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Conserved domains on  [gi|4505941|ref|NP_000929|]
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DNA-directed RNA polymerase II subunit RPB2 isoform 1 [Homo sapiens]

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

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;
27-1172 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: 1282.59  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhaSGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565    2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    106 SPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565   69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565  144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565  210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565  286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565  366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    504 TLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565  440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565  520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    662 VEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565  596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565  669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    822 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565  749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    898 TSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 977
Cdd:PRK08565  825 HGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    978 IGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDD 1057
Cdd:PRK08565  905 VGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1058 KIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC 1137
Cdd:PRK08565  984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVC 1063
                        1130      1140      1150
                  ....*....|....*....|....*....|....*
gi 4505941   1138 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172
Cdd:PRK08565 1064 PIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
27-1172 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 1282.59  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhaSGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565    2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    106 SPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565   69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565  144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565  210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565  286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565  366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    504 TLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565  440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565  520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    662 VEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565  596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565  669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    822 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565  749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    898 TSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 977
Cdd:PRK08565  825 HGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    978 IGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDD 1057
Cdd:PRK08565  905 VGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1058 KIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC 1137
Cdd:PRK08565  984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVC 1063
                        1130      1140      1150
                  ....*....|....*....|....*....|....*
gi 4505941   1138 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172
Cdd:PRK08565 1064 PIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
39-1172 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: 1254.39  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    39 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhasgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 118
Cdd:cd00653    1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   119 TYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 198
Cdd:cd00653   70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   199 KMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 278
Cdd:cd00653  146 QRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   279 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 358
Cdd:cd00653  202 --------------------------------------ALKYIGKRF--------------------------------- 210
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   359 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 438
Cdd:cd00653  211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   439 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEG 517
Cdd:cd00653  287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   518 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 597
Cdd:cd00653  366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   598 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 677
Cdd:cd00653  382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   678 tpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 757
Cdd:cd00653  395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   758 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 837
Cdd:cd00653  460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   838 QGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 914
Cdd:cd00653  536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615
                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   915 GYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKG 994
Cdd:cd00653  616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLG 695
                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   995 EIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1074
Cdd:cd00653  696 KFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQP 774
                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941  1075 MEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYA 1154
Cdd:cd00653  775 LKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYA 848
                       1130
                 ....*....|....*...
gi 4505941  1155 CKLLFQELMSMSIAPRMM 1172
Cdd:cd00653  849 FKLLFQELQSMNIDPRLK 866
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
567-1171 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: 785.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     567 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 646
Cdd:TIGR03670    1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     647 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 726
Cdd:TIGR03670   80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     727 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 806
Cdd:TIGR03670  150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     807 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 882
Cdd:TIGR03670  230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     883 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 962
Cdd:TIGR03670  309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     963 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 1042
Cdd:TIGR03670  386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    1043 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1122
Cdd:TIGR03670  465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*....
gi 4505941    1123 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1171
Cdd:TIGR03670  545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
30-1173 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 700.71  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    30 ISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQaeaqhaSGEVEepprylLKFEQIYLSKPTHwerdgapspmM 109
Cdd:COG0085    7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDF------TGNLS------LEFGDYRLGEPKY----------T 64
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   110 PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllngltdrdlcelnecpldpgGYFIING 189
Cdd:COG0085   65 PEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------------------------GTFIING 116
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   190 SEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARggqgaKKSAIGQRIVAtlpyiKQEVP 268
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-----KDGTIYVRIDR-----KRKIP 178
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   269 IIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGSRgAKPGvtKEKRIKYAKEVL---- 343
Cdd:COG0085  179 VTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYRK-LRPG--EPPTIERAEQLLdnlf 249
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   344 ---QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK 409
Cdd:COG0085  250 fdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   410 NLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkahqaraGVSQVLNRLTFASTLSHLRR 484
Cdd:COG0085  330 RMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRR 389
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   485 LN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilEFleewsmenleei 556
Cdd:COG0085  390 LSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------ 444
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   557 spaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQKLLLK 636
Cdd:COG0085  445 --------------------------------------------------------------GFIETPYRKVENGKVTDE 462
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   637 krhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK--------------EVAYCST--YTHCEIHP 700
Cdd:COG0085  463 -------------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgEEVLVPPeeVDYMDVSP 517
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   701 SMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP--------------QKPLVttRSMEY 766
Cdd:COG0085  518 KQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RVGDR 587
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   767 LR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY--KEQESKKGfdQEEVfekp 832
Cdd:COG0085  588 VEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeiEARDTKLG--PEEI---- 661
                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   833 TREtcqgmrhaI-------YDKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELESTNR----------RYtKRDCSTF 895
Cdd:COG0085  662 TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELTPEERllraifgekaRE-VRDTSLR 730
                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   896 LRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIIN 968
Cdd:COG0085  731 VPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLN 810
                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   969 PHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYY 1048
Cdd:COG0085  811 PLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYY 889
                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941  1049 QRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYqvhvcnlCGimaia 1128
Cdd:COG0085  890 LKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV-------CG----- 957
                       1210      1220      1230      1240
                 ....*....|....*....|....*....|....*....|....*
gi 4505941  1129 ntRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1173
Cdd:COG0085  958 --RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
707-1080 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: 553.29  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     707 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 786
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     787 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYDKLDDDGLIAPGVRVSGDDVI 866
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     867 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 944
Cdd:pfam00562  155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     945 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 1023
Cdd:pfam00562  235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 4505941    1024 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1080
Cdd:pfam00562  315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
27-1172 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 1282.59  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhaSGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565    2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    106 SPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565   69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565  144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565  210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565  286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565  366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    504 TLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565  440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565  520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    662 VEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565  596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565  669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    822 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565  749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    898 TSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 977
Cdd:PRK08565  825 HGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    978 IGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDD 1057
Cdd:PRK08565  905 VGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1058 KIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC 1137
Cdd:PRK08565  984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVC 1063
                        1130      1140      1150
                  ....*....|....*....|....*....|....*
gi 4505941   1138 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172
Cdd:PRK08565 1064 PIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
39-1172 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: 1254.39  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    39 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhasgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 118
Cdd:cd00653    1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   119 TYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 198
Cdd:cd00653   70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   199 KMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 278
Cdd:cd00653  146 QRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   279 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 358
Cdd:cd00653  202 --------------------------------------ALKYIGKRF--------------------------------- 210
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   359 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 438
Cdd:cd00653  211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   439 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEG 517
Cdd:cd00653  287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   518 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 597
Cdd:cd00653  366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   598 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 677
Cdd:cd00653  382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   678 tpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 757
Cdd:cd00653  395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   758 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 837
Cdd:cd00653  460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   838 QGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 914
Cdd:cd00653  536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615
                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   915 GYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKG 994
Cdd:cd00653  616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLG 695
                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   995 EIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1074
Cdd:cd00653  696 KFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQP 774
                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941  1075 MEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYA 1154
Cdd:cd00653  775 LKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYA 848
                       1130
                 ....*....|....*...
gi 4505941  1155 CKLLFQELMSMSIAPRMM 1172
Cdd:cd00653  849 FKLLFQELQSMNIDPRLK 866
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
567-1171 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: 785.76  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     567 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 646
Cdd:TIGR03670    1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     647 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 726
Cdd:TIGR03670   80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     727 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 806
Cdd:TIGR03670  150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     807 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 882
Cdd:TIGR03670  230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     883 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 962
Cdd:TIGR03670  309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     963 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 1042
Cdd:TIGR03670  386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    1043 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1122
Cdd:TIGR03670  465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*....
gi 4505941    1123 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1171
Cdd:TIGR03670  545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
565-1172 0e+00

