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Conserved domains on  [gi|45545335|gb|AAS67515|]
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DNA-dependent RNA polymerase II second largest subunit, partial [Ramularia punctiformis]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 1000145)

DNA-directed RNA polymerase subunit B family protein similar to fungal DNA-directed RNA polymerase II subunit RPB2

CATH:  3.90.1110.10|3.90.1070.20
EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0000428|GO:0008270|GO:0003677|GO:0006351
PubMed:  11839495
SCOP:  4003708

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-935 0e+00

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK08565:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1103  Bit Score: 970.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335     1 SEKVLIAQERSAAN--IVQVFKKKGTNTPVmAELRSAVeRGTRliSSTTVKLynqavnaNNPGqTIKGSLPYIKTDIPIA 78
Cdd:PRK08565  148 SERVIVSQEDLAPNrvLVDKGEAGSSITHT-AKVISSR-AGYR--AQVTVER-------RKDG-TIYVSFPAVPGKIPFV 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    79 IIFRALGVVSDEDILNHIVNKEDTQmlEMLKPCLEEAF-VVQDRDNALDFIGRRGQQTGTKDRRIRYARDIMQKEFLPHI 157
Cdd:PRK08565  216 ILMRALGLETDRDIVYAVSLDPEIQ--QELLPSLEQASsIAATVEDALDYIGKRVAIGQPREYRIERAEQILDKYLLPHL 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   158 SQEEGSETKKAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLHRCVEGGRDFNI 237
Cdd:PRK08565  294 GTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   238 TLAIKTNILTSGLRYCLATGNWGdqkkasSAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCP 317
Cdd:PRK08565  374 RAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICP 447

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   318 AETPEGQACGLVKNLSLMCYVTVGTPGEPLTDFMRQRGMDLLEEYDPVLEPKSTKVFINGTWVGVHKNAGQLTETLRSLR 397
Cdd:PRK08565  448 FETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELR 527

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   398 RKGLLSFEVTI--IRDVREREIRVFTDAGRVCRPLFVVDNkpdaaerGSLVLRQDQVAKLQqdqenaaslRGiseedkal 475
Cdd:PRK08565  528 RSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLK---------KG-------- 583

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   476 hSYGWMGLVNEGVVEYLDAEEEETAMIIMTPEDL-DEHralrsgaeyddpksdphrrikpkpnmqvhtwTHCEIHPAMIL 554
Cdd:PRK08565  584 -ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLtPEH-------------------------------THLEIWPPAIL 631

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   555 GICASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIAS 634
Cdd:PRK08565  632 GITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLS 711

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   635 YSGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSVVESFERPERAATMKMKHGSYDKLDDDGIVSPGCRVSGGD 714
Cdd:PRK08565  712 YTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGD 791

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   715 MLIGKTAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTTNTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGT 794
Cdd:PRK08565  792 VLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGV 871

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   795 IGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQRGF 874
Cdd:PRK08565  872 IGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGT 951

                         890       900       910       920       930       940
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545335   875 EVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:PRK08565  952 EVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-935 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 970.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335     1 SEKVLIAQERSAAN--IVQVFKKKGTNTPVmAELRSAVeRGTRliSSTTVKLynqavnaNNPGqTIKGSLPYIKTDIPIA 78
Cdd:PRK08565  148 SERVIVSQEDLAPNrvLVDKGEAGSSITHT-AKVISSR-AGYR--AQVTVER-------RKDG-TIYVSFPAVPGKIPFV 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    79 IIFRALGVVSDEDILNHIVNKEDTQmlEMLKPCLEEAF-VVQDRDNALDFIGRRGQQTGTKDRRIRYARDIMQKEFLPHI 157
Cdd:PRK08565  216 ILMRALGLETDRDIVYAVSLDPEIQ--QELLPSLEQASsIAATVEDALDYIGKRVAIGQPREYRIERAEQILDKYLLPHL 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   158 SQEEGSETKKAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLHRCVEGGRDFNI 237
Cdd:PRK08565  294 GTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   238 TLAIKTNILTSGLRYCLATGNWGdqkkasSAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCP 317
Cdd:PRK08565  374 RAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICP 447

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   318 AETPEGQACGLVKNLSLMCYVTVGTPGEPLTDFMRQRGMDLLEEYDPVLEPKSTKVFINGTWVGVHKNAGQLTETLRSLR 397
Cdd:PRK08565  448 FETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELR 527

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   398 RKGLLSFEVTI--IRDVREREIRVFTDAGRVCRPLFVVDNkpdaaerGSLVLRQDQVAKLQqdqenaaslRGiseedkal 475
Cdd:PRK08565  528 RSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLK---------KG-------- 583

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   476 hSYGWMGLVNEGVVEYLDAEEEETAMIIMTPEDL-DEHralrsgaeyddpksdphrrikpkpnmqvhtwTHCEIHPAMIL 554
Cdd:PRK08565  584 -ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLtPEH-------------------------------THLEIWPPAIL 631

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   555 GICASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIAS 634
Cdd:PRK08565  632 GITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLS 711

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   635 YSGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSVVESFERPERAATMKMKHGSYDKLDDDGIVSPGCRVSGGD 714
Cdd:PRK08565  712 YTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGD 791

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   715 MLIGKTAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTTNTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGT 794
Cdd:PRK08565  792 VLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGV 871

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   795 IGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQRGF 874
Cdd:PRK08565  872 IGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGT 951

                         890       900       910       920       930       940
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545335   875 EVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:PRK08565  952 EVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-935 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: 841.84  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   1 SEKVLIAQERSAANIVQVFKKKGTntpVMAELRSAVERGTRLISSTTVKLYNqavnannPGQTIKGSLPYIKtdipiaii 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVEDSKGK---RIYTKTSIPSYSPYRGSWLEVKSDK-------KKDRIYVRIDLKR-------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  81 fralgvvsdedilnhivnkedtqmlemlkpcleeafvvqdRDNALDFIGRRGqqtgtkdrriryardimqkeflphisqe 160
Cdd:cd00653 199 ----------------------------------------QEEALKYIGKRF---------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 161 egsetkkaFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLHRCVEGGRDFNITLA 240
Cdd:cd00653 211 --------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLL 282

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 241 IKTNILTSGLRYCLATGNWGDQKKASSaKAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAE 319
Cdd:cd00653 283 INSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIE 361

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 320 TPEGQACGLVKNLSLMCYVTvgtpgepltdfmrqrgmdlleeydpvlepkstkvfingtwvgvhknagqltetlrslrrk 399
Cdd:cd00653 362 TPEGENCGLVKNLALMARIS------------------------------------------------------------ 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 400 gllsfevtiirdvrereirvftdaGRVCRPLFVVDNKpdaaergslvlrqdqvaklqqdqenaaslrgiseedkalhsyg 479
Cdd:cd00653 382 ------------------------GRIERPYRIVEKE------------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 480 wmglvnegvveyldaeeeetamiimtpedldehralrsgaeyddpksdphrrikpkpnmqvhtWTHCEIHPAMILGICAS 559
Cdd:cd00653 395 ---------------------------------------------------------------VTHIEISPSQILSVAAS 411

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 560 IIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIASYSGYN 639
Cdd:cd00653 412 LIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYN 491

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 640 QEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGmsvvESFERPERAATMKMKHGSYDKLDDDGIVSPGCRVSGGDMLIGK 719
Cdd:cd00653 492 FEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGK 567

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 720 TAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTT---NTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGTIG 796
Cdd:cd00653 568 ITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVIS 647

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 797 ITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQRGFEV 876
Cdd:cd00653 648 KILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEV 727

                       890       900       910       920       930
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 45545335 877 MYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:cd00653 728 LYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRF 786
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 373-935 0e+00

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 649.01  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   373 VFINGTWVGVHKNAGQLTETLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVDNkpdaaerGSLVLRQDQV 452
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   453 AKLQQDQenaaslrgiseedkalhsYGWMGLVNEGVVEYLDAEEEETAMIIMTPEDL-DEHralrsgaeyddpksdphrr 531
Cdd:TIGR03670  74 EKLKEGE------------------LTWDDLVKQGVIEYLDAEEEENAYIALDPEELtPEH------------------- 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   532 ikpkpnmqvhtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATT 611
Cdd:TIGR03670 117 ------------THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKT 184

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   612 RSMEFLKFRDLPAGQNAIVAIASYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSVVESFERPERAATMKMK 691
Cdd:TIGR03670 185 RVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRG 264

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   692 HGSYDKLDDDGIVSPGCRVSGGDMLIGKTAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTTNTEGLRFAKV 771
Cdd:TIGR03670 265 EEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKV 344

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   772 RTRVTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATP 851
Cdd:TIGR03670 345 RVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTP 424

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   852 FTDVTVTSISMILADHGFQQRGFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDG 931
Cdd:TIGR03670 425 FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREG 504


                  ....
gi 45545335   932 GLRF 935
Cdd:TIGR03670 505 GLRF 508
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 557-929 0e+00

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: 527.48  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   557 CASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIASYS 636
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   637 GYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSvVESFERPEraatmKMKHGSYDKLDDDGIVSPGCRVSGGDML 716
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPI-EEITRDIP-----NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   717 IGKTAPMAPDAEELGMRT-KMQVKRDVSTPLRSTENGVVDQVLL-TTNTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGT 794
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGeKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   795 IGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFT--DVTVTSISMILADHGFQQR 872
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYY 314

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 45545335   873 GFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRAR 929
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 72-935 2.36e-178

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: 543.16  E-value: 2.36e-178
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   72 KTDIPIAIIFRALGVVSDEDILNHIVnkeDTQMLEMLKPCLEEAfVVQDRDNALDFIGRR---GQQtgtkdRRIRYARDI 148
Cdd:COG0085  174 KRKIPVTVLLRALGLETDEEILEAFG---DDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGEP-----PTIERAEQL 244

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  149 MQKEF-------LPHI-----------SQEEGSETKKAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVF 210
Cdd:COG0085  245 LDNLFfdpkrydLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQF 324

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  211 RLKFVQLVKEMK--MYLHrcveGGRDFNITLAIKTNILTSGLRYCLATGnwgdqkkassakaGVSQVLNRYTYASTLSHL 288
Cdd:COG0085  325 RVGLSRMERVVRerMTTQ----DVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHK 387

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  289 RRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpgepltdfmrqrgmdlle 360
Cdd:COG0085  388 RRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN--------------------- 442

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  361 EYdpvlepkstkvfingtwvgvhknagqltetlrslrrkgllsfevtiirdvrereirvftdaGRVCRPLFVVDNkpdaa 440
Cdd:COG0085  443 EY-------------------------------------------------------------GFIETPYRKVEN----- 456

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  441 ergslvlrqdqvaklqqdqenaaslrgiseedkalhsygwmGLVNEGVvEYLDAEEEETAMIIMTPEDLDEHRAL----- 515
Cdd:COG0085  457 -----------------------------------------GKVTDEI-EYLTADEEENYYIAQANAPLDEDGNFleerv 494

