|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
38-1133 |
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: 1101.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFE 431
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIK 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 432 YLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLM 511
Cdd:cd00653 294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 512 NHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkvlrekripp 591
Cdd:cd00653 372 KNLALMARIS---------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 592 wmevvlipmtgkpslypglflfttpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIA 671
Cdd:cd00653 382 -------------------------------------------GRIERPYRIVE--------KEVTHIEISPSQILSVAA 410
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 672 NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGY 751
Cdd:cd00653 411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 752 DMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNL 831
Cdd:cd00653 491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITP 570
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 832 NTGESFV--------------MYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLW 897
Cdd:cd00653 571 KGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 898 PAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTE 977
Cdd:cd00653 651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKE 726
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 978 RLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDR 1057
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 33469941 1058 LFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1133
Cdd:cd00653 807 LTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
563-621 |
1.88e-23 |
|
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: 94.47 E-value: 1.88e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 33469941 563 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 621
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 super family |
cl37712 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
1.03e-10 |
|
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: 61.98 E-value: 1.03e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 264 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 335
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 33469941 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. ... |
38-1133 |
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: 1101.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFE 431
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIK 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 432 YLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLM 511
Cdd:cd00653 294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 512 NHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkvlrekripp 591
Cdd:cd00653 372 KNLALMARIS---------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 592 wmevvlipmtgkpslypglflfttpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIA 671
Cdd:cd00653 382 -------------------------------------------GRIERPYRIVE--------KEVTHIEISPSQILSVAA 410
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 672 NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGY 751
Cdd:cd00653 411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 752 DMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNL 831
Cdd:cd00653 491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITP 570
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 832 NTGESFV--------------MYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLW 897
Cdd:cd00653 571 KGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 898 PAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTE 977
Cdd:cd00653 651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKE 726
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 978 RLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDR 1057
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 33469941 1058 LFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1133
Cdd:cd00653 807 LTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
38-1134 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 603.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQA-------IPPFEFAFKDERI---SFTILDAVISPptvpkgtickeanVYPAECRGRR 107
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVgepEIKEADGSERP-------------ITPMEARLRN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 108 STYRGKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMP 185
Cdd:PRK08565 81 LTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 186 RRnfpiamIRPKWKTRGPGYTqygvsmhcvreeHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFAL 253
Cdd:PRK08565 161 NR------VLVDKGEAGSSIT------------HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILM 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 254 KAL-----------VSfSDYQIFQELIKGKEDdsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQ 322
Cdd:PRK08565 219 RALgletdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIER 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 323 AAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKI 398
Cdd:PRK08565 281 AEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 399 AFDKKAQKTSvSMNTDNLMRiftMGIdLTKPFEYLFATGN-LRSKTGLG-LLqdsglcvvaDKLNFIRYLSHFRCV---- 472
Cdd:PRK08565 360 QLEKSYARGR-KLDLRAIVR---PDI-ITERIRHALATGNwVGGRTGVSqLL---------DRTNYLSTLSHLRRVvspl 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 473 HRG-ADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVvTQFVYTASIPALLCNLGVTPIDGAPHRSYS 551
Cdd:PRK08565 426 SRGqPHFE------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI-SVGVDEEEVEEILYELGVVPVEEAREEEYI 498
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 552 ECYPVLLDGVMVGWVDKDLApgIADSLRHFKvlREKRIPPWMEVVLIPMTGKPSLYpglfLFTTPCRLVRPVQNLALGKE 631
Cdd:PRK08565 499 SWSRVYLNGRLIGYHPDGEE--LAEKIRELR--RSGKISDEVNVAYIETGEINEVY----VNCDSGRVRRPLIVVENGKP 570
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 632 ELIGTM-EQIFMNVAIFEDEVFAGV------------------------TTHQELFPHSLLSVIANFIPFSDHNQSPRNM 686
Cdd:PRK08565 571 KLTREHvEKLKKGELTFDDLVKMGVieyldaeeeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNT 650
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 687 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 766
Cdd:PRK08565 651 YQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIER 730
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 767 GFAhgsvyKSEFIDL--SEKIK----QGD-----SSLVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD------------ 823
Cdd:PRK08565 731 GLA-----RSTFFRTyeTEERKypggQEDkieipEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDvligktspprfl 803
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 824 PYYSYLNLNTGE----SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPA 899
Cdd:PRK08565 804 EELEELSLGLQErrdtSVTV--RHGEKGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQ 878
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 900 EDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERL 979
Cdd:PRK08565 879 EDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVM 954
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 980 YSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLF 1059
Cdd:PRK08565 955 YDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLL 1034
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33469941 1060 NCSDRSVAHVCVKCGSllspllekppPSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:PRK08565 1035 DSSDKTTIYVCELCGH----------IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
670-1029 |
4.98e-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: 528.64 E-value: 4.98e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 670 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 749
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 750 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 828
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 829 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 893
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 894 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 973
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 33469941 974 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 1029
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
556-1134 |
8.06e-145 |
|
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: 448.32 E-value: 8.06e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 556 VLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGK 630
Cdd:TIGR03670 1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 631 EELigtmEQIFMNVAIFEDEVFAGVT------------------------THQELFPHSLLSVIANFIPFSDHNQSPRNM 686
Cdd:TIGR03670 71 EHV----EKLKEGELTWDDLVKQGVIeyldaeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 687 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 766
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 767 GFAHGS---VYKSEFID----LSEKIKQGDSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYL 829
Cdd:TIGR03670 227 GLARSTffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 830 NLNTGE------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMP 903
Cdd:TIGR03670 304 EFGLVTerrrdtSVTV--RHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMP 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 904 FTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGI 983
Cdd:TIGR03670 379 FTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGI 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 984 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:TIGR03670 455 TGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 33469941 1064 RSVAHVCVKCGSLlspllekpppSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:TIGR03670 535 KYVVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
38-1132 |
1.17e-111 |
|
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: 372.13 E-value: 1.17e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFtiLDAVISPPTVpkgtickeanvYPAECRGRRSTYRGKLTAD 117
Cdd:COG0085 16 LLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKY-----------TPEECKERDLTYAAPLYVK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 118 INWAVNGIskGIIKQ---FLGYVPIMVKSklcnlrnlppqaliehheeaeemgGYFIINGIEKVIRMLImprrnfpiami 194
Cdd:COG0085 83 VRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQL----------- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 195 rpkwkTRGPG--YTQYGVSMHcvREEHSA--VNMNLHYLE-----NGTVMLNFIYRKELFFLPLgfaLKALVSFSDYQIF 265
Cdd:COG0085 126 -----VRSPGvyFVEEEDKSG--KDLYSAkvIPSRGAWLEfetdkDGTIYVRIDRKRKIPVTVL---LRALGLETDEEIL 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 266 qELIKGKEDDSFLRNSVsqmlrivMEEGCSTQKQVLNYLGEcfRVKLNVPdwyPNEQAAE-----FLFNQC--------- 331
Cdd:COG0085 196 -EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYR--KLRPGEP---PTIERAEqlldnLFFDPKrydlahvgr 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 332 --------ICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLM-F----------LKEKLEgw 392
Cdd:COG0085 263 ykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNqFrvglsrmervVRERMT-- 340
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 393 lVSikiafDKKAQKTSVSMNTdnlmRIFTMGIdltKPFeylFATgnlrsktglgllqdSGLCVVADKLNFIRYLSHFRCV 472
Cdd:COG0085 341 -TQ-----DVEAITPQSLINI----RPVVAAI---KEF---FGS--------------SQLSQFMDQTNPLSELTHKRRL 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 473 ----------HRgADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLtavcevvtqfvytasipALLCNLGV--- 539
Cdd:COG0085 391 salgpgglsrER-AGFE------VRDVHPSHYGRMCPIETPEGPNIGLIGSL-----------------ALYARVNEygf 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 540 --TPidgaphrsysecYPVLLDGVM---VGWVDKD------LAPGIADsLRHFKVLREKRIPpwmevvlipmtgkpSLYP 608
Cdd:COG0085 447 ieTP------------YRKVENGKVtdeIEYLTADeeenyyIAQANAP-LDEDGNFLEERVL--------------VRYR 499
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 609 GLFLFTTPcrlvrpvqnlalgkeeligtmeqifmnvaifeDEVfagvtTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 688
Cdd:COG0085 500 GEEVLVPP--------------------------------EEV-----DYMDVSPKQIVSVATSLIPFLEHDDANRALMG 542
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 689 CQMGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLVR--------------PSMydyyDMDNYPIGTN 740
Cdd:COG0085 543 ANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIVRvgdrvekgdvladgPAT----DNGELALGQN 610
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 741 AIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----KIKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFI 815
Cdd:COG0085 611 LLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRI 684
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 816 GAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSK------------ENCVVDNIKVCSNDTGS----GKF 864
Cdd:COG0085 685 GAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVN 758
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 865 KCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLC 944
Cdd:COG0085 759 KLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRR 838
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 945 HDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTN 1023
Cdd:COG0085 839 VATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQ 913
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 1024 QPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVkcgsllsplLEkpppswsamRNRKynctlcsr 1103
Cdd:COG0085 914 QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV---------YE---------AIVK-------- 967
|
1210 1220
....*....|....*....|....*....
