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Conserved domains on  [gi|489205283|ref|WP_003114335|]
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DNA-directed RNA polymerase subunit beta [Pseudomonas aeruginosa]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 11478603)

DNA-directed RNA polymerase subunit beta catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Graphical summary

 Zoom to residue level

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List of domain hits

Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
1-1357 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


:

Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 2256.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    1 MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEqfrDVGLHAAFKSVFPIISYSGNAALEYVGYRLG 80
Cdd:PRK00405    1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   81 EPAFDVKECVLRGVTFAVPLRVKVRLIifdressNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVF 160
Cdd:PRK00405   78 EPKYDVEECKERGLTYSAPLRVKLRLI-------NKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVY 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  161 FDHDRGKThSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKget 240
Cdd:PRK00405  151 FDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKE--- 226
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  241 lnlelvpqrlrgevasidikdgsgkviveqgrritarhinqlekagvsqLEVPFDYLIGRTIAKAIVHPATGEIIAECNT 320
Cdd:PRK00405  227 -------------------------------------------------IEVPVEYLLGKVLAEDIVDEETGