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Conserved domains on  [gi|147903615|ref|NP_001083372|]
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polymerase (RNA) II (DNA directed) polypeptide B, 140kDa L homeolog [Xenopus laevis]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RNA_pol_Rpb2_7 super family cl27131
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
27-923 0e+00

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.


The actual alignment was detected with superfamily member PRK08565:

Pssm-ID: 331952  Cd Length: 1103  Bit Score: 896.62  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhtTGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565    2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  106 SPMMPNEARLRNLTYSAPLYVDITktVVKEGEEQiqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565   69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTAECRSCLENSSRPTssiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565  144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565  210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565  286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565  366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  504 TLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565  440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565  520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  662 VEYIDTLEEETVMLAMTPDDLQEKgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565  596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565  669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  822 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565  749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
                         890       900
                  ....*....|....*....|....*.
gi 147903615  898 TSETGIVDQVMVTLNQEGYKFCKIRV 923
Cdd:PRK08565  825 HGEKGIVDTVLITESPEGNKLVKVRV 850
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
27-923 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291  Cd Length: 1103  Bit Score: 896.62  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhtTGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565    2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  106 SPMMPNEARLRNLTYSAPLYVDITktVVKEGEEQiqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565   69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTAECRSCLENSSRPTssiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565  144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565  210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565  286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565  366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  504 TLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565  440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565  520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  662 VEYIDTLEEETVMLAMTPDDLQEKgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565  596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565  669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  822 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565  749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
                         890       900
                  ....*....|....*....|....*.
gi 147903615  898 TSETGIVDQVMVTLNQEGYKFCKIRV 923
Cdd:PRK08565  825 HGEKGIVDTVLITESPEGNKLVKVRV 850
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
39-923 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  Cd Length: 866  Bit Score: 788.30  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  39 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhttgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 118
Cdd:cd00653    1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 119 TYSAPLYVDITKTVVKEGEeqiqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 198
Cdd:cd00653   70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 199 KMATNTVYVFakkDSKYAYTAECRSCLENSSRPTSSIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 278
Cdd:cd00653  146 QRSPNVIIVE---DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 279 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 358
Cdd:cd00653  202 --------------------------------------ALKYIGKRF--------------------------------- 210
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 359 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 438
Cdd:cd00653  211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 439 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMICPAETPEG 517
Cdd:cd00653  287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 518 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 597
Cdd:cd00653  366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 598 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkrrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 677
Cdd:cd00653  382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 678 tpddlqekgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 757
Cdd:cd00653  395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 758 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 837
Cdd:cd00653  460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 838 QGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 914
Cdd:cd00653  536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615

                 ....*....
gi 147903615 915 GYKFCKIRV 923
Cdd:cd00653  616 GNKLVKVYI 624
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription];
15-923 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription];


Pssm-ID: 223163  Cd Length: 1060  Bit Score: 711.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   15 DEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaqhttgeVEEPPRYLLKFEQIYLS 94
Cdd:COG0085     3 DSYTGKKRIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPI------------ESYNGNTELEYGSYRLG 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   95 KPthwerdgapSPMMPNEARLRNLTYSAPLYVDITKtVVKEGEEQIQTQhqKTFIGKIPIMLRstycllngltdrdlcel 174
Cdd:COG0085    71 EP---------PKFYPEECRLRGLTYSAPLYVKLRL-VVNETGEEIKEQ--EVYMGDIPLMTR----------------- 121
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  175 necpldpGGYFIINGSEKVLIAQEKMATNTVYV--FAKKDSKYAYTAecrSCLENSSrptSSIWVSMlarggqgAKKSAI 252
Cdd:COG0085   122 -------GGYFIINGTERVIVSQEHRSPGVIFVekKDKTGSKVLYVA---RVIPYRG---SWLEFEF-------DPKDNL 181
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  253 GQRIVAtlpyiKQEVPIIIVFRALGFVSDRDILEHI----IYDFEDPEMMEMVKPSLDEA--FVIQEQNvALNFIGSRGA 326
Cdd:COG0085   182 YVRIDR-----KRKIPVTILLRALGLETDEEIIEAFggdeLTDLVPPEGEEALLEIYEEAkgEKITARN-ALELIGSRVF 255
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  327 KPGVT--KEKRIKYAKEVLQKEMLPHVGVS----DFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLL 400
Cdd:COG0085   256 VVKRYdaKEGRYKRAKYVLDKELLPHLGEAgeryDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELL 335
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  401 AFLFRGMFKNLLKEVRIYAQKFIDRgkdfnlELAIKTRIISDGLKYSLATGNWGdqkkahqaRAGVSQVLNRLTFASTLS 480
Cdd:COG0085   336 ENLFRVGLSRMERDVKERLEKADKR------DTLVPQDLINAKPIHALITGFFG--------RSQLSQFMDQTNPLSELS 401
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  481 HLRRLNS-PIGRDGKLAKPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYIS-VGSQPSPILEFL-EEWSMENLEEIS 557
Cdd:COG0085   402 HKRRLSAlGLSRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINeYGFLETPYRKVLdGSLVVDEIEYLS 481
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  558 paaiADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDiivSEVSMIRDIRER----EIRIYTDAGRICRPLLIVEKQKL 633
Cdd:COG0085   482 ----ADEEDVYVIGQANGTLDEPGELVEELVECRRGGS---GEVSVADPEGVDymdvSPKQVVSVGRSLIPFLEHDDANR 554
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  634 LLKRRHIDQLKEREYnnYSWQDLVASGVvEYIDTLEEETVMLAMTPDDlqekgvaycstYTHCEIHPSMILGVCASIIPF 713
Cdd:COG0085   555 ALMGSNMQRQAVPLL--RTEAPLVGTGM-EYLDAEDSGAAVIAKRPGV-----------VTHVEISPIVILGIEASLIPY 620
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  714 PDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTrsmeylrfRELPAGINSIVAIASYTGYNQEDS 793
Cdd:COG0085   621 PEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFMPWNGYNYEDA 692
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  794 VIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTREtcqgmrHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVtl 873
Cdd:COG0085   693 IIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVS------EEALRNLDEDGIIRIGAEVKGGDILVGKVT-- 764
                         890       900       910       920       930
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 147903615  874 PENEDELESTNRRYT-----KRDCSTFLRTSETGIVDQVMVTLNQEG----YKFCKIRV 923
Cdd:COG0085   765 PKGETELTPEERLLRifgekVRDTSLRVPHGEEGIVDDVQVFTREDGdpgvNKLVKVYV 823
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
38-441 9.96e-179

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: 282429  Cd Length: 396  Bit Score: 527.72  E-value: 9.96e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   38 GLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHTTGEVEeppRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRN 117
Cdd:pfam04563   1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRN 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  118 LTYSAPLYVDITKtVVKEGEEQIqtqHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 197
Cdd:pfam04563  78 LTYSAPLYVDLEL-SVYNGEDIK---PIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQ 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  198 EKMATNTVYVFAKKD-SKYAYTAECRSCLENSSRPTSSIWVSMLARggqgakksAIGQRIVATLPYIKQEVPIIIVFRAL 276
Cdd:pfam04563 154 EHRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVNVLEY--------LSNGTIYFKFPYIKKEIPIVIILRAL 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  277 GFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVI--QEQNVALNFIGSRGAKP---GVTKEKRIKYAKEVLQKEMLPHV 351
Cdd:pfam04563 226 GFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHL 305
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  352 GVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNL 431
Cdd:pfam04563 306 GTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLML 385
                         410
                  ....*....|
gi 147903615  432 ELAIKTRIIS 441
Cdd:pfam04563 386 QLLVNAKPIT 395
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
567-923 7.78e-130

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  Cd Length: 599  Bit Score: 407.88  E-value: 7.78e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  567 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKER 646
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  647 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 726
Cdd:TIGR03670  80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  727 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 806
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  807 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 882
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 147903615  883 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRV 346
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
27-923 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291  Cd Length: 1103  Bit Score: 896.62  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhtTGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565    2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  106 SPMMPNEARLRNLTYSAPLYVDITktVVKEGEEQiqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565   69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTAECRSCLENSSRPTssiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565  144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565  210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565  286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565  366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  504 TLWGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565  440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565  520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  662 VEYIDTLEEETVMLAMTPDDLQEKgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565  596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565  669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  822 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565  749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
                         890       900
                  ....*....|....*....|....*.
gi 147903615  898 TSETGIVDQVMVTLNQEGYKFCKIRV 923
Cdd:PRK08565  825 HGEKGIVDTVLITESPEGNKLVKVRV 850
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
39-923 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  Cd Length: 866  Bit Score: 788.30  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  39 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhttgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 118
Cdd:cd00653    1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 119 TYSAPLYVDITKTVVKEGEeqiqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 198
Cdd:cd00653   70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 199 KMATNTVYVFakkDSKYAYTAECRSCLENSSRPTSSIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 278
Cdd:cd00653  146 QRSPNVIIVE---DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 279 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 358
Cdd:cd00653  202 --------------------------------------ALKYIGKRF--------------------------------- 210
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 359 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 438
Cdd:cd00653  211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 439 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMICPAETPEG 517
Cdd:cd00653  287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 518 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 597
Cdd:cd00653  366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 598 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkrrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 677
Cdd:cd00653  382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 678 tpddlqekgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 757
Cdd:cd00653  395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 758 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 837
Cdd:cd00653  460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 838 QGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 914
Cdd:cd00653  536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615

                 ....*....
gi 147903615 915 GYKFCKIRV 923
Cdd:cd00653  616 GNKLVKVYI 624
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription];
15-923 0e+00

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription];


Pssm-ID: 223163  Cd Length: 1060  Bit Score: 711.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   15 DEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaqhttgeVEEPPRYLLKFEQIYLS 94
Cdd:COG0085     3 DSYTGKKRIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPI------------ESYNGNTELEYGSYRLG 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   95 KPthwerdgapSPMMPNEARLRNLTYSAPLYVDITKtVVKEGEEQIQTQhqKTFIGKIPIMLRstycllngltdrdlcel 174
Cdd:COG0085    71 EP---------PKFYPEECRLRGLTYSAPLYVKLRL-VVNETGEEIKEQ--EVYMGDIPLMTR----------------- 121
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  175 necpldpGGYFIINGSEKVLIAQEKMATNTVYV--FAKKDSKYAYTAecrSCLENSSrptSSIWVSMlarggqgAKKSAI 252
Cdd:COG0085   122 -------GGYFIINGTERVIVSQEHRSPGVIFVekKDKTGSKVLYVA---RVIPYRG---SWLEFEF-------DPKDNL 181
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  253 GQRIVAtlpyiKQEVPIIIVFRALGFVSDRDILEHI----IYDFEDPEMMEMVKPSLDEA--FVIQEQNvALNFIGSRGA 326
Cdd:COG0085   182 YVRIDR-----KRKIPVTILLRALGLETDEEIIEAFggdeLTDLVPPEGEEALLEIYEEAkgEKITARN-ALELIGSRVF 255
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  327 KPGVT--KEKRIKYAKEVLQKEMLPHVGVS----DFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLL 400
Cdd:COG0085   256 VVKRYdaKEGRYKRAKYVLDKELLPHLGEAgeryDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRRLRLVGELL 335
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  401 AFLFRGMFKNLLKEVRIYAQKFIDRgkdfnlELAIKTRIISDGLKYSLATGNWGdqkkahqaRAGVSQVLNRLTFASTLS 480
Cdd:COG0085   336 ENLFRVGLSRMERDVKERLEKADKR------DTLVPQDLINAKPIHALITGFFG--------RSQLSQFMDQTNPLSELS 401
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  481 HLRRLNS-PIGRDGKLAKPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYIS-VGSQPSPILEFL-EEWSMENLEEIS 557
Cdd:COG0085   402 HKRRLSAlGLSRERAGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARINeYGFLETPYRKVLdGSLVVDEIEYLS 481
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  558 paaiADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDiivSEVSMIRDIRER----EIRIYTDAGRICRPLLIVEKQKL 633
Cdd:COG0085   482 ----ADEEDVYVIGQANGTLDEPGELVEELVECRRGGS---GEVSVADPEGVDymdvSPKQVVSVGRSLIPFLEHDDANR 554
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  634 LLKRRHIDQLKEREYnnYSWQDLVASGVvEYIDTLEEETVMLAMTPDDlqekgvaycstYTHCEIHPSMILGVCASIIPF 713
Cdd:COG0085   555 ALMGSNMQRQAVPLL--RTEAPLVGTGM-EYLDAEDSGAAVIAKRPGV-----------VTHVEISPIVILGIEASLIPY 620
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  714 PDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTrsmeylrfRELPAGINSIVAIASYTGYNQEDS 793
Cdd:COG0085   621 PEHNQSPYNLYKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFMPWNGYNYEDA 692
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  794 VIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTREtcqgmrHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVtl 873
Cdd:COG0085   693 IIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVS------EEALRNLDEDGIIRIGAEVKGGDILVGKVT-- 764
                         890       900       910       920       930
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 147903615  874 PENEDELESTNRRYT-----KRDCSTFLRTSETGIVDQVMVTLNQEG----YKFCKIRV 923
Cdd:COG0085   765 PKGETELTPEERLLRifgekVRDTSLRVPHGEEGIVDDVQVFTREDGdpgvNKLVKVYV 823
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
38-441 9.96e-179

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: 282429  Cd Length: 396  Bit Score: 527.72  E-value: 9.96e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   38 GLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHTTGEVEeppRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRN 117
Cdd:pfam04563   1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRN 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  118 LTYSAPLYVDITKtVVKEGEEQIqtqHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 197
Cdd:pfam04563  78 LTYSAPLYVDLEL-SVYNGEDIK---PIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQ 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  198 EKMATNTVYVFAKKD-SKYAYTAECRSCLENSSRPTSSIWVSMLARggqgakksAIGQRIVATLPYIKQEVPIIIVFRAL 276
Cdd:pfam04563 154 EHRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVNVLEY--------LSNGTIYFKFPYIKKEIPIVIILRAL 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  277 GFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVI--QEQNVALNFIGSRGAKP---GVTKEKRIKYAKEVLQKEMLPHV 351
Cdd:pfam04563 226 GFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHL 305
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  352 GVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNL 431
Cdd:pfam04563 306 GTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLML 385
                         410
                  ....*....|
gi 147903615  432 ELAIKTRIIS 441
Cdd:pfam04563 386 QLLVNAKPIT 395
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
27-547 7.17e-140

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587  Cd Length: 494  Bit Score: 430.53  E-value: 7.17e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaqhttgEVEEPPRYLLKFEQIYLSKPTHWERDGAPS 106
Cdd:PRK09606   6 RVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPI-----------ETEIEDGVYVELGKIRVGKPVVKEADGSER 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 107 PMMPNEARLRNLTYSAPLYVDITktVVKEGEEQiqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFI 186
Cdd:PRK09606  75 EIYPMEARLRNLTYSAPLYLEMS--PVEGGEEE---EPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFI 149
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 187 INGSEKVLIAQEKMATNTVYVfaKKDSKYAYTAECRSCLenSSRPTSSIWVSmLARGGQGakksaigqRIVATLPYIKQE 266
Cdd:PRK09606 150 VNGSERVLMTLEDLAPNKILV--EKDERYGDRIEVAKVF--SQRRGYRALVT-VERNRDG--------LLEVSFPSVPGS 216
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 267 VPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAfVIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVLQKE 346
Cdd:PRK09606 217 IPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVA-PGQTKEYRIKRAEYVIDRY 291
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 347 MLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426
Cdd:PRK09606 292 LLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN 371
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 427 KDFNLELAIKTRIISDGLKYSLATGNW-GdqkkahqARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTL 505
Cdd:PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNWvG-------GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444
                        490       500       510       520
                 ....*....|....*....|....*....|....*....|..
gi 147903615 506 WGMICPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEE 547
Cdd:PRK09606 445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
567-923 7.78e-130

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  Cd Length: 599  Bit Score: 407.88  E-value: 7.78e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  567 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLKER 646
Cdd:TIGR03670   1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  647 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 726
Cdd:TIGR03670  80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  727 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 806
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  807 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 882
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 147903615  883 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRV 346
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
565-923 2.25e-120

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972  Cd Length: 605  Bit Score: 383.16  E-value: 2.25e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 565 TKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIiVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKRRHIDQLK 644
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEI-SEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLK 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 645 EREYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKgvaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTY 724
Cdd:PRK07225  84 NGEL---TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-------HTHLEIDPSLILGIGAGMIPYPEHNASPRITM 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 725 QSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRG 804
Cdd:PRK07225 154 GAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERG 233
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615 805 FFRSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDEL 880
Cdd:PRK07225 234 LGRSHFFRTYEGEERRYPGGQEDRFEIPDKDV-RGYRGEeAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfLEEPDDFG 312
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 147903615 881 ESTNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923
Cdd:PRK07225 313 ISPEKR---RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRV 352
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
707-923 5.75e-85

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: 306936  Cd Length: 370  Bit Score: 280.56  E-value: 5.75e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  707 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 786
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYALNKFQRSDQNTYVLCYPQKPLVKTGAVEKGGFGELPLGQNAIVAVMSYT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  787 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYDKLDDDGLIAPGVRVSGDDVI 866
Cdd:pfam00562  81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARDTKLG-PIEEITRDPPNV-----SEEAYKKLDEDGIVRVGAEVKPGDIL 154
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 147903615  867 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRV 923
Cdd:pfam00562 155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPHGEEGVVDDVLVTLNPGGNKMVKVYI 212
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
201-394 6.63e-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: 309623  Cd Length: 185  Bit Score: 192.95  E-value: 6.63e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  201 ATNTVYVFAKKDSKyaytaecrsclenssrPTSSIWVSMLARGGQGAKKSAIGQR-IVATLPYIKQEVPIIIVFRALGFV 279
Cdd:pfam04561   1 RSNGIYVEKELDKN----------------GIGATYTSSLISNRGSWLKLEIDGKtLIWSRPSKKRKIPIVIFLKALGLV 64
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  280 SDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGsRGAKPGVTKEKRIKYAKEVLQK-----EMLPHVGVS 354
Cdd:pfam04561  65 SDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLN 143
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 147903615  355 DFCETK--KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLD 394
Cdd:pfam04561 144 EPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
567-629 5.91e-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: 309626  Cd Length: 62  Bit Score: 115.14  E-value: 5.91e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 147903615  567 IFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIvSEVSMIRDIREREIRIYTDAGRICRPLLIVE 629
Cdd:pfam04566   1 VFLNGTLIGVHRDPEELVRTLRKLRRSGKIS-EEVSIVRDIRQKEVYINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
468-531 1.73e-27