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  516 --RSGAEYDDPKSDPHrrikpkpnmqvhtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVtltnynvr 593
Cdd:COG0085  495 lvRYRGEEVLVPPEEV--------------DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPL-------- 552

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  594 MDTMANVLYYP--------------QKPLAttRSMEFLKFRD------------LPAGQNAIVAIASYSGYNQEDSVIMN 647
Cdd:COG0085  553 LRPEAPLLHYPlqkfqrsnqgtcinQRPIV--RVGDRVEKGDvladgpatdngeLALGQNLLVAFMPWEGYNYEDAIIIS 630

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  648 QSSIDRGLFRSLFYRAYMDQEKR--VGMSVVeSFERPERAATMkmkhgsYDKLDDDGIVSPGCRVSGGDMLIGKTAP--- 722
Cdd:COG0085  631 ERLVKDDVLTSIHIEEYEIEARDtkLGPEEI-TRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkge 703

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  723 MAPDAEELGMR----TKMQVKRDVSTPLRSTENGVVDQVLLTTNTEG-------LRFAKVRTRVTKVPQIGDKFASRHGQ 791
Cdd:COG0085  704 TELTPEERLLRaifgEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGN 783

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  792 KGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQ 871
Cdd:COG0085  784 KGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPP 863

                        890       900       910       920       930       940
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45545335  872 RGFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:COG0085  864 DGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-935 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 970.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335     1 SEKVLIAQERSAAN--IVQVFKKKGTNTPVmAELRSAVeRGTRliSSTTVKLynqavnaNNPGqTIKGSLPYIKTDIPIA 78
Cdd:PRK08565  148 SERVIVSQEDLAPNrvLVDKGEAGSSITHT-AKVISSR-AGYR--AQVTVER-------RKDG-TIYVSFPAVPGKIPFV 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    79 IIFRALGVVSDEDILNHIVNKEDTQmlEMLKPCLEEAF-VVQDRDNALDFIGRRGQQTGTKDRRIRYARDIMQKEFLPHI 157
Cdd:PRK08565  216 ILMRALGLETDRDIVYAVSLDPEIQ--QELLPSLEQASsIAATVEDALDYIGKRVAIGQPREYRIERAEQILDKYLLPHL 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   158 SQEEGSETKKAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLHRCVEGGRDFNI 237
Cdd:PRK08565  294 GTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   238 TLAIKTNILTSGLRYCLATGNWGdqkkasSAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCP 317
Cdd:PRK08565  374 RAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICP 447

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   318 AETPEGQACGLVKNLSLMCYVTVGTPGEPLTDFMRQRGMDLLEEYDPVLEPKSTKVFINGTWVGVHKNAGQLTETLRSLR 397
Cdd:PRK08565  448 FETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELR 527

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   398 RKGLLSFEVTI--IRDVREREIRVFTDAGRVCRPLFVVDNkpdaaerGSLVLRQDQVAKLQqdqenaaslRGiseedkal 475
Cdd:PRK08565  528 RSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLK---------KG-------- 583

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   476 hSYGWMGLVNEGVVEYLDAEEEETAMIIMTPEDL-DEHralrsgaeyddpksdphrrikpkpnmqvhtwTHCEIHPAMIL 554
Cdd:PRK08565  584 -ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLtPEH-------------------------------THLEIWPPAIL 631

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   555 GICASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIAS 634
Cdd:PRK08565  632 GITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLS 711

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   635 YSGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSVVESFERPERAATMKMKHGSYDKLDDDGIVSPGCRVSGGD 714
Cdd:PRK08565  712 YTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGD 791

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   715 MLIGKTAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTTNTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGT 794
Cdd:PRK08565  792 VLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGV 871

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   795 IGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQRGF 874
Cdd:PRK08565  872 IGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGT 951

                         890       900       910       920       930       940
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545335   875 EVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:PRK08565  952 EVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-935 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: 841.84  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   1 SEKVLIAQERSAANIVQVFKKKGTntpVMAELRSAVERGTRLISSTTVKLYNqavnannPGQTIKGSLPYIKtdipiaii 80
Cdd:cd00653 137 TEKVIINQEQRSPNVIIVEDSKGK---RIYTKTSIPSYSPYRGSWLEVKSDK-------KKDRIYVRIDLKR-------- 198

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  81 fralgvvsdedilnhivnkedtqmlemlkpcleeafvvqdRDNALDFIGRRGqqtgtkdrriryardimqkeflphisqe 160
Cdd:cd00653 199 ----------------------------------------QEEALKYIGKRF---------------------------- 210

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 161 egsetkkaFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLHRCVEGGRDFNITLA 240
Cdd:cd00653 211 --------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLL 282

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 241 IKTNILTSGLRYCLATGNWGDQKKASSaKAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAE 319
Cdd:cd00653 283 INSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIE 361

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 320 TPEGQACGLVKNLSLMCYVTvgtpgepltdfmrqrgmdlleeydpvlepkstkvfingtwvgvhknagqltetlrslrrk 399
Cdd:cd00653 362 TPEGENCGLVKNLALMARIS------------------------------------------------------------ 381

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 400 gllsfevtiirdvrereirvftdaGRVCRPLFVVDNKpdaaergslvlrqdqvaklqqdqenaaslrgiseedkalhsyg 479
Cdd:cd00653 382 ------------------------GRIERPYRIVEKE------------------------------------------- 394

                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 480 wmglvnegvveyldaeeeetamiimtpedldehralrsgaeyddpksdphrrikpkpnmqvhtWTHCEIHPAMILGICAS 559
Cdd:cd00653 395 ---------------------------------------------------------------VTHIEISPSQILSVAAS 411

