 HPIVFKKADPKKRGSVASVRSSAEISVRPdSTSWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-E 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 268 LIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNV-PDWYPNEQAAEFLFNQCICIHLK----SNTEK 342
Cdd:pfam04563 236 LICYDVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKK 315
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1713222114 343 FYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQK-----TSVSMNTDNL 416
Cdd:pfam04563 316 AYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSpddlmLQLLVNAKPI 394
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
783-1109 |
1.59e-49 |
|
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: 191.80 E-value: 1.59e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 783 IGTNAIVAVISYTGYDMEDAMIVNkaswERGF---AHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 859
Cdd:TIGR02013 673 LGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 860 FIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSKEncVVDN--------------IKVCSNDTGS--- 907
Cdd:TIGR02013 749 RIGAEVKAGDilvgkvtpkgeteltPEEKLLRAIFGE------KARD--VRDTslrvppgvegtvidVKVFSREQGDelp 820
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 908 -GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKS 983
Cdd:TIGR02013 821 pGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKR 900
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 984 AALHGLCHdATPfIFseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGA 1063
Cdd:TIGR02013 901 LGRKGVPI-ATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGP 976
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 1713222114 1064 RDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1109
Cdd:TIGR02013 977 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
709-1109 |
3.85e-43 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 171.43 E-value: 3.85e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 709 PHSLLSVIANFIPFSDHNQSPRnmyqCQMGK--QTMGFPLL--------------------------------------- 747
Cdd:CHL00207 514 PIQVFSIAESLIPFLEHNDANR----ALMGSnmQRQAVPLLypekpivgtgyekqialdsgmtiisltegivvsvsayki 589
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 748 TYQDRSDNKL-YRLQ----------TPQSPLVRPS--------MYDYYDMDN--YPIGTNAIVAVISYTGYDMEDAMIVN 806
Cdd:CHL00207 590 IIQDDNNRYIhYYLQkyqrsnqntcINYRPIVWVGekinigqiLADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILIN 669
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 807 KAswergFAHGSVYKSEFIDLSEKI----KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGD-------PYYSYL 875
Cdd:CHL00207 670 KR-----LVYEDLFTSIHIEKYEIElrqtKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDilvgkitPKGESD 744
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 876 NLNTGESFVMYYKSKENCVVDN--------------IKVCSNDTGSGKFKCVCITMRV----PRNPTIGDKFASRHGQKG 937
Cdd:CHL00207 745 QLPEGKLLRAIFGEKAKDVKDTslrmpnggygrvikVEIFSRSKGDELKFGYYLKIRVfiaqIRKIQVGDKLAGRHGNKG 824
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 938 ILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAalHGLCHDATPFIFSEENSALE---YFGEMLKA 1014
Cdd:CHL00207 825 IISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAG--DNLNKRFKILPFDEMYGSEYsriLINNKLNQ 902
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1015 AG--------YNFY--GTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFG 1084
Cdd:CHL00207 903 ASiknneywlFNSYhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFG 982
|
490 500
....*....|....*....|....*
gi 1713222114 1085 EMERDALLAHGTSFLLHDRLFNCSD 1109
Cdd:CHL00207 983 EMEVWALEAFGAAYTLKELLTIKSD 1007
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
924-1100 |
3.29e-36 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 149.10 E-value: 3.29e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 924 TIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKsaalhGL-CHDATPfIF- 998
Cdd:PRK00405 881 QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAAK-----GLgIKFATP-VFd 954
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 999 --SEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRN 1076
Cdd:PRK00405 955 gaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029
|
170 180
....*....|....*....|....