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 750.25  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    565 TKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIiVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLK 644
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEI-SEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLK 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    645 EREYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTY 724
Cdd:PRK07225   84 NGEL---TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-------HTHLEIDPSLILGIGAGMIPYPEHNASPRITM 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    725 QSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRG 804
Cdd:PRK07225  154 GAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERG 233
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    805 FFRSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDEL 880
Cdd:PRK07225  234 LGRSHFFRTYEGEERRYPGGQEDRFEIPDKDV-RGYRGEeAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfLEEPDDFG 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    881 ESTNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG 960
Cdd:PRK07225  313 ISPEKR---RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESG 389
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    961 ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDaVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ 1040
Cdd:PRK07225  390 VVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSG-EDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAE 468
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1041 IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN 1120
Cdd:PRK07225  469 IFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCA 548
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|..
gi 4505941   1121 LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172
Cdd:PRK07225  549 KCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLE 600
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
30-1173 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 700.71  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    30 ISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQaeaqhaSGEVEepprylLKFEQIYLSKPTHwerdgapspmM 109
Cdd:COG0085    7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDF------TGNLS------LEFGDYRLGEPKY----------T 64
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   110 PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllngltdrdlcelnecpldpgGYFIING 189
Cdd:COG0085   65 PEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------------------------GTFIING 116
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   190 SEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARggqgaKKSAIGQRIVAtlpyiKQEVP 268
Cdd:COG0085  117 TERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-----KDGTIYVRIDR-----KRKIP 178
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   269 IIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGSRgAKPGvtKEKRIKYAKEVL---- 343
Cdd:COG0085  179 VTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYRK-LRPG--EPPTIERAEQLLdnlf 249
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   344 ---QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK 409
Cdd:COG0085  250 fdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   410 NLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkahqaraGVSQVLNRLTFASTLSHLRR 484
Cdd:COG0085  330 RMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRR 389
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   485 LN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilEFleewsmenleei 556
Cdd:COG0085  390 LSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------ 444
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   557 spaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQKLLLK 636
Cdd:COG0085  445 --------------------------------------------------------------GFIETPYRKVENGKVTDE 462
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   637 krhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK--------------EVAYCST--YTHCEIHP 700
Cdd:COG0085  463 -------------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgEEVLVPPeeVDYMDVSP 517
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   701 SMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP--------------QKPLVttRSMEY 766
Cdd:COG0085  518 KQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RVGDR 587
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   767 LR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY--KEQESKKGfdQEEVfekp 832
Cdd:COG0085  588 VEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeiEARDTKLG--PEEI---- 661
                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   833 TREtcqgmrhaI-------YDKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELESTNR----------RYtKRDCSTF 895
Cdd:COG0085  662 TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELTPEERllraifgekaRE-VRDTSLR 730
                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   896 LRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIIN 968
Cdd:COG0085  731 VPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLN 810
                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   969 PHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYY 1048
Cdd:COG0085  811 PLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYY 889
                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941  1049 QRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYqvhvcnlCGimaia 1128
Cdd:COG0085  890 LKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV-------CG----- 957
                       1210      1220      1230      1240
                 ....*....|....*....|....*....|....*....|....*
gi 4505941  1129 ntRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1173
Cdd:COG0085  958 --RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
707-1080 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: 553.29  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     707 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 786
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     787 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYDKLDDDGLIAPGVRVSGDDVI 866
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     867 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 944
Cdd:pfam00562  155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     945 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 1023
Cdd:pfam00562  235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 4505941    1024 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1080
Cdd:pfam00562  315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
38-441 6.86e-178