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 309625  Cd Length: 67  Bit Score: 108.35  E-value: 1.73e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 147903615  468 QVLNRLTFASTLSHLRRLNSPIG---RDGKLAKPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAY 531
Cdd:pfam04565   1 QVLDRTNPLSELSHLRRVSSLRGglfRERKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
30-880 2.16e-25

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  Cd Length: 1065  Bit Score: 113.22  E-value: 2.16e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615    30 ISSYFDEKGLVRQQLDSFDEFIQMS----------VQRIVEDAPPIdlqaeaQHTTGeveeppRYLLKFEQIYLSKPTHw 99
Cdd:TIGR02013   11 IPEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPI------EDYTG------NIELEYLSYRLGEPKY- 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   100 erdgapspmMPNEARLRNLTYSAPLYVDiTKTVVKEGEEQIQTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpl 179
Cdd:TIGR02013   78 ---------SVEECKERGLTYSAPLKVK-LRLINKEEDGTKEIKEQDVYMGDIPLM-----------TDR---------- 126
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   180 dpgGYFIINGSEKVLIAQEKMATNTVYvfakkDSKYAYTAECRSCLENSSRPTSSIWVSMlarggQGAKKSAIGQRIVAt 259
Cdd:TIGR02013  127 ---GTFIINGAERVVVSQLHRSPGVFF-----SSEKDTTKSGKVLFSARIIPYRGSWLEF-----ETDKKDVLYVRIDR- 192
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   260 lpyiKQEVPIIIVFRALGFVSDRDILEHiiydFEDPEMME---MVKPSL--DEAFVIQeqnvalnfigSRGAKPG--VTK 332
Cdd:TIGR02013  193 ----KRKLPATVLLRALGYTIDTLILNR----LGSGEYIRntlRKDPTNseEEALVEI----------YRKLRPGepPTV 254
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   333 EKrikyAKEVLQKEM-------LPHVG---VSDFCETKKAYFLGYMVHRLLLAAL--------GRRELDDRDHYGNKRLD 394
Cdd:TIGR02013  255 EA----ARSLLENLFfdpkrydLGRVGrykLNKKLGLDVPESIGVLTKEDIIATIkyliklrnGKGEIDDIDHLGNRRIR 330
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   395 LAGPLLAFLFRGMFKNLLKEVRiyaqkfiDRGKDFNLELA-----IKTRIISDGLKYSLATGNwgdqkkahqaragVSQV 469
Cdd:TIGR02013  331 SVGELLQNQFRVGLARMERIVR-------ERMSTQDTDTLtpqdlINAKPISAAIKEFFGSSQ-------------LSQF 390
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   470 LNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYISVgsqpspiLEFL 545
Cdd:TIGR02013  391 MDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE-------YGFI 463
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   546 EewsmenleeiSPAAIADATKIFVNGCWVGIHKDPEQlmntlRKLRRQMDIIVSEVSMIRDirereiriytdagricrpl 625
Cdd:TIGR02013  464 E----------TPYRKVKDGKVVVTDEIDYLTADEED-----NYVIAQANAPLDENGRFVE------------------- 509
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   626 livekqklllkrrhidqlkereynnyswqDLVASGVVEYIDTLEEETVmlamtpddlqekgvaycstyTHCEIHPSMILG 705
Cdd:TIGR02013  510 -----------------------------DLVVARYRGEITLVSPDQV--------------------DYMDVSPKQVVS 540
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   706 VCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------GV---------YITNFHVRMD 745
Cdd:TIGR02013  541 VAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVveyvdakriVIRYDEDEEE 620
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   746 TLAHVLYYP--------------QKPLVTT-------------RSMEylrFRELPAGINSIVAIASYTGYNQEDSVIMNR 798
Cdd:TIGR02013  621 PDGGIDIYRllkyqrsnqdtcinQRPIVSVgdrveagdvladgPSTD---LGELALGRNVLVAFMPWNGYNYEDAILISE 697
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   799 SAVDRGFFRSVFYRSYK--EQESKKGfdQEEVfekpTRETCQGMRHAIyDKLDDDGLIAPGVRVSGDDVIIGKTVtlPEN 876
Cdd:TIGR02013  698 RLVKDDVFTSIHIEEYEveARDTKLG--PEEI----TRDIPNVSEEAL-RNLDENGIVRIGAEVKAGDILVGKVT--PKG 768