gi 33469941 1104 SDTIDTVSVPYVFRYFVAELAAMNIKVKL 1132
Cdd:COG0085 968 GENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
563-621 |
1.88e-23 |
|
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: 94.47 E-value: 1.88e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 33469941 563 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 621
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
1.03e-10 |
|
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: 61.98 E-value: 1.03e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 264 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 335
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 33469941 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. ... |
38-1133 |
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: 1101.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFTILDAVISPPTVPKGtiCKEANVYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 118 INWAVNGISK-GIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653 79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 193 MIRPKWKTRGPGYTQYGVSMHCVREEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 272 keddsflrnsvsqmlrivmeegcstQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTR 351
Cdd:cd00653 199 -------------------------QEEALKYIGK-----------------------------------RFEDLIYMIR 218
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 352 KLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFE 431
Cdd:cd00653 219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIK 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 432 YLFATGNLRSKTGLglLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLM 511
Cdd:cd00653 294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 512 NHLTAVCEVVtqfvytasipallcnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkvlrekripp 591
Cdd:cd00653 372 KNLALMARIS---------------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 592 wmevvlipmtgkpslypglflfttpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIA 671
Cdd:cd00653 382 -------------------------------------------GRIERPYRIVE--------KEVTHIEISPSQILSVAA 410
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 672 NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGY 751
Cdd:cd00653 411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 752 DMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNL 831
Cdd:cd00653 491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITP 570
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 832 NTGESFV--------------MYYKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLW 897
Cdd:cd00653 571 KGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 898 PAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTE 977
Cdd:cd00653 651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKE 726
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 978 RLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDR 1057
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 33469941 1058 LFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 1133
Cdd:cd00653 807 LTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
38-1134 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 603.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQA-------IPPFEFAFKDERI---SFTILDAVISPptvpkgtickeanVYPAECRGRR 107
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVgepEIKEADGSERP-------------ITPMEARLRN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 108 STYRGKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMP 185
Cdd:PRK08565 81 LTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 186 RRnfpiamIRPKWKTRGPGYTqygvsmhcvreeHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFAL 253
Cdd:PRK08565 161 NR------VLVDKGEAGSSIT------------HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILM 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 254 KAL-----------VSfSDYQIFQELIKGKEDdsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQ 322
Cdd:PRK08565 219 RALgletdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIER 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 323 AAEFLFNQCIcIHLKSNTE----KFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKI 398
Cdd:PRK08565 281 AEQILDKYLL-PHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 399 AFDKKAQKTSvSMNTDNLMRiftMGIdLTKPFEYLFATGN-LRSKTGLG-LLqdsglcvvaDKLNFIRYLSHFRCV---- 472
Cdd:PRK08565 360 QLEKSYARGR-KLDLRAIVR---PDI-ITERIRHALATGNwVGGRTGVSqLL---------DRTNYLSTLSHLRRVvspl 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 473 HRG-ADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVvTQFVYTASIPALLCNLGVTPIDGAPHRSYS 551
Cdd:PRK08565 426 SRGqPHFE------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI-SVGVDEEEVEEILYELGVVPVEEAREEEYI 498
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 552 ECYPVLLDGVMVGWVDKDLApgIADSLRHFKvlREKRIPPWMEVVLIPMTGKPSLYpglfLFTTPCRLVRPVQNLALGKE 631
Cdd:PRK08565 499 SWSRVYLNGRLIGYHPDGEE--LAEKIRELR--RSGKISDEVNVAYIETGEINEVY----VNCDSGRVRRPLIVVENGKP 570
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 632 ELIGTM-EQIFMNVAIFEDEVFAGV------------------------TTHQELFPHSLLSVIANFIPFSDHNQSPRNM 686
Cdd:PRK08565 571 KLTREHvEKLKKGELTFDDLVKMGVieyldaeeeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNT 650
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 687 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 766
Cdd:PRK08565 651 YQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIER 730
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 767 GFAhgsvyKSEFIDL--SEKIK----QGD-----SSLVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD------------ 823
Cdd:PRK08565 731 GLA-----RSTFFRTyeTEERKypggQEDkieipEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDvligktspprfl 803
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 824 PYYSYLNLNTGE----SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPA 899
Cdd:PRK08565 804 EELEELSLGLQErrdtSVTV--RHGEKGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQ 878
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 900 EDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERL 979
Cdd:PRK08565 879 EDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVM 954
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 980 YSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLF 1059
Cdd:PRK08565 955 YDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLL 1034
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33469941 1060 NCSDRSVAHVCVKCGSllspllekppPSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:PRK08565 1035 DSSDKTTIYVCELCGH----------IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
670-1029 |
4.98e-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: 528.64 E-value: 4.98e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 670 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 749
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 750 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 828
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 829 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 893
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 894 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 973
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 33469941 974 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 1029
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
556-1134 |
8.06e-145 |
|
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: 448.32 E-value: 8.06e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 556 VLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGK 630
Cdd:TIGR03670 1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 631 EELigtmEQIFMNVAIFEDEVFAGVT------------------------THQELFPHSLLSVIANFIPFSDHNQSPRNM 686
Cdd:TIGR03670 71 EHV----EKLKEGELTWDDLVKQGVIeyldaeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 687 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 766
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 767 GFAHGS---VYKSEFID----LSEKIKQGDSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYL 829
Cdd:TIGR03670 227 GLARSTffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 830 NLNTGE------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMP 903
Cdd:TIGR03670 304 EFGLVTerrrdtSVTV--RHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMP 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 904 FTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGI 983
Cdd:TIGR03670 379 FTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGI 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 984 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:TIGR03670 455 TGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 33469941 1064 RSVAHVCVKCGSLlspllekpppSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:TIGR03670 535 KYVVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
555-1134 |
2.51e-129 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 407.81 E-value: 2.51e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 555 PVLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN------ 625
Cdd:PRK07225 6 KVYVNGKLIGTHDD--PEELVEEIR--EARRSGEISEEVNVSYKEETNE------VIINTDAGRARRPlivVENgepllt 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 626 -----------------LALGKEELIGTMEQIFMNVAIFEDEVFAGvTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 688
Cdd:PRK07225 76 eehieklkngeltfddlVKQGVIEYLDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 689 CQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGF 768
Cdd:PRK07225 155 AGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 769 AHGSVYKSefIDLSEKIKQGDSSLVFGIKPGDPR------VLQKLDDDGLPFIGAKLQYGD--------PyySYLNLNTG 834
Cdd:PRK07225 235 GRSHFFRT--YEGEERRYPGGQEDRFEIPDKDVRgyrgeeAYRHLDEDGLVNPETEVKEGDvligktspP--RFLEEPDD 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 835 E----------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPF 904