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: 527.72  E-value: 6.86e-178
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941      38 GLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEeppRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRN 117
Cdd:pfam04563    1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRN 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     118 LTYSAPLYVDITKTVIKEGEEQlqtqHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 197
Cdd:pfam04563   78 LTYSAPLYVDLELSVYNGEDIK----PIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQ 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     198 EKMATNTVYVFAKKD-SKYAYTGECRSCLENSSRPTSTIWVSMLARggqgakksAIGQRIVATLPYIKQEVPIIIVFRAL 276
Cdd:pfam04563  154 EHRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVNVLEY--------LSNGTIYFKFPYIKKEIPIVIILRAL 225
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     277 GFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVI--QEQNVALNFIGSRGAKP---GVTKEKRIKYAKEVLQKEMLPHV 351
Cdd:pfam04563  226 GFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHL 305
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     352 GVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNL 431
Cdd:pfam04563  306 GTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLML 385
                          410
                   ....*....|
gi 4505941     432 ELAIKTRIIS 441
Cdd:pfam04563  386 QLLVNAKPIT 395
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
27-547 4.85e-138

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 427.83  E-value: 4.85e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaqhasgEVEEPPRYLLKFEQIYLSKPTHWERDGAPS 106
Cdd:PRK09606    6 RVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPI-----------ETEIEDGVYVELGKIRVGKPVVKEADGSER 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    107 PMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFI 186
Cdd:PRK09606   75 EIYPMEARLRNLTYSAPLYLEMS--PVEGGEEE---EPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFI 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    187 INGSEKVLIAQEKMATNTVYVfaKKDSKYAYTGECRSCLenSSRPTSTIWVSmLARGGQGakksaigqRIVATLPYIKQE 266
Cdd:PRK09606  150 VNGSERVLMTLEDLAPNKILV--EKDERYGDRIEVAKVF--SQRRGYRALVT-VERNRDG--------LLEVSFPSVPGS 216
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    267 VPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAfVIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVLQKE 346
Cdd:PRK09606  217 IPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVA-PGQTKEYRIKRAEYVIDRY 291
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    347 MLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426
Cdd:PRK09606  292 LLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN 371
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    427 KDFNLELAIKTRIISDGLKYSLATGNW-GdqkkahqARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTL 505
Cdd:PRK09606  372 RELSIKTAVRSDVLTERLEHAMATGNWvG-------GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|..
gi 4505941    506 WGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEE 547
Cdd:PRK09606  445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
30-1112 5.81e-71

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: 258.05  E-value: 5.81e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941      30 ISSYFDEKGLVRQQLDSFDEFIQMS----------VQRIVEDAPPIdlqaeaQHASGeveeppRYLLKFEQIYLSKPTHw 99
Cdd:TIGR02013   11 IPEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPI------EDYTG------NIELEYLSYRLGEPKY- 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     100 erdgapspmMPNEARLRNLTYSAPLYVDiTKTVIKEGEEQLQTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpl 179
Cdd:TIGR02013   78 ---------SVEECKERGLTYSAPLKVK-LRLINKEEDGTKEIKEQDVYMGDIPLM-----------TDR---------- 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     180 dpgGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKyaytgecRSCLENSSR--PTSTIWVSMlarggQGAKKSAIGQRIV 257
Cdd:TIGR02013  127 ---GTFIINGAERVVVSQLHRSPGVFFSSEKDTTK-------SGKVLFSARiiPYRGSWLEF-----ETDKKDVLYVRID 191
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     258 AtlpyiKQEVPIIIVFRALGFVSDRDILEHiiydFEDPEMME---MVKPSL--DEAFVIQeqnvalnfigSRGAKPG--V 330
Cdd:TIGR02013  192 R-----KRKLPATVLLRALGYTIDTLILNR----LGSGEYIRntlRKDPTNseEEALVEI----------YRKLRPGepP 252
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     331 TKEKrikyAKEVLQKEM-------LPHVG---VSDFCETKKAYFLGYMVHRLLLAAL--------GRRELDDRDHYGNKR 392
Cdd:TIGR02013  253 TVEA----ARSLLENLFfdpkrydLGRVGrykLNKKLGLDVPESIGVLTKEDIIATIkyliklrnGKGEIDDIDHLGNRR 328
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     393 LDLAGPLLAFLFRGMFKNLLKEVRiyaqkfiDRGKDFNLELA-----IKTRIISDGLKYSLATGNwgdqkkahqaragVS 467
Cdd:TIGR02013  329 IRSVGELLQNQFRVGLARMERIVR-------ERMSTQDTDTLtpqdlINAKPISAAIKEFFGSSQ-------------LS 388
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     468 QVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVgsqpspiLE 543
Cdd:TIGR02013  389 QFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE-------YG 461
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     544 FLEewsmenleeiSPAAIADATKIFVNGCWVGIHKDPEQlmntlRKLRRQMDIIVSEVSMIRDirereiriytdagricr 623
Cdd:TIGR02013  462 FIE----------TPYRKVKDGKVVVTDEIDYLTADEED-----NYVIAQANAPLDENGRFVE----------------- 509
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     624 pllivekqklllkkrhidqlkereynnyswqDLVASGVVEYIDTLEEETVmlamtpddlqekevaycstyTHCEIHPSMI 703
Cdd:TIGR02013  510 -------------------------------DLVVARYRGEITLVSPDQV--------------------DYMDVSPKQV 538
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     704 LGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------GV---------YITNFHVR 743
Cdd:TIGR02013  539 VSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVveyvdakriVIRYDEDE 618
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     744 MDTLAHVLYYP--------------QKPLVTT-------------RSMEylrFRELPAGINSIVAIASYTGYNQEDSVIM 796
Cdd:TIGR02013  619 EEPDGGIDIYRllkyqrsnqdtcinQRPIVSVgdrveagdvladgPSTD---LGELALGRNVLVAFMPWNGYNYEDAILI 695
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     797 NRSAVDRGFFRSVFYRSYK--EQESKKGfdQEEVfekpTRETCQGMRHAIyDKLDDDGLIAPGVRVSGDDVIIGKTVtlP 874
Cdd:TIGR02013  696 SERLVKDDVFTSIHIEEYEveARDTKLG--PEEI----TRDIPNVSEEAL-RNLDENGIVRIGAEVKAGDILVGKVT--P 766
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     875 ENEDELESTNRRYTK---------RDCSTFLRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASR 938
Cdd:TIGR02013  767 KGETELTPEEKLLRAifgekardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGR 846
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     939 HGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--ATPFNDAVNVQKISNLLS 1016
Cdd:TIGR02013  847 HGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPVFDGASEEEIKEYLE 926
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    1017 DYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIA 1096
Cdd:TIGR02013  927 KAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1006
                         1210
                   ....*....|....*.
gi 4505941    1097 HGAAQFLRERLFEASD 1112
Cdd:TIGR02013 1007 YGAAYTLQEMLTVKSD 1022
rpoB CHL00207
RNA polymerase beta subunit; Provisional
84-1116 2.75e-57

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 216.50  E-value: 2.75e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     84 YLLKFEQIYLSKPthwerdgapsPMMPNEARLRNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMlrstycll 163
Cdd:CHL00207   45 LLLFGKNYKLKYP----------KYNLLSAKSYDSNYSIQIYLPLKFINLKTNK----IKFINYLIGNLPKM-------- 102
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    164 nglTDRdlcelnecpldpgGYFIINGSEKVLIAQeKMATNTVYVFAKKDSKYaytgecRSCLENSSRPTSTIWVSMLARg 243
Cdd:CHL00207  103 ---TQR-------------GTFIINGLERVIVSQ-IIRSPGIYFKKEIKKNS------NKIYSATLIPNRGSWIKFELD- 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    244 gqgaKKSAIGQRIVATLpyikqEVPIIIVFRALGfVSDRDILEHIIYDFEDP-------------------EMMEMVKPS 304
Cdd:CHL00207  159 ----KNKEIWIRIDKNR-----KKPLIIFLKALG-LTDQDIYSRLTKSEFLKklkpillnsnsytneeillEIYKNLSPI 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    305 LDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCEtkkayflgyMVHRLLLAALGRRELDD 384
Cdd:CHL00207  229 EPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILS---------IIDKLINLKINKGNFDD 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    385 RDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKF-IDRGKDFNLelaIKTRIISDGLKYSLATGNwgdqkkahqar 463
Cdd:CHL00207  300 IDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICdIDSLSKFNL---INPKPLIALIREFFGSSQ----------- 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    464 agVSQVLNRLTFASTLSHLRRLNS--PIGRDgKLAKP---RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqp 538
Cdd:CHL00207  366 --LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLATNARIN----- 437
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    539 spILEFLEE--WSMENLeeispaaiadatKIFVNGCWVGIHKDPEQLMNTLrklrrqmdiivsevsmIRDIREREIRiyt 616
Cdd:CHL00207  438 --KFGFIETpfYKVING------------KVKKFGNPIYLTADSEDLYRIA----------------PNDINLNKNN--- 484
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    617 dagricrpllivekqklLLKKRHIdqlkEREYNNyswqdlvasgvvEYIDTLEEETVMLAMTPDDlqekevaycstythc 696
Cdd:CHL00207  485 -----------------YFKKNII----PVRYKQ------------EFKTVNPSKVDFIAISPIQ--------------- 516
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    697 eihpsmILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG---------------------------------VYITNF--H 741
Cdd:CHL00207  517 ------VFSIAESLIPFLEHNDANRALMGSNMQRQAVPllypekpivgtgyekqialdsgmtiisltegivVSVSAYkiI 590
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    742 VRMDTLAHVLYYPQK-------------PLV----------TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNR 798
Cdd:CHL00207  591 IQDDNNRYIHYYLQKyqrsnqntcinyrPIVwvgekinigqILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINK 670
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    799 SAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGKTVTLPENED 878
Cdd:CHL00207  671 RLVYEDLFTSIHIEKYEIELRQTKLGSEEI----TRNIPNVSEYSLK-NLDENGIISIGSKVLAGDILVGKITPKGESDQ 745
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    879 ELEST--------NRRYTKrDCSTFLRTSETGIVDQVMVTLNQEG--YKF-----CKIRVRSVRIPQIGDKFASRHGQKG 943
Cdd:CHL00207  746 LPEGKllraifgeKAKDVK-DTSLRMPNGGYGRVIKVEIFSRSKGdeLKFgyylkIRVFIAQIRKIQVGDKLAGRHGNKG 824
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    944 TCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA--------------VNV 1008
Cdd:CHL00207  825 IISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMygseysrilinnklNQA 903
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1009 QKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGE 1088
Cdd:CHL00207  904 SIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGE 983
                        1130      1140
                  ....*....|....*....|....*...
gi 4505941   1089 MERDCQIAHGAAQFLRERLFEASDPYQV 1116
Cdd:CHL00207  984 MEVWALEAFGAAYTLKELLTIKSDDMQG 1011
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
201-394 6.23e-56

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: 192.18  E-value: 6.23e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     201 ATNTVYVFAKKDSKyaytgecrsclenssrPTSTIWVSMLARGGQGAKKSAIGQR-IVATLPYIKQEVPIIIVFRALGFV 279
Cdd:pfam04561    1 RSNGIYVEKELDKN----------------GIIATYTSSLISNRGSWLKLEIDGKtLIWSRPSKKRKIPIVIFLKALGLV 64
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     280 SDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSrGAKPGVTKEKRIKYAKEVLQK-----EMLPHVGVS 354
Cdd:pfam04561   65 SDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLN 143
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 4505941     355 DFCETK--KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLD 394
Cdd:pfam04561  144 EPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
43-1107 2.66e-47

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 184.92  E-value: 2.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     43 QLDSFDEFIQMSV-------QRIVEDAPPIdlqaeaQHASGeveeppRYLLKFEQIYLSKPTHWERdgapspmmpnEARL 115
Cdd:PRK00405   31 QLDSFDWFLQLDVppedeglEEVFRSIFPI------EDFNG------NLSLEFVSYELGEPKYDVE----------ECKE 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    116 RNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpldpgGYFIINGSEKVLI 195
Cdd:PRK00405   89 RGLTYSAPLRVKLRLINKETGE----IKEQEVYMGDIPLM-----------TEN-------------GTFIINGTERVIV 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    196 AQekmatnTVY---VFAKKDSKYAYTGEcrscLENSSR--PTstiwvsmlaRGG----QGAKKSAIGQRIVatlpyIKQE 266
Cdd:PRK00405  141 SQ------LHRspgVYFDHDKDKTSSGK----LLYSARiiPY---------RGSwlefEFDPKDILYVRID-----RRRK 196
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    267 VPIIIVFRALGFvSDRDILEhIIYDFED-PEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQK 345
Cdd:PRK00405  197 LPVTVLLRALGY-SDEEILD-LFYEKEEfGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEK 274
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    346 E--------------ML-----PHVgvsdfcETKKAYF-----------LG----YMV-HRL---------------LLA 375
Cdd:PRK00405  275 DptssreealveiyrRLrpgepPTV------EAARSLLenlffdpkrydLSkvgrYKLnKKLgldededvrvltkedIIA 348
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    376 AL--------GRRELDDRDHYGNKRLDLAGPLLAFLFR-GMfknllkeVRIyaQKFI-DR--GKDFN----LELaIKTRI 439
Cdd:PRK00405  349 TIkylinlrnGKGEVDDIDHLGNRRVRSVGELLQNQFRiGL-------SRM--ERAVrERmsLQDLDtltpQDL-INAKP 418
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    440 ISDGLKYSLATgnwgdqkkaHQaragVSQVL---NRLtfaSTLSHLRRLNS--PIG----------RDgklakprqLHNT 504
Cdd:PRK00405  419 VVAAIKEFFGS---------SQ----LSQFMdqtNPL---SELTHKRRLSAlgPGGltreragfevRD--------VHPT 474
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    505 LWGMVCPAETPEGHAVGLVKNLALMAYI-SVGsqpspileFLEewsmenleeiSPaaiadaTKIFVNGcwvgihkdpeql 583
Cdd:PRK00405  475 HYGRICPIETPEGPNIGLINSLATYARVnEYG--------FIE----------TP------YRKVVDG------------ 518
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    584 mntlrklrrqmdIIVSEVSMIRDIREREIRI------YTDAGRICRPLLIVekqklllkkrhidqlkeREYNNYswqDLV 657
Cdd:PRK00405  519 ------------KVTDEIVYLTADEEDNYVIaqanapLDEDGRFVDELVTA-----------------RYKGEF---VLV 566
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    658 ASGVVEYIDtleeetvmlamtpddlqekevaycstythceIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQA----- 732
Cdd:PRK00405  567 PPEEVDYMD-------------------------------VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAvpllr 615
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    733 ---------M-----------------GV---------YITNFHVRMDTLAHVLY-------------YPQKPLVTTR-- 762
Cdd:PRK00405  616 peaplvgtgMerrvardsgavvvakrdGVveyvdasriVVRVEELDPGEDGVDIYnlikfqrsnqntcINQRPIVKVGdr 695
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    763 -----------SMEYlrfRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrSYKEQE-----SKKGfdQE 826
Cdd:PRK00405  696 vekgdvladgpSTDN---GELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSI---HIEEYEieardTKLG--PE 767
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    827 EVfekpTREtcqgmrhaIYD-------KLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDEL------------Estnrry 887
Cdd:PRK00405  768 EI----TRD--------IPNvseealrNLDESGIVRIGAEVKPGDILVGK-VT-PKGETELtpeekllraifgE------ 827
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    888 tK----RDCStfLR--TSETGIVDQVMV-TLNQEGY-------KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQED 953
Cdd:PRK00405  828 -KardvKDTS--LRvpHGEEGTVIDVKVfTRIEQGDelppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVED 904
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    954 MPFTCEGiTP-DIIINPHAIPSRMTIGHLIECLQGKVSANKGE-IgdATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNG 1031
Cdd:PRK00405  905 MPYLEDG-TPvDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIkF--ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDG 981
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1032 FTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMErdcqI----AHGAAQFLRERL 1107
Cdd:PRK00405  982 RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEME----VwaleAYGAAYTLQEML 1057
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
1082-1174 2.99e-42

RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.


Pssm-ID: 461355 [Multi-domain]  Cd Length: 87  Bit Score: 148.89  E-value: 2.99e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    1082 GGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYACKLLFQE 1161
Cdd:pfam04560    1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYN------KCPICKGETDISPGYIPESFKLLFQE 74
                           90
                   ....*....|...
gi 4505941    1162 LMSMSIAPRMMSV 1174
Cdd:pfam04560   75 LQSLGIDPRLLLE 87
rpoB CHL00001
RNA polymerase beta subunit
38-1112 1.54e-38

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 156.60  E-value: 1.54e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941     38 GLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaQHASGEVEepprYLLKFEQIYLSKPTHWERDgapspmmpneARLRN 117
Cdd:CHL00001   14 GFNQIQFEGFCRFIDQGLTEELSKFPKI------EDTDQEIE----FQLFVETYQLVEPLIKERD----------AVYES 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    118 LTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMlrstycllngltdrdlcelnecplDPGGYFIINGSEKVLIAQ 197
Cdd:CHL00001   74 LTYSSELYVPAGLIWKKSRDMQEQT----VFIGNIPLM------------------------NSLGTFIINGIYRVVINQ 125
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    198 eKMATNTVYVFAKKDSK--YAYTGEC------RSCLENSSRptSTIWVsmlarggqgakksaigqRIVAtlpyiKQEVPI 269
Cdd:CHL00001  126 -ILRSPGIYYRSELDHNgiSVYTGTIisdwggRLELEIDRK--ARIWA-----------------RVSR-----KQKISI 180
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    270 IIVFRALGFvSDRDILEHIIYdfedPEMMemvkpsldeafviqeqnvaLNFIGSRGAKPGVTKEKRIkyakeVLQKEMLP 349
Cdd:CHL00001  181 LVLLSAMGL-NLREILDNVCY----PEIF-------------------LSFLNDKEKKKIGSKENAI-----LEFYQQFA 231
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    350 HVGV------SDFCETKKAYF-----LGY-----MVHRL---------------LLAA--------LGRRELDDRDHYGN 390
Cdd:CHL00001  232 CVGGdpvfseSLCKELQKKFFqqrceLGRigrrnMNRKLnldipenntfllpqdVLAAadyligmkFGMGTLDDIDHLKN 311
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    391 KRLDLAGPLLaflfRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLkyslaTGNWGDQKKAHQaragVSQVL 470
Cdd:CHL00001  312 KRIRSVADLL----QDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPL-----TTTYESFFGSHP----LSQFL 378
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    471 NRLTFASTLSHLRRLNS--PIGRDGKLA--KPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYI-SVGSQPSPILEFL 545
Cdd:CHL00001  379 DQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIgHWGSLESPFYEIS 458
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    546 EEWSMENLEEISPAaiadatkifvngcwvgihKDpEQLMntlrklrrqmdiIVSEVSMI--RDIREREIriyTDAgricr 623
Cdd:CHL00001  459 ERSKEERMVYLSPS------------------ED-EYYM------------IAAGNSLAlnQGIQEEQV---VPA----- 499
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    624 pllivekqklllkkRHidqlkEREYNNYSWQdlvasgvveyidtleeetvmlamtpddlqekEVAYCStythceIHPSMI 703
Cdd:CHL00001  500 --------------RY-----RQEFLTIAWE-------------------------------QIHLRS------IFPFQY 523
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    704 LGVCASIIPFPDHNQSPRNTYQSAMGKQAM----------------------GV-----------YI------------- 737
Cdd:CHL00001  524 FSIGASLIPFLEHNDANRALMGSNMQRQAVplsrsekcivgtglerqvaldsGVvaiaehegkiiYTdtdkiilsgngdt 603
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    738 TNFHVRM------DTLAHvlyypQKPLVttRSMEYLRFRELPA------------GINSIVAIASYTGYNQEDSVIMNRS 799
Cdd:CHL00001  604 LSIPLVMyqrsnkNTCMH-----QKPQV--RRGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDAVLISER 676
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    800 AVDRGFFRSVFYRSYKEQ--ESKKGFdqeevfEKPTRETCQ----GMRHaiydkLDDDGLIAPGVRVSGDDVIIGKtVTL 873
Cdd:CHL00001  677 LVYEDIYTSFHIRKYEIQthVTSQGP------ERITKEIPHleahLLRN-----LDKNGIVMLGSWVETGDILVGK-LTP 744
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    874 PENEDELESTNRR----------YTKRDCSTFLRTSETGIVDQVMvTLNQEGYKFCKIRVRSVRIPQ-----IGDKFASR 938
Cdd:CHL00001  745 QEAEESSYAPEGRllraifgiqvSTSKETCLKLPIGGRGRVIDVR-WIQKKGGSSYNPETIHVYILQkreiqVGDKVAGR 823
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    939 HGQKGTCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVsankGEIGDA----TPFnDAVNVQKIS- 1012
Cdd:CHL00001  824 HGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLA----GDLLNRhyriAPF-DERYEQEASr 897
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1013 NLLSDYGYHLR--------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGR 1078
Cdd:CHL00001  898 KLVFSELYEASkqtanpwvfepeypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGR 977
                        1210      1220      1230
                  ....*....|....*....|....*....|....
gi 4505941   1079 SRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1112
Cdd:CHL00001  978 SKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
378-1112 1.55e-34

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 144.68  E-value: 1.55e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    378 GRRELDDRDHYGNKRLDLAGPLLAflfrgmfkNLLKEVRIYAQKFIdRGKDFNLELAIKTRIISDGLKYSLATGNWGDQK 457
Cdd:PRK09603  450 NQGKIDDRDHLGNRRIRAVGELLA--------NELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFF 520
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    458 KAHQaragVSQVLNRLTFASTLSHLRRLnSPIGrDGKLAK------PRQLHNTLWGMVCPAETPEGHAVGLVKNLAlmAY 531
Cdd:PRK09603  521 MGGQ----LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS--TF 592
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    532 ISVGSqpspiLEFLEewsmenleeispaaiADATKIfVNGcwvgihkdpeqlmntlrklrrqmdIIVSEVSMIRDIRERE 611
Cdd:PRK09603  593 TRVND-----LGFIE---------------APYKKV-VDG------------------------KVVGETIYLTAIQEDS 627
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    612 IRIYTDAGRIcrpllivekqklllkkrhidqlkerEYNNYSWQDLvasgvveyIDTLEEETVMLAmtpddlqEKevaycS 691
Cdd:PRK09603  628 HIIAPASTPI-------------------------DEEGNILGDL--------IETRVEGEIVLN-------EK-----S 662
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    692 TYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------------- 733
Cdd:PRK09603  663 KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswgaikanragvvekid 742
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    734 ------------GVYITNFHVRMDTLAHV-LYYPQKPLVTT-------------RSMEYlrfRELPAGINSIVAIASYTG 787
Cdd:PRK09603  743 skniyilgegkeEAYIDAYSLQKNLRTNQnTSFNQVPIVKVgdkveagqiiadgPSMDR---GELALGKNVRVAFMPWNG 819
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    788 YNQEDSVIMNRSAVDRGFFRSV--FYRSYKEQESKKGFdqeevfEKPTRETcQGMRHAIYDKLDDDGLIAPGVRVSGDDV 865
Cdd:PRK09603  820 YNFEDAIVVSERITKDDIFTSThiYEKEVDARELKHGV------EEFTADI-PDVKEEALAHLDESGIVKVGTYVSAGMI 892
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    866 IIGKTV------TLPENE---------------------DELEST---------------------------------NR 885
Cdd:PRK09603  893 LVGKTSpkgeikSTPEERllraifgdkaghvvnkslycpPSLEGTvidvkvftkkgyekdarvlsayeeekakldmehFD 972
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    886 RYTKRDCSTFLRT----------SETGIVDQVM----------------VTLN----------QEGY------------- 916
Cdd:PRK09603  973 RLTMLNREELLRVssllsqaileEPFSHNGKDYkegdqipkeeiasinrFTLAslvkkyskevQNHYeitknnfleqkkv 1052
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    917 -----------------------KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIP 973
Cdd:PRK09603 1053 lgeeheeklsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVP 1132
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    974 SRMTIGHLIECLQGKVSANKG-----------------------EIGD-------------------------------- 998
Cdd:PRK09603 1133 SRMNIGQILEMHLGLVGKEFGkqiasmledktkdfakelrakmlEIANainekdpltihalencsdeelleyakdwskgv 1212
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    999 --ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPME 1076
Cdd:PRK09603 1213 kmAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVG 1292
                         970       980       990
                  ....*....|....*....|....*....|....*.
gi 4505941   1077 GRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1112
Cdd:PRK09603 1293 GKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
567-629 3.57e-30