                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 560 IIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIASYSGYN 639
Cdd:cd00653 412 LIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYN 491

                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 640 QEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGmsvvESFERPERAATMKMKHGSYDKLDDDGIVSPGCRVSGGDMLIGK 719
Cdd:cd00653 492 FEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGK 567

                       730       740       750       760       770       780       790       800
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 720 TAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTT---NTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGTIG 796
Cdd:cd00653 568 ITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVIS 647

                       810       820       830       840       850       860       870       880
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335 797 ITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQRGFEV 876
Cdd:cd00653 648 KILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEV 727

                       890       900       910       920       930
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 45545335 877 MYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:cd00653 728 LYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRF 786
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 373-935 0e+00

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 649.01  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   373 VFINGTWVGVHKNAGQLTETLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVDNkpdaaerGSLVLRQDQV 452
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   453 AKLQQDQenaaslrgiseedkalhsYGWMGLVNEGVVEYLDAEEEETAMIIMTPEDL-DEHralrsgaeyddpksdphrr 531
Cdd:TIGR03670  74 EKLKEGE------------------LTWDDLVKQGVIEYLDAEEEENAYIALDPEELtPEH------------------- 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   532 ikpkpnmqvhtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATT 611
Cdd:TIGR03670 117 ------------THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKT 184

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   612 RSMEFLKFRDLPAGQNAIVAIASYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSVVESFERPERAATMKMK 691
Cdd:TIGR03670 185 RVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRG 264

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   692 HGSYDKLDDDGIVSPGCRVSGGDMLIGKTAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTTNTEGLRFAKV 771
Cdd:TIGR03670 265 EEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKV 344

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   772 RTRVTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATP 851
Cdd:TIGR03670 345 RVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTP 424

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   852 FTDVTVTSISMILADHGFQQRGFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDG 931
Cdd:TIGR03670 425 FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREG 504


                  ....
gi 45545335   932 GLRF 935
Cdd:TIGR03670 505 GLRF 508
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 369-935 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 630.07  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  369 KSTKVFINGTWVGVHKNAGQLTETLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVDNkpdaaerGSLVLR 448
Cdd:PRK07225   3 RKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  449 QDQVAKLQQDQENaaslrgiseedkalhsygWMGLVNEGVVEYLDAEEEETAMIIMTPEDL-DEHralrsgaeyddpksd 527
Cdd:PRK07225  76 EEHIEKLKNGELT------------------FDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH--------------- 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  528 phrrikpkpnmqvhtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKP 607
Cdd:PRK07225 123 ----------------THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVP 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  608 LATTRSMEFLKFRDLPAGQNAIVAIASYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSVVESFERPERAAT 687
Cdd:PRK07225 187 LVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVR 266

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  688 MKMKHGSYDKLDDDGIVSPGCRVSGGDMLIGKTAPMAPDAEELGMRTKMQVKRDVSTPLRSTENGVVDQVLLTTNTEGLR 767
Cdd:PRK07225 267 GYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSR 346

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  768 FAKVRTRVTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEG 847
Cdd:PRK07225 347 LVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRV 426

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  848 DATPFTDVTVTSISMILADHGFQQRGFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGR 927
Cdd:PRK07225 427 DGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGR 506


                 ....*...
gi 45545335  928 ARDGGLRF 935
Cdd:PRK07225 507 AREGGLRF 514
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 557-929 0e+00

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: 527.48  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   557 CASIIPFPDHNQSPRNTYQSAMGKQAMGVTLTNYNVRMDTMANVLYYPQKPLATTRSMEFLKFRDLPAGQNAIVAIASYS 636
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   637 GYNQEDSVIMNQSSIDRGLFRSLFYRAYMDQEKRVGMSvVESFERPEraatmKMKHGSYDKLDDDGIVSPGCRVSGGDML 716
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPI-EEITRDIP-----NVSEEALKKLDEDGIVRVGAEVKPGDIL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   717 IGKTAPMAPDAEELGMRT-KMQVKRDVSTPLRSTENGVVDQVLL-TTNTEGLRFAKVRTRVTKVPQIGDKFASRHGQKGT 794
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGeKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   795 IGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFT--DVTVTSISMILADHGFQQR 872
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYY 314

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 45545335   873 GFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRAR 929
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 72-935 2.36e-178

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: 543.16  E-value: 2.36e-178
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   72 KTDIPIAIIFRALGVVSDEDILNHIVnkeDTQMLEMLKPCLEEAfVVQDRDNALDFIGRR---GQQtgtkdRRIRYARDI 148
Cdd:COG0085  174 KRKIPVTVLLRALGLETDEEILEAFG---DDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGEP-----PTIERAEQL 244

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  149 MQKEF-------LPHI-----------SQEEGSETKKAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVF 210
Cdd:COG0085  245 LDNLFfdpkrydLAHVgrykinkklglDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQF 324

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  211 RLKFVQLVKEMK--MYLHrcveGGRDFNITLAIKTNILTSGLRYCLATGnwgdqkkassakaGVSQVLNRYTYASTLSHL 288
Cdd:COG0085  325 RVGLSRMERVVRerMTTQ----DVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHK 387

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  289 RRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpgepltdfmrqrgmdlle 360
Cdd:COG0085  388 RRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN--------------------- 442

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  361 EYdpvlepkstkvfingtwvgvhknagqltetlrslrrkgllsfevtiirdvrereirvftdaGRVCRPLFVVDNkpdaa 440
Cdd:COG0085  443 EY-------------------------------------------------------------GFIETPYRKVEN----- 456