Cdd:PRK07225 311 FgispekrretSVTM--RSGEEGIVDTVILTETEEGS---RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPF 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 905 TESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENSalEYFGEMLKAAGYNFYGTERLYSGIS 984
Cdd:PRK07225 386 TESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAF--SGEDE--EDLREALEKLGFEHTGKEVMYDGIT 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 985 GLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDR 1064
Cdd:PRK07225 462 GEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDK 541
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 33469941 1065 SVAHVCVKCGSLlspllekpppswsAMRNRKYN---CTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:PRK07225 542 VEIYVCAKCGMI-------------AIYDKKRNrkyCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
38-1132 |
1.17e-111 |
|
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: 372.13 E-value: 1.17e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKDERISFtiLDAVISPPTVpkgtickeanvYPAECRGRRSTYRGKLTAD 117
Cdd:COG0085 16 LLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKY-----------TPEECKERDLTYAAPLYVK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 118 INWAVNGIskGIIKQ---FLGYVPIMVKSklcnlrnlppqaliehheeaeemgGYFIINGIEKVIRMLImprrnfpiami 194
Cdd:COG0085 83 VRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQL----------- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 195 rpkwkTRGPG--YTQYGVSMHcvREEHSA--VNMNLHYLE-----NGTVMLNFIYRKELFFLPLgfaLKALVSFSDYQIF 265
Cdd:COG0085 126 -----VRSPGvyFVEEEDKSG--KDLYSAkvIPSRGAWLEfetdkDGTIYVRIDRKRKIPVTVL---LRALGLETDEEIL 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 266 qELIKGKEDDSFLRNSVsqmlrivMEEGCSTQKQVLNYLGEcfRVKLNVPdwyPNEQAAE-----FLFNQC--------- 331
Cdd:COG0085 196 -EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYR--KLRPGEP---PTIERAEqlldnLFFDPKrydlahvgr 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 332 --------ICIHLKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFLM-F----------LKEKLEgw 392
Cdd:COG0085 263 ykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNqFrvglsrmervVRERMT-- 340
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 393 lVSikiafDKKAQKTSVSMNTdnlmRIFTMGIdltKPFeylFATgnlrsktglgllqdSGLCVVADKLNFIRYLSHFRCV 472
Cdd:COG0085 341 -TQ-----DVEAITPQSLINI----RPVVAAI---KEF---FGS--------------SQLSQFMDQTNPLSELTHKRRL 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 473 ----------HRgADFAkmrtttVRRLLPESWGFLCPVHTPDGEPCGLMNHLtavcevvtqfvytasipALLCNLGV--- 539
Cdd:COG0085 391 salgpgglsrER-AGFE------VRDVHPSHYGRMCPIETPEGPNIGLIGSL-----------------ALYARVNEygf 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 540 --TPidgaphrsysecYPVLLDGVM---VGWVDKD------LAPGIADsLRHFKVLREKRIPpwmevvlipmtgkpSLYP 608
Cdd:COG0085 447 ieTP------------YRKVENGKVtdeIEYLTADeeenyyIAQANAP-LDEDGNFLEERVL--------------VRYR 499
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 609 GLFLFTTPcrlvrpvqnlalgkeeligtmeqifmnvaifeDEVfagvtTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 688
Cdd:COG0085 500 GEEVLVPP--------------------------------EEV-----DYMDVSPKQIVSVATSLIPFLEHDDANRALMG 542
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 689 CQMGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLVR--------------PSMydyyDMDNYPIGTN 740
Cdd:COG0085 543 ANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIVRvgdrvekgdvladgPAT----DNGELALGQN 610
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 741 AIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----KIKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFI 815
Cdd:COG0085 611 LLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRI 684
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 816 GAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSK------------ENCVVDNIKVCSNDTGS----GKF 864
Cdd:COG0085 685 GAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVN 758
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 865 KCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLC 944
Cdd:COG0085 759 KLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRR 838
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 945 HDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTN 1023
Cdd:COG0085 839 VATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQ 913
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 1024 QPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVkcgsllsplLEkpppswsamRNRKynctlcsr 1103
Cdd:COG0085 914 QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV---------YE---------AIVK-------- 967
|
1210 1220
....*....|....*....|....*....
gi 33469941 1104 SDTIDTVSVPYVFRYFVAELAAMNIKVKL 1132
Cdd:COG0085 968 GENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
37-416 |
1.46e-67 |
|
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: 233.04 E-value: 1.46e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 37 ELTRAHVESFNYAVHEGLGLAVQAIPPFEFAFK-------DERISFTILDAVISPPTVPKGTIcKEANVYPAECRGRRST 109
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEiqhpgenGDKLSLKFGQIRLGKPMFDETDG-STREIYPQECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 110 YRGKLTADINWAVNGISKGI-IKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRN 188
Cdd:pfam04563 80 YSAPLYVDLELSVYNGEDIKpIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRN 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 189 FPIAMIRPKWKTRGPGYTQYGVSMHCVRE-EHSAVNMnLHYLENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqE 267
Cdd:pfam04563 160 HPIVFKKADPKKRGSVASVRSSAEISVRPdSTSWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-E 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 268 LIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNV-PDWYPNEQAAEFLFNQCICIHLK----SNTEK 342
Cdd:pfam04563 236 LICYDVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKK 315
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 33469941 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 ... |
737-1063 |
1.39e-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: 1.39e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 737 IGTNAIVAVISYTGYDMEDAMIVNkaswERGF---AHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 813
Cdd:TIGR02013 673 LGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 814 FIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSKEncVVDN--------------IKVCSNDTGS--- 861
Cdd:TIGR02013 749 RIGAEVKAGDilvgkvtpkgeteltPEEKLLRAIFGE------KARD--VRDTslrvppgvegtvidVKVFSREQGDelp 820
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 862 -GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKS 937
Cdd:TIGR02013 821 pGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKR 900
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 938 AALHGLCHdATPfIFseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGA 1017
Cdd:TIGR02013 901 LGRKGVPI-ATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGP 976
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 33469941 1018 RDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:TIGR02013 977 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
458-1063 |
1.29e-43 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 172.97 E-value: 1.29e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 458 DKLNFIRYLSH-FRCVHRGAD-FAKMRTTT-VRRLLPESWGFLCPVHTPDGEPCGLMNHLTaVCEVVTQFvytasipall 534
Cdd:CHL00207 371 DQTNPLSELTHkRRISILGPGgLDKDRISFaVRDIHPSHYGRICPIETPEGPNCGLIGSLA-TNARINKF---------- 439
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 535 cNLGVTPidgaphrsyseCYPVLldgvmVGWVDKDLAPGI--ADSLRHFKVLrekrippwmevvlipmtgkpslyPGlfl 612
Cdd:CHL00207 440 -GFIETP-----------FYKVI-----NGKVKKFGNPIYltADSEDLYRIA-----------------------PN--- 476
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 613 fttpcrlvrpvqNLALGKEELIgtmeqIFMNVAIFEDEVFAGVTTHQELF----PHSLLSVIANFIPFSDHNQSPRnmyq 688
Cdd:CHL00207 477 ------------DINLNKNNYF-----KKNIIPVRYKQEFKTVNPSKVDFiaisPIQVFSIAESLIPFLEHNDANR---- 535
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 689 CQMGK--QTMGFPLL---------------------------------------TYQDRSDNKL-YRLQ----------T 716
Cdd:CHL00207 536 ALMGSnmQRQAVPLLypekpivgtgyekqialdsgmtiisltegivvsvsaykiIIQDDNNRYIhYYLQkyqrsnqntcI 615
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 717 PQSPLVRPS--------MYDYYDMDN--YPIGTNAIVAVISYTGYDMEDAMIVNKAswergFAHGSVYKSEFIDLSEKI- 785
Cdd:CHL00207 616 NYRPIVWVGekinigqiLADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILINKR-----LVYEDLFTSIHIEKYEIEl 690
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 786 ---KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGD-------PYYSYLNLNTGESFVMYYKSKENCVVDN---- 851
Cdd:CHL00207 691 rqtKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDilvgkitPKGESDQLPEGKLLRAIFGEKAKDVKDTslrm 770
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 852 ----------IKVCSNDTGSGKFKCVCITMRV----PRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNP 917
Cdd:CHL00207 771 pnggygrvikVEIFSRSKGDELKFGYYLKIRVfiaqIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNP 850
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 918 HGFPSRMTIGMLIESMAGKSAalHGLCHDATPFIFSEENSALE---YFGEMLKAAG--------YNFY--GTERLYSGIS 984
Cdd:CHL00207 851 LGVPSRMNVGQLFECLLGLAG--DNLNKRFKILPFDEMYGSEYsriLINNKLNQASiknneywlFNSYhpGKMVLRDGRT 928
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 33469941 985 GLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:CHL00207 929 GYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD 1007
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
878-1054 |
3.00e-36 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 149.10 E-value: 3.00e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 878 TIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKsaalhGL-CHDATPfIF- 952
Cdd:PRK00405 881 QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAAK-----GLgIKFATP-VFd 954
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 953 --SEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRN 1030
Cdd:PRK00405 955 gaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029
|
170 180
....*....|....*....|....