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: 113.62  E-value: 3.57e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4505941     567 IFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIvSEVSMIRDIREREIRIYTDAGRICRPLLIVE 629
Cdd:pfam04566    1 VFLNGNLIGVHRDPEELVETLRKLRRSGKIS-EEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
368-1112 2.88e-28

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 124.35  E-value: 2.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    368 MVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFR-GMFKNLLKEVRIYAQKFIDR--GKDFnlelaIKTRIISDGL 444
Cdd:PRK14844  449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRtGLLKLERAVVDSMSTSSLDKvsPSDF-----INPKVLTNVL 523
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    445 KyslatgnwgDQKKAHQaragVSQVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAV 520
Cdd:PRK14844  524 R---------DFFNSSQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    521 GLVKNLALMAYIS-VGSQPSPILEFLEEWSMENLEEISPA-----AIADAT-KIFVNGCWVgihkdpeQLMNTLRKLRRQ 593
Cdd:PRK14844  591 GLINSLAIYARINkYGFIESPYRKVVNRVVTDQIEYLSAIdeglyYIADTSaKLDENNCFV-------DDMLYCRYAGSF 663
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    594 MDIIVSEVSMIrDIREREIrIYTDAGRIcrPLLivekqklllkkrhidqlkereYNNYSWQDLVASGVVEYIDTLEEETV 673
Cdd:PRK14844  664 VMVSSDQVSYI-DVSPKQV-ISVAASLI--PFL---------------------ENDDANRALMGSNMQRQAVPLLKPTA 718
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    674 MLAMTPddlQEKEVAYCSTythceihpSMILGVCASIIPFPDHNQSPRNTYQSAmGKQAMGVYItnFHVR-MDTLAHVLY 752
Cdd:PRK14844  719 PLVATG---MESFVASGSG--------AVVLAKRDGIVDSSDSNSIVIRAFDKE-RVNYLDVDI--YHLRkFQRSNHNTC 784
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    753 YPQKPLVttRSMEYLR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrsYKEQESK 820
Cdd:PRK14844  785 INQKPLV--CVGDYVKegdviadgpainSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSI----HIEEFEC 858
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    821 KGFDQEEVFEKPTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGK-----TVTLP--------------------- 874
Cdd:PRK14844  859 VVHDTPLGSEKITRAIPGVNEENLY-HLDDSGIVKIGTRVGPGYILVGKvtpkpSLSLPpetkllmtifgeksfdcadss 937
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    875 -----------------------ENE-----------------------------DELE-------STNRR--------- 886
Cdd:PRK14844  938 lytspdvegtvidvqvftrrgveENErallikqkeindfekerdyiinvtseyfyDELKkllinsgSQDREkfdsiereq 1017
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    887 -----YTKRDCSTFLRTSETGIVDQVMVTLNQ---------EGYKFCKIRVRSVRI-------PQIGDKFASRHGQKGTC 945
Cdd:PRK14844 1018 wwgigLKNQSISEQVKSLKKDFDEKVSHAIAQfkrkveklhEGYDLPQGVSMSVKVfiavkhsLQPGDKMAGRHGNKGVI 1097
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    946 GIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG--------KVS--------------------------- 990
Cdd:PRK14844 1098 SRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgeKVGnildeinkiksafckgirslnddnftk 1177
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941    991 -------------ANKGEIGDA---TPFNDAVN----------------------------------------VQKIS-N 1013
Cdd:PRK14844 1178 faaayldnkkienIDDDEITASvlnTPNKNALNdelnelvenylnscksaysnlrnflievyscgsnvsicnnIRDISdN 1257
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4505941   1014 LLSDYGYHLR------------------------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRA 1063
Cdd:PRK14844 1258 NLIEFARKLRdgipvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARS 1337
                         970       980       990      1000
                  ....*....|....*....|....*....|....*....|....*....
gi 4505941   1064 RGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1112
Cdd:PRK14844 1338 VGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
468-531 4.92e-28

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: 107.61  E-value: 4.92e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4505941     468 QVLNRLTFASTLSHLRRLNSPIG---RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAY 531
Cdd:pfam04565    1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
653-700 3.98e-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: 93.37  E-value: 3.98e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 4505941     653 WQDLVASGVVEYIDTLEEETVMLAMTPDDL-----QEKEVAYCSTYTHCEIHP 700
Cdd:pfam04567    1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLeessrEEREGPYAHTYTHCEIHP 53
 
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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