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  441 ergslvlrqdqvaklqqdqenaaslrgiseedkalhsygwmGLVNEGVvEYLDAEEEETAMIIMTPEDLDEHRAL----- 515
Cdd:COG0085  457 -----------------------------------------GKVTDEI-EYLTADEEENYYIAQANAPLDEDGNFleerv 494

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  516 --RSGAEYDDPKSDPHrrikpkpnmqvhtwTHCEIHPAMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVtltnynvr 593
Cdd:COG0085  495 lvRYRGEEVLVPPEEV--------------DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPL-------- 552

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  594 MDTMANVLYYP--------------QKPLAttRSMEFLKFRD------------LPAGQNAIVAIASYSGYNQEDSVIMN 647
Cdd:COG0085  553 LRPEAPLLHYPlqkfqrsnqgtcinQRPIV--RVGDRVEKGDvladgpatdngeLALGQNLLVAFMPWEGYNYEDAIIIS 630

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  648 QSSIDRGLFRSLFYRAYMDQEKR--VGMSVVeSFERPERAATMkmkhgsYDKLDDDGIVSPGCRVSGGDMLIGKTAP--- 722
Cdd:COG0085  631 ERLVKDDVLTSIHIEEYEIEARDtkLGPEEI-TRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkge 703

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  723 MAPDAEELGMR----TKMQVKRDVSTPLRSTENGVVDQVLLTTNTEG-------LRFAKVRTRVTKVPQIGDKFASRHGQ 791
Cdd:COG0085  704 TELTPEERLLRaifgEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGN 783

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  792 KGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQ 871
Cdd:COG0085  784 KGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPP 863

                        890       900       910       920       930       940
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45545335  872 RGFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:COG0085  864 DGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-248 1.66e-86

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: 282.35  E-value: 1.66e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335     1 SEKVLIAQERSAANIVQVFKKK-GTNTPVMAELRSAVERGTRLISSTTVKLYNqavnaNNPGQTIKGSLPYIKTDIPIAI 79
Cdd:pfam04563 146 SEKVIVAQEHRSRNHPIVFKKAdPKKRGSVASVRSSAEISVRPDSTSWVNVLE-----YLSNGTIYFKFPYIKKEIPIVI 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    80 IFRALGVVSDEDILNHIVNKE-DTQMLEMLKPCLEEAFVV--QDRDNALDFIGRRG---QQTG-TKDRRIRYARDIMQKE 152
Cdd:pfam04563 221 ILRALGFTSDREIFELICYDVnDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGraiFRMGrPREPRIKYAEEILQKE 300

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   153 FLPHISQEEGSETKKAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLHRCVEGG 232
Cdd:pfam04563 301 VLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSP 380

                         250
                  ....*....|....*.
gi 45545335   233 RDFNITLAIKTNILTS 248
Cdd:pfam04563 381 DDLMLQLLVNAKPITS 396
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-355 4.03e-80

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 268.74  E-value: 4.03e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    1 SEKVLIAQERSAAN-IVQVFKKKGTNTPVMAELRSaVERGTR-LIsstTVKLynqavnanNPGQTIKGSLPYIKTDIPIA 78
Cdd:PRK09606 153 SERVLMTLEDLAPNkILVEKDERYGDRIEVAKVFS-QRRGYRaLV---TVER--------NRDGLLEVSFPSVPGSIPFV 220

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   79 IIFRALGVVSDEDILNHIVNKEDTQMlEMLkPCLEEAfVVQDRDNALDFIGRRGQQTGTKDRRIRYARDIMQKEFLPHIS 158
Cdd:PRK09606 221 ILMRALGLETDEEIVEAVSDDPEIVK-FML-ENLEEA-EVDTQEEALEYIGKRVAPGQTKEYRIKRAEYVIDRYLLPHLG 297

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  159 QEEGSETKKAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLHRCVEGGRDFNIT 238
Cdd:PRK09606 298 VEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIK 377

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335  239 LAIKTNILTSGLRYCLATGNWgdqkkaSSAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPA 318
Cdd:PRK09606 378 TAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPS 451

                        330       340       350
                 ....*....|....*....|....*....|....*..
gi 45545335  319 ETPEGQACGLVKNLSLMCYVTVGTPGEPLTDFMRQRG 355
Cdd:PRK09606 452 ETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELG 488
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 62-935 2.48e-61

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: 226.47  E-value: 2.48e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335     62 QTIKGSLPYIKTD----IPIAIIFRALGVVSDEDILNHIVNKEDTQMLEMLKPCL--EEAFVV----------QDRDNAL 125
Cdd:TIGR02013  179 ETDKKDVLYVRIDrkrkLPATVLLRALGYTIDTLILNRLGSGEYIRNTLRKDPTNseEEALVEiyrklrpgepPTVEAAR 258

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    126 DFIgrrgQQTGTKDRRI---RYARDIMQKEFLPHISQEEGSETKKAFF--LGYMVN-RMlqcalGRTEEDDRDHFGKKRL 199
Cdd:TIGR02013  259 SLL----ENLFFDPKRYdlgRVGRYKLNKKLGLDVPESIGVLTKEDIIatIKYLIKlRN-----GKGEIDDIDHLGNRRI 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    200 DLAGPLMAQVFRLKFVQL---VKEmKMYLhrcveggRDFNiTLA----IKTNILTSGLRYCLATGNwgdqkkassakagV 272
Cdd:TIGR02013  330 RSVGELLQNQFRVGLARMeriVRE-RMST-------QDTD-TLTpqdlINAKPISAAIKEFFGSSQ-------------L 387