gi 33469941 1031 VQGGIRFGEMERDALLAHGTSFLL 1054
Cdd:PRK00405 1030 QFGGQRFGEMEVWALEAYGAAYTL 1053
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
38-544 |
5.77e-32 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 131.61 E-value: 5.77e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 38 LTRAHVESFNYAVHEGLGLAVQAIPPFEFAFKD-ERISFTilDAVISPPTVpkgticKEAN-----VYPAECRGRRSTYR 111
Cdd:PRK09606 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDgVYVELG--KIRVGKPVV------KEADgsereIYPMEARLRNLTYS 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 112 GKLTADINWAVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML-------IM 184
Cdd:PRK09606 90 APLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLedlapnkIL 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 185 PRRNFPIAMIRPKWKTrgpgYTQY-GVSMHCVREEHSavnmnlhyleNGTVMLNFIY-RKELFFLPLgfaLKALVSFSDy 262
Cdd:PRK09606 170 VEKDERYGDRIEVAKV----FSQRrGYRALVTVERNR----------DGLLEVSFPSvPGSIPFVIL---MRALGLETD- 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 263 qifQELIKGKEDDsflRNSVSQMLRIVMEEGCSTQKQVLNYLGEcfRVKLNVPDWYPNEQaAEFLFNQCICIHLKSNTEK 342
Cdd:PRK09606 232 ---EEIVEAVSDD---PEIVKFMLENLEEAEVDTQEEALEYIGK--RVAPGQTKEYRIKR-AEYVIDRYLLPHLGVEPEV 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 343 F----YMLCLMTRKLFALAKGECMEDNPDSLVNQEVLTPGQLFlmflkEKLegwlvsIKIAF-----DKKAQKTSVSM-N 412
Cdd:PRK09606 303 RrakaHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLM-----EDL------FRVAFnrlarDVKYQLERANMrN 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 413 TDNLMRIFTMGIDLTKPFEYLFATGNLRS-KTGLGLLqdsglcvvADKLNFIRYLSHFRCV---------HRGAdfakmr 482
Cdd:PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNWVGgRTGVSQL--------LDRTDYMATLSHLRRVvsplsrsqpHFEA------ 437
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33469941 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 |
7.77e-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: 7.77e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 33469941 455 VVADKLNFIRYLSHFRCVH--RGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCE 519
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
738-1063 |
2.83e-31 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 133.10 E-value: 2.83e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 738 GTNAIVAVISYTGYDMEDAMIVNkaswERgFAHGSVYKSEFIDLSE----KIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 813
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLIS----ER-LVYEDIYTSFHIRKYEiqthVTSQGPERITKEIPHLEAHLLRNLDKNGIV 726
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 814 FIGAKLQYGD-------PYYSYLNLNTGESFVMY-------YKSKENC----------VVDNIKVCSNDTGSGKFKCVCI 869
Cdd:CHL00001 727 MLGSWVETGDilvgkltPQEAEESSYAPEGRLLRaifgiqvSTSKETClklpiggrgrVIDVRWIQKKGGSSYNPETIHV 806
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 870 TMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATP 949
Cdd:CHL00001 807 YILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAP 886
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 950 F--IFSEENSALEYFGEMLKA---AGY------NFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGAR 1018
Cdd:CHL00001 887 FdeRYEQEASRKLVFSELYEAskqTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPY 966
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 33469941 1019 DRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:CHL00001 967 ALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
861-1063 |
5.19e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 123.11 E-value: 5.19e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 861 SGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE---SMAGK- 936
Cdd:PRK09603 1072 NGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlGLVGKe 1151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 937 ----------------------------------------------SAALHGLCHD-------ATPfIFseENSALEYFG 963
Cdd:PRK09603 1152 fgkqiasmledktkdfakelrakmleianainekdpltihalencsDEELLEYAKDwskgvkmAIP-VF--EGISQEKFY 1228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 964 EMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERD 1043
Cdd:PRK09603 1229 KLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
|
250 260
....*....|....*....|
gi 33469941 1044 ALLAHGTSFLLHDRLFNCSD 1063
Cdd:PRK09603 1309 ALEAYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
563-621 |
1.88e-23 |
|
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: 94.47 E-value: 1.88e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 33469941 563 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 621
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1033-1135 |
3.20e-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: 3.20e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 1033 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGsllspllekpppswsAMRNRKYnCTLCSRSDTIDTVSV 1112
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCG---------------LYAAYNK-CPICKGETDISPGYI 64
|
90 100
....*....|....*....|...
gi 33469941 1113 PYVFRYFVAELAAMNIKVKLDVV 1135
Cdd:pfam04560 65 PESFKLLFQELQSLGIDPRLLLE 87
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
880-1063 |
2.50e-20 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 98.16 E-value: 2.50e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 880 GDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAG--------------------KSAA 939
Cdd:PRK14844 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgekvgnildeinkiKSAF 1163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 940 LHGL--------------------------------------------------------CHDATPFIFS---------- 953
Cdd:PRK14844 1164 CKGIrslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnsCKSAYSNLRNflievyscgs 1243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 954 -----------EENSALEY----------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 1000
Cdd:PRK14844 1244 nvsicnnirdiSDNNLIEFarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 33469941 1001 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:PRK14844 1324 KLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
186-375 |
1.03e-10 |
|
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: 61.98 E-value: 1.03e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 186 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33469941 264 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 335
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 33469941 336 LKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 375
Cdd:pfam04561 146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