gi 1713222114 1077 VQGGIRFGEMERDALLAHGTSFLL 1100
Cdd:PRK00405 1030 QFGGQRFGEMEVWALEAYGAAYTL 1053
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
38-544 |
6.12e-32 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 131.61 E-value: 6.12e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKD-ERISFTilDAVISPPTVpkgticKEAN-----VYPAECRGRRSTYR 111
Cdd:PRK09606 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDgVYVELG--KIRVGKPVV------KEADgsereIYPMEARLRNLTYS 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 112 GKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML-------IM 184
Cdd:PRK09606 90 APLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLedlapnkIL 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 185 PRRNFPIAMIRPKWKTrgpgYTQY-GVSMHCVREEHSavnmnlhyleNGTVMLNFIY-RKELFFLPLgfaLKALVSFSDy 262
Cdd:PRK09606 170 VEKDERYGDRIEVAKV----FSQRrGYRALVTVERNR----------DGLLEVSFPSvPGSIPFVIL---MRALGLETD- 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 263 qifQELIKGKEDDsflRNSVSQMLRIVMEEGCSTQKQVLNYLGEcfRVKLNVPDWYPNEQaAEFLFNQCICIHLKSNTEK 342
Cdd:PRK09606 232 ---EEIVEAVSDD---PEIVKFMLENLEEAEVDTQEEALEYIGK--RVAPGQTKEYRIKR-AEYVIDRYLLPHLGVEPEV 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 343 F----YMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFlmflkEKLegwlvsIKIAF-----DKKAQKTSVSM-N 412
Cdd:PRK09606 303 RrakaHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLM-----EDL------FRVAFnrlarDVKYQLERANMrN 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 413 TDNLMRIFTMGIDLTKPFEYLFATGNLRS-KTGLGLLqdsglcvvADKLNFIRYLSHFRCV---------HRGAdfakmr 482
Cdd:PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNWVGgRTGVSQL--------LDRTDYMATLSHLRRVvsplsrsqpHFEA------ 437
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1713222114 483 tttvRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPaLLCNLGVTPIDG 544
Cdd:PRK09606 438 ----RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKE-ILKELGVEPERG 494
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
455-519 |
8.09e-32 |
|
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: 118.40 E-value: 8.09e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1713222114 455 VVADKLNFIRYLSHFRCVH--RGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCE 519
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
784-1109 |
2.63e-31 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 133.49 E-value: 2.63e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 784 GTNAIVAVISYTGYDMEDAMIVNkaswERgFAHGSVYKSEFIDLSE----KIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 859
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLIS----ER-LVYEDIYTSFHIRKYEiqthVTSQGPERITKEIPHLEAHLLRNLDKNGIV 726
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 860 FIGAKLQYGD-------PYYSYLNLNTGESFVMY-------YKSKENC----------VVDNIKVCSNDTGSGKFKCVCI 915
Cdd:CHL00001 727 MLGSWVETGDilvgkltPQEAEESSYAPEGRLLRaifgiqvSTSKETClklpiggrgrVIDVRWIQKKGGSSYNPETIHV 806
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 916 TMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATP 995
Cdd:CHL00001 807 YILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAP 886
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 996 F--IFSEENSALEYFGEMLKA---AGY------NFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGAR 1064
Cdd:CHL00001 887 FdeRYEQEASRKLVFSELYEAskqTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPY 966
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1713222114 1065 DRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1109
Cdd:CHL00001 967 ALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
907-1109 |
5.60e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 123.11 E-value: 5.60e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 907 SGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE---SMAGK- 982
Cdd:PRK09603 1072 NGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlGLVGKe 1151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 983 ----------------------------------------------SAALHGLCHD-------ATPfIFseENSALEYFG 1009
Cdd:PRK09603 1152 fgkqiasmledktkdfakelrakmleianainekdpltihalencsDEELLEYAKDwskgvkmAIP-VF--EGISQEKFY 1228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1010 EMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERD 1089
Cdd:PRK09603 1229 KLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
|
250 260
....*....|....*....|
gi 1713222114 1090 ALLAHGTSFLLHDRLFNCSD 1109
Cdd:PRK09603 1309 ALEAYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1079-1181 |
3.21e-22 |
|
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: 91.88 E-value: 3.21e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1079 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGsllspllekpppswsAMRNRKYnCTLCSRSDTIDTVSV 1158
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCG---------------LYAAYNK-CPICKGETDISPGYI 64
|
90 100
....*....|....*....|...
gi 1713222114 1159 PYVFRYFVAELAAMNIKVKLDVV 1181
Cdd:pfam04560 65 PESFKLLFQELQSLGIDPRLLLE 87
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
926-1109 |
2.66e-20 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 98.16 E-value: 2.66e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 926 GDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAG--------------------KSAA 985
Cdd:PRK14844 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgekvgnildeinkiKSAF 1163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 986 LHGL--------------------------------------------------------CHDATPFIFS---------- 999
Cdd:PRK14844 1164 CKGIrslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnsCKSAYSNLRNflievyscgs 1243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 1000 -----------EENSALEY----------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 1046
Cdd:PRK14844 1244 nvsicnnirdiSDNNLIEFarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1713222114 1047 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1109
Cdd:PRK14844 1324 KLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
563-667 |
9.24e-16 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 72.52 E-value: 9.24e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 563 VGWVDKDLAPGIADSLRHFKslalsprlqcsgvilahcslrlpcssnspasvsqvagitgahhhawVLREKRIPPWMEVV 642
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLK----------------------------------------------VEGEHGVPLTLEIG 34
|
90 100
....*....|....*....|....*
gi 1713222114 643 LIPMTgKPSLYPGLFLFTTPCRLVR 667
Cdd:pfam06883 35 YVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
6.91e-11 |
|
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: 62.36 E-value: 6.91e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1713222114 264 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 335
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1713222114 336 LKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 375
Cdd:pfam04561 146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