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    273 SQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMC-----------Y 337
Cdd:TIGR02013  388 SQFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYArvneygfietpY 467

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    338 VTVgTPGEPLTDfMRQRGMDLLEEYDPVLEPKSTKVFINGTWVGVHKNA---GQLTETLRSlrrkgllsfEVTIIrDVRE 414
Cdd:TIGR02013  468 RKV-KDGKVVVT-DEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAryrGEITLVSPD---------QVDYM-DVSP 535

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    415 REIrvfTDAGRVCRPLFVVDnkpDA--AERGSLVLRQdQVAKLQQDqenaASLRGISEEDKALHSYGWMGLVNE-GVVEY 491
Cdd:TIGR02013  536 KQV---VSVAASLIPFLEHD---DAnrALMGSNMQRQ-AVPLLRSE----APLVGTGMEAKVARDSGAVIVAKRgGVVEY 604

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    492 LDAEEeetaMIIMTPEDLDEhralrsgaeyddpksdphrrikpkPNMQVHTWthceihpamilgicaSIIPFPDHNQSpr 571
Cdd:TIGR02013  605 VDAKR----IVIRYDEDEEE------------------------PDGGIDIY---------------RLLKYQRSNQD-- 639

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    572 ntyqsamgkqamgvtlTNYNvrmdtmanvlyypQKP-------------LATTRSMEFlkfRDLPAGQNAIVAIASYSGY 638
Cdd:TIGR02013  640 ----------------TCIN-------------QRPivsvgdrveagdvLADGPSTDL---GELALGRNVLVAFMPWNGY 687

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    639 NQEDSVIMNQSSIDRGLFRSLFYRAY--MDQEKRVGmsvVESFER--PEraatmkMKHGSYDKLDDDGIVSPGCRVSGGD 714
Cdd:TIGR02013  688 NYEDAILISERLVKDDVFTSIHIEEYevEARDTKLG---PEEITRdiPN------VSEEALRNLDENGIVRIGAEVKAGD 758

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    715 MLIGKTAPMA---PDAEELGMRT----KMQVKRDVSTPLRSTENGVVDQVLLTTNTEG-------LRFAKVRTRVTKVPQ 780
Cdd:TIGR02013  759 ILVGKVTPKGeteLTPEEKLLRAifgeKARDVRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQ 838

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    781 IGDKFASRHGQKGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVGALQGQEGD--ATP-FTDVTV 857
Cdd:TIGR02013  839 VGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASE 918

                          890       900       910       920       930       940       950
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45545335    858 TSISMILADHGFQQRGFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:TIGR02013  919 EEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 996
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 617-935 6.53e-46

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 179.13  E-value: 6.53e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   617 LKFRDLPAGQNAIVAIASYSGYNQEDSVIMNQSSIDRGLFRSL---FYRAYMDQEKrvgmsvvesfERPERAATMKMKHG 693
Cdd:CHL00207  639 IDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIhieKYEIELRQTK----------LGSEEITRNIPNVS 708

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   694 SYD--KLDDDGIVSPGCRVSGGDMLIGKTAPMaPDAEELGmRTKM------QVKRDV-STPLRSTENG---VVDQVLLTT 761
Cdd:CHL00207  709 EYSlkNLDENGIISIGSKVLAGDILVGKITPK-GESDQLP-EGKLlraifgEKAKDVkDTSLRMPNGGygrVIKVEIFSR 786

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   762 NTeGLR-----FAKVRTRVTKVP--QIGDKFASRHGQKGTIG-ITYRQeDMPFSADGLVPDIIINPHAIPSRMTIAHLIE 833
Cdd:CHL00207  787 SK-GDElkfgyYLKIRVFIAQIRkiQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLFE 864

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   834 CLLSKVGALQGQEGDATPFTDVTVTSISMILADHGFQQRGFE---------------VMYNGHTGKKLNAQVFLGPTYYQ 898
Cdd:CHL00207  865 CLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKnneywlfnsyhpgkmVLRDGRTGYKFKNPVTVGIAYML 944

                         330       340       350
                  ....*....|....*....|....*....|....*..
gi 45545335   899 RLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:CHL00207  945 KLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRF 981
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 58-200 7.04e-45

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: 159.82  E-value: 7.04e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335    58 NNPGQTIKGSLPYIKTDIPIAIIFRALGVVSDEDILNHIV-NKEDTQMLEMLKPCLEEAFVVQDRDNALDFIGRRGQQTG 136
Cdd:pfam04561  35 EIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLCyDFNDPQMLELLKPELEEAENIYTQEEALDYIGKGFALRR 114

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545335   137 TKDRRIRYARDIMQK-----EFLPHISQEEGSETK--KAFFLGYMVNRMLQCALGRTEEDDRDHFGKKRLD 200
Cdd:pfam04561 115 GEEPRLQRAREILYSrdpkyNLNKHLGLNEPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 625-935 4.66e-39

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 157.57  E-value: 4.66e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   625 GQNAIVAIASYSGYNQEDSVIMNQSSIDRGLFRSLFyraymdqekrvgmsvVESFErperAATMKMKHG----------- 693
Cdd:PRK00405  716 GQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIH---------------IEEYE----IEARDTKLGpeeitrdipnv 776

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   694 ---SYDKLDDDGIVSPGCRVSGGDMLIGKTAP-----MAPdaEELGMRTKMQVK-RDV-STPLR--STENG-VVDQVLLT 760
Cdd:PRK00405  777 seeALRNLDESGIVRIGAEVKPGDILVGKVTPkgeteLTP--EEKLLRAIFGEKaRDVkDTSLRvpHGEEGtVIDVKVFT 854

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   761 TNTEG-------LRFAKVRTRVTKVPQIGDKFASRHGQKGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIE 833
Cdd:PRK00405  855 RIEQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILE 934

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   834 CLLSKVGALQGQEGdATP-FTDVTVTSISMILADHGFQQRGFEVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARA 912
Cdd:PRK00405  935 THLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARS 1013

                         330       340
                  ....*....|....*....|...
gi 45545335   913 RGPLQVLTRQPVEGRARDGGLRF 935
Cdd:PRK00405 1014 TGPYSLVTQQPLGGKAQFGGQRF 1036
rpoB CHL00001
RNA polymerase beta subunit
 625-934 2.31e-33

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 139.27  E-value: 2.31e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   625 GQNAIVAIASYSGYNQEDSVIMNQSSIDRGLFRSLFYRAYmdqekrvGMSVVESFERPERAaTMKMKHGSYDK---LDDD 701
Cdd:CHL00001  652 GKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-------EIQTHVTSQGPERI-TKEIPHLEAHLlrnLDKN 723

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   702 GIVSPGCRVSGGDMLIGKTAP-MAPDAEE----------LGmrtkMQVKRDVSTPLRSTENG---VVD------QVLLTT 761
Cdd:CHL00001  724 GIVMLGSWVETGDILVGKLTPqEAEESSYapegrllraiFG----IQVSTSKETCLKLPIGGrgrVIDvrwiqkKGGSSY 799

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   762 NTEGLRFAKVRTRvtKVpQIGDKFASRHGQKGTIG-ITYRQeDMPFSADGLVPDIIINPHAIPSRMTIAHLIECLLSKVG 840
Cdd:CHL00001  800 NPETIHVYILQKR--EI-QVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAG 875

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   841 ALQGQEGDATPFtdvtvtsismilaDHGFQQ---RG------------------FEVMY-------NGHTGKKLNAQVFL 892
Cdd:CHL00001  876 DLLNRHYRIAPF-------------DERYEQeasRKlvfselyeaskqtanpwvFEPEYpgksrlfDGRTGDPFEQPVTI 942

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 45545335   893 GPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLR 934
Cdd:CHL00001  943 GKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQR 984
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 373-434 9.74e-31

RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 114.77  E-value: 9.74e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545335   373 VFINGTWVGVHKNAGQLTETLRSLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVD 434
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 274-337 1.23e-30

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: 114.93  E-value: 1.23e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45545335   274 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 337
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
175-935 1.92e-27

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 120.80  E-value: 1.92e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   175 VNRMLQCALGRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQLVKEMKMYLhRCVEGGRDFNITL-AIKTNILTSGLRYC 253
Cdd:PRK09603  441 VKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKL-TTMSGAFDSLMPHdLVNSKMITSTIMEF 519

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   254 LATGNwgdqkkassakagVSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGL 328
Cdd:PRK09603  520 FMGGQ-------------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGL 585

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   329 VKNLSLMCYVT-VGTPGEPLTDFMRQRGMD------LLEEYDPVLEPKSTKVFINGTWVGvhknagQLTETlrslRRKGL 401
Cdd:PRK09603  586 INTLSTFTRVNdLGFIEAPYKKVVDGKVVGetiyltAIQEDSHIIAPASTPIDEEGNILG------DLIET----RVEGE 655

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   402 LSF----EVTIIrDVREREIrVFTDAGRVcrPlFVVDNKPDAAERGSLVLRQdQVAKLQQDQENAASlrGIsEEDKALHS 477
Cdd:PRK09603  656 IVLneksKVTLM-DLSSSML-VGVAASLI--P-FLEHDDANRALMGTNMQRQ-AVPLLRSDAPIVGT--GI-EKIIARDS 726

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   478 YGWMGLVNEGVVEYLDA-------EEEETAMIimtpedldEHRALRSGAEYDDPKSDPHRRIkpkpnmqVHTWTHCEIHP 550
Cdd:PRK09603  727 WGAIKANRAGVVEKIDSkniyilgEGKEEAYI--------DAYSLQKNLRTNQNTSFNQVPI-------VKVGDKVEAGQ 791

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   551 AMILGicasiipfPDhnqsprntyqsamgkqamgvtltnynvrMDTmanvlyypqkplattrsmeflkfRDLPAGQNAIV 630
Cdd:PRK09603  792 IIADG--------PS----------------------------MDR-----------------------GELALGKNVRV 812

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   631 AIASYSGYNQEDSVIMNQSSIDRGLFRSL-FYRAYMD-QEKRVGmsvVESFER--PEraatmkMKHGSYDKLDDDGIVSP 706
Cdd:PRK09603  813 AFMPWNGYNFEDAIVVSERITKDDIFTSThIYEKEVDaRELKHG---VEEFTAdiPD------VKEEALAHLDESGIVKV 883

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   707 GCRVSGGDMLIGKTAP---MAPDAEE------LGMRTKMQVKRDVSTPlRSTENGVVDQVLLTTN--------------- 762
Cdd:PRK09603  884 GTYVSAGMILVGKTSPkgeIKSTPEErllraiFGDKAGHVVNKSLYCP-PSLEGTVIDVKVFTKKgyekdarvlsayeee 962

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   763 -----------------TEGLRF------------AKVRTRVTK----VPQ----------------------------- 780
Cdd:PRK09603  963 kakldmehfdrltmlnrEELLRVssllsqaileepFSHNGKDYKegdqIPKeeiasinrftlaslvkkyskevqnhyeit 1042