                   ....
gi 147903615   877 EDEL 880
Cdd:TIGR02013  769 ETEL 772
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
653-700 2.09e-22

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: 309627  Cd Length: 52  Bit Score: 93.36  E-value: 2.09e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 147903615  653 WQDLVASGVVEYIDTLEEETVMLAMTPDDL----QEKGVAYCSTYTHCEIHP 700
Cdd:pfam04567   1 WSDLLKEGVIEYLDAEEEETSMIAMTPEDLeesrEEKEGERTHTYTHCEIHP 52
rpoB CHL00001
RNA polymerase beta subunit
38-559 8.27e-18

RNA polymerase beta subunit


Pssm-ID: 214330  Cd Length: 1070  Bit Score: 88.81  E-value: 8.27e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   38 GLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaQHTTGEVEepprYLLKFEQIYLSKPTHWERDgapspmmpneARLRN 117
Cdd:CHL00001   14 GFNQIQFEGFCRFIDQGLTEELSKFPKI------EDTDQEIE----FQLFVETYQLVEPLIKERD----------AVYES 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  118 LTYSAPLYVDITKTVVKEGEEQIQTqhqkTFIGKIPIMlrstycllngltdrdlcelnecplDPGGYFIINGSEKVLIAQ 197
Cdd:CHL00001   74 LTYSSELYVPAGLIWKKSRDMQEQT----VFIGNIPLM------------------------NSLGTFIINGIYRVVINQ 125
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  198 eKMATNTVYVFAKKDSK--YAYTA----ECRSCLENSSRPTSSIWVsmlarggqgakksaigqRIVAtlpyiKQEVPIII 271
Cdd:CHL00001  126 -ILRSPGIYYRSELDHNgiSVYTGtiisDWGGRLELEIDRKARIWA-----------------RVSR-----KQKISILV 182
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  272 VFRALGFvSDRDILEHIIYdfedPEMMemvkpsldeafviqeqnvaLNFIGSRGAKPGVTKEKRIkyakeVLQKEMLPHV 351
Cdd:CHL00001  183 LLSAMGL-NLREILDNVCY----PEIF-------------------LSFLNDKEKKKIGSKENAI-----LEFYQQFACV 233
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  352 GV------SDFCETKKAYF-----LGY-----MVHRL---------------LLAA--------LGRRELDDRDHYGNKR 392
Cdd:CHL00001  234 GGdpvfseSLCKELQKKFFqqrceLGRigrrnMNRKLnldipenntfllpqdVLAAadyligmkFGMGTLDDIDHLKNKR 313
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  393 LDLAGPLLaflfRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLkyslaTGNWGDQKKAHQaragVSQVLNR 472
Cdd:CHL00001  314 IRSVADLL----QDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPL-----TTTYESFFGSHP----LSQFLDQ 380
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  473 LTFASTLSHLRRLNS--PIGRDGKLA--KPRQLHNTLWGMICPAETPEGHAVGLVKNLALMAYI-SVGSQPSPILEFLEE 547
Cdd:CHL00001  381 TNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIgHWGSLESPFYEISER 460
                         570
                  ....*....|..
gi 147903615  548 WSMENLEEISPA 559
Cdd:CHL00001  461 SKEERMVYLSPS 472
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
43-530 2.42e-15

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749  Cd Length: 1112  Bit Score: 80.92  E-value: 2.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   43 QLDSFDEFIQMSV-------QRIVEDAPPIdlqaeaQHTTGeveeppRYLLKFEQIYLSKPTHWERdgapspmmpnEARL 115
Cdd:PRK00405   31 QLDSFDWFLQLDVppedeglEEVFRSIFPI------EDFNG------NLSLEFVSYELGEPKYDVE----------ECKE 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  116 RNLTYSAPLYVDITKTVVKEGEeqiqTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpldpgGYFIINGSEKVLI 195
Cdd:PRK00405   89 RGLTYSAPLRVKLRLINKETGE----IKEQEVYMGDIPLM-----------TEN-------------GTFIINGTERVIV 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  196 AQekmatntVYVFAKKDS----KYAYTAE---CR-SCLENSSRPTSSIWVsmlarggqgakksaigqrivatlpYI--KQ 265
Cdd:PRK00405  141 SQlhr-spgVYFDHDKDKtssgKLLYSARiipYRgSWLEFEFDPKDILYV------------------------RIdrRR 195
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  266 EVPIIIVFRALGFvSDRDILEhIIYDFED-PEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQ 344
Cdd:PRK00405  196 KLPVTVLLRALGY-SDEEILD-LFYEKEEfGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLE 273
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  345 KE--------------ML-----PHVgvsdfcETKKAYF-----------LG----YMV-HRL---------------LL 374
Cdd:PRK00405  274 KDptssreealveiyrRLrpgepPTV------EAARSLLenlffdpkrydLSkvgrYKLnKKLgldededvrvltkedII 347
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  375 AAL--------GRRELDDRDHYGNKRLDLAGPLLAFLFR-GMfknllkeVRIyaQKFI-DR--GKDFN----LELaIKTR 438
Cdd:PRK00405  348 ATIkylinlrnGKGEVDDIDHLGNRRVRSVGELLQNQFRiGL-------SRM--ERAVrERmsLQDLDtltpQDL-INAK 417
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  439 IISDGLKYSLATgnwgdqkkaHQaragVSQVL---NRLtfaSTLSHLRRLNS--PIG----------RDgklakprqLHN 503
Cdd:PRK00405  418 PVVAAIKEFFGS---------SQ----LSQFMdqtNPL---SELTHKRRLSAlgPGGltreragfevRD--------VHP 473
                         570       580
                  ....*....|....*....|....*..
gi 147903615  504 TLWGMICPAETPEGHAVGLVKNLALMA 530
Cdd:PRK00405  474 THYGRICPIETPEGPNIGLINSLATYA 500
rpoB CHL00207
RNA polymerase beta subunit; Provisional
84-877 3.06e-14

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397  Cd Length: 1077  Bit Score: 77.05  E-value: 3.06e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615   84 YLLKFEQIYLSKPthwerdgapsPMMPNEARLRNLTYSAPLYVDITKTVVKEGeeqiQTQHQKTFIGKIPIMlrstycll 163
Cdd:CHL00207   45 LLLFGKNYKLKYP----------KYNLLSAKSYDSNYSIQIYLPLKFINLKTN----KIKFINYLIGNLPKM-------- 102
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  164 nglTDRdlcelnecpldpgGYFIINGSEKVLIAQeKMATNTVYVFAKKDSKYaytaecRSCLENSSRPTSSIWVSMLARg 243
Cdd:CHL00207  103 ---TQR-------------GTFIINGLERVIVSQ-IIRSPGIYFKKEIKKNS------NKIYSATLIPNRGSWIKFELD- 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  244 gqgaKKSAIGQRIVATLpyikqEVPIIIVFRALGfVSDRDILEHIIYDFEDP-------------------EMMEMVKPS 304
Cdd:CHL00207  159 ----KNKEIWIRIDKNR-----KKPLIIFLKALG-LTDQDIYSRLTKSEFLKklkpillnsnsytneeillEIYKNLSPI 228
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  305 LDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCEtkkayflgyMVHRLLLAALGRRELDD 384
Cdd:CHL00207  229 EPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILS---------IIDKLINLKINKGNFDD 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  385 RDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKF-IDRGKDFNLelaIKTRIISDGLKYSLATGNwgdqkkahqar 463
Cdd:CHL00207  300 IDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICdIDSLSKFNL---INPKPLIALIREFFGSSQ----------- 365
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  464 agVSQVLNRLTFASTLSHLRRLNS--PIGRDgKLAKP---RQLHNTLWGMICPAETPEGHAVGLVKNLALMAYISvgsqp 538
Cdd:CHL00207  366 --LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLATNARIN----- 437
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  539 spILEFLEE--WSMENLeeispaaiadatKIFVNGCWVGIHKDPEQLMNTLRKlrrqmDIIVSEVSMIRDIRereiriyt 616
Cdd:CHL00207  438 --KFGFIETpfYKVING------------KVKKFGNPIYLTADSEDLYRIAPN-----DINLNKNNYFKKNI-------- 490
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  617 dagricrpLLIVEKQKLLLKrrhidqlkereynNYSWQDLVAsgvveyidtleeetvmlamtpddlqekgvaycstythc 696
Cdd:CHL00207  491 --------IPVRYKQEFKTV-------------NPSKVDFIA-------------------------------------- 511
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  697 eIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG---------------------------------VYITNF--H 741
Cdd:CHL00207  512 -ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPllypekpivgtgyekqialdsgmtiisltegivVSVSAYkiI 590
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  742 VRMDTLAHVLYYPQK-------------PLV----------TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNR 798
Cdd:CHL00207  591 IQDDNNRYIHYYLQKyqrsnqntcinyrPIVwvgekinigqILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINK 670
                         810       820       830       840       850       860       870
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147903615  799 SAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGKTVTLPENE 877
Cdd:CHL00207  671 RLVYEDLFTSIHIEKYEIELRQTKLGSEEI----TRNIPNVSEYSLK-NLDENGIISIGSKVLAGDILVGKITPKGESD 744
PRK09603 PRK09603
bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
378-870 5.54e-13

bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed


Pssm-ID: 181983  Cd Length: 2890  Bit Score: 73.42  E-value: 5.54e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  378 GRRELDDRDHYGNKRLDLAGPLLAflfrgmfkNLLKEVRIYAQKFIdRGKDFNLELAIKTRIISDGLKYSLATGNWGDQK 457
Cdd:PRK09603  450 NQGKIDDRDHLGNRRIRAVGELLA--------NELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFF 520
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  458 KAHQaragVSQVLNRLTFASTLSHLRRLnSPIGrDGKLAK------PRQLHNTLWGMICPAETPEGHAVGLVKNLAlmAY 531
Cdd:PRK09603  521 MGGQ----LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS--TF 592
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  532 ISVGSqpspiLEFLEewsmenleeispaaiADATKIfVNGcwvgihkdpeqlmntlrklrrqmdIIVSEVSMIRDIRERE 611
Cdd:PRK09603  593 TRVND-----LGFIE---------------APYKKV-VDG------------------------KVVGETIYLTAIQEDS 627
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  612 IRIYTDAGRIcrpllivekqklllkrrhidqlkerEYNNYSWQDLvasgvveyIDTLEEETVMLAmtpddlqEKgvaycS 691
Cdd:PRK09603  628 HIIAPASTPI-------------------------DEEGNILGDL--------IETRVEGEIVLN-------EK-----S 662
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  692 TYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------------- 733
Cdd:PRK09603  663 KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswgaikanragvvekid 742
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  734 ------------GVYITNFHVRMDTLAHV-LYYPQKPLVTT-------------RSMEYlrfRELPAGINSIVAIASYTG 787
Cdd:PRK09603  743 skniyilgegkeEAYIDAYSLQKNLRTNQnTSFNQVPIVKVgdkveagqiiadgPSMDR---GELALGKNVRVAFMPWNG 819
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  788 YNQEDSVIMNRSAVDRGFFRSV--FYRSYKEQESKKGfdqeevFEKPTRETcQGMRHAIYDKLDDDGLIAPGVRVSGDDV 865
Cdd:PRK09603  820 YNFEDAIVVSERITKDDIFTSThiYEKEVDARELKHG------VEEFTADI-PDVKEEALAHLDESGIVKVGTYVSAGMI 892

                  ....*
gi 147903615  866 IIGKT 870
Cdd:PRK09603  893 LVGKT 897
PRK14844 PRK14844
bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
368-874 6.67e-13

bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional


Pssm-ID: 173305  Cd Length: 2836  Bit Score: 73.12  E-value: 6.67e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  368 MVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFR-GMFKNLLKEVRIYAQKFIDR--GKDFnlelaIKTRIISDGL 444
Cdd:PRK14844  449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRtGLLKLERAVVDSMSTSSLDKvsPSDF-----INPKVLTNVL 523
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  445 KyslatgnwgDQKKAHQaragVSQVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMICPAETPEGHAV 520
Cdd:PRK14844  524 R---------DFFNSSQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  521 GLVKNLALMAYIS-VGSQPSPILEFLEEWSMENLEEISPA-----AIADAT-KIFVNGCWVgihkdpeQLMNTLRKLRRQ 593
Cdd:PRK14844  591 GLINSLAIYARINkYGFIESPYRKVVNRVVTDQIEYLSAIdeglyYIADTSaKLDENNCFV-------DDMLYCRYAGSF 663
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  594 MDIIVSEVSMIrDIREREIrIYTDAGRIcrPLLIVEKQKLLL-----KRRHIDQLKEReynnyswQDLVASGVVEYIDTl 668
Cdd:PRK14844  664 VMVSSDQVSYI-DVSPKQV-ISVAASLI--PFLENDDANRALmgsnmQRQAVPLLKPT-------APLVATGMESFVAS- 731
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  669 EEETVMLAmtpddlQEKGVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMgVYITNFHVRMDTLA 748
Cdd:PRK14844  732 GSGAVVLA------KRDGIVDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPL-VCVGDYVKEGDVIA 804
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147903615  749 hvlyypQKPLVTTrsmeylrfRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrsYKEQESKKGFDQEEV 828
Cdd:PRK14844  805 ------DGPAINS--------GELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSI----HIEEFECVVHDTPLG 866
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*.
gi 147903615  829 FEKPTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGKTVTLP 874
Cdd:PRK14844  867 SEKITRAIPGVNEENLY-HLDDSGIVKIGTRVGPGYILVGKVTPKP 911
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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