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   781 -----------------------------------------------IGDKFASRHGQKGTIGITYRQEDMPFSADGLVP 813
Cdd:PRK09603 1043 knnfleqkkvlgeeheeklsilekddilpngvikkvklyiatkrklkVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPV 1122

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   814 DIIINPHAIPSRMTIAHLIECLLSKVGALQGQE-----------------------GDATPFTDVTVTSISMILAD---- 866
Cdd:PRK09603 1123 DIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQiasmledktkdfakelrakmleiANAINEKDPLTIHALENCSDeell 1202

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   867 -----------------HGFQQRGFEV--------------MYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGP 915
Cdd:PRK09603 1203 eyakdwskgvkmaipvfEGISQEKFYKlfelakiamdgkmdLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGP 1282

                         970       980
                  ....*....|....*....|
gi 45545335   916 LQVLTRQPVEGRARDGGLRF 935
Cdd:PRK09603 1283 YSLVTHQPVGGKALFGGQRF 1302
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 480-550 7.83e-23

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 92.22  E-value: 7.83e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545335   480 WMGLVNEGVVEYLDAEEEETAMIIMTPEDLDEHralrsgaeyddpksdpHRRIKPKPNmqVHTWTHCEIHP 550
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEES----------------SREEREGPY--AHTYTHCEIHP 53
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
184-935 2.75e-18

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 90.84  E-value: 2.75e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   184 GRTEEDDRDHFGKKRLDLAGPLMAQVFRLKFVQL----VKEMKMYLHRCVEGGrDFnitlaIKTNILTSGLRyclatgnw 259
Cdd:PRK14844  459 GQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLeravVDSMSTSSLDKVSPS-DF-----INPKVLTNVLR-------- 524

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   260 gDQKKASSakagVSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLm 335
Cdd:PRK14844  525 -DFFNSSQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI- 598

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   336 cYVTVGTPGepltdfmrqrgmdlleeydpVLEPKSTKVfingtwvgVHKNAGQLTETLRSLRrKGLLSFEVTiirDVRER 415
Cdd:PRK14844  599 -YARINKYG--------------------FIESPYRKV--------VNRVVTDQIEYLSAID-EGLYYIADT---SAKLD 645

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   416 EIRVFTDAGRVCRplfvvdnkpdaaERGSLVLrqdqvaklqqdqenaaslrgiseedkalhsygwmglVNEGVVEYLDAE 495
Cdd:PRK14844  646 ENNCFVDDMLYCR------------YAGSFVM------------------------------------VSSDQVSYIDVS 677

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   496 EEET----AMIIMTPEDLDEHRALRSgaeyddpkSDPHRRIKP--KPNMQ-VHTWTHCEIHP---AMILGICASIIPFPD 565
Cdd:PRK14844  678 PKQVisvaASLIPFLENDDANRALMG--------SNMQRQAVPllKPTAPlVATGMESFVASgsgAVVLAKRDGIVDSSD 749

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   566 HNQSPRNTYQSAmGKQAMGVTLtnYNVRMDTMAN-VLYYPQKPLatTRSMEFLKFRDL----PA--------GQNAIVAI 632
Cdd:PRK14844  750 SNSIVIRAFDKE-RVNYLDVDI--YHLRKFQRSNhNTCINQKPL--VCVGDYVKEGDViadgPAinsgelalGQNLLVAF 824

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   633 ASYSGYNQEDSVIMNQSSIDRGLFRSLfyraYMDQEKRVGMSVVESFERPERAATMKMKHGSYdKLDDDGIVSPGCRVSG 712
Cdd:PRK14844  825 MSWQGYNFEDSIIISSEVVKKDLFTSI----HIEEFECVVHDTPLGSEKITRAIPGVNEENLY-HLDDSGIVKIGTRVGP 899

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   713 GDMLIGKTAP------------------------------MAPDAEELGMRTKMQVKRDVSTPLRS-------------T 749
Cdd:PRK14844  900 GYILVGKVTPkpslslppetkllmtifgeksfdcadsslyTSPDVEGTVIDVQVFTRRGVEENERAllikqkeindfekE 979

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   750 ENGVVD-----------QVLLTTNTE----------------GLR----------------------FAKVRTRVTKVP- 779
Cdd:PRK14844  980 RDYIINvtseyfydelkKLLINSGSQdrekfdsiereqwwgiGLKnqsiseqvkslkkdfdekvshaIAQFKRKVEKLHe 1059

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   780 ----------------------QIGDKFASRHGQKGTIGITYRQEDMPFSADGLVPDIIINPHAIPSRMTIAHLIEC--- 834
Cdd:PRK14844 1060 gydlpqgvsmsvkvfiavkhslQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILEThvg 1139

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   835 -----LLSKVGALQGQ----------------EGDATPF----------------------------------------- 852
Cdd:PRK14844 1140 wackkLGEKVGNILDEinkiksafckgirslnDDNFTKFaaayldnkkienidddeitasvlntpnknalndelnelven 1219

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545335   853 -----------------------TDVTVTS-----------------------------------ISMILADHGFQQRGF 874
Cdd:PRK14844 1220 ylnscksaysnlrnflievyscgSNVSICNnirdisdnnliefarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQ 1299

                         970       980       990      1000      1010      1020
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545335   875 EVMYNGHTGKKLNAQVFLGPTYYQRLRHMVDDKIHARARGPLQVLTRQPVEGRARDGGLRF 935
Cdd:PRK14844 1300 AVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRF 1360
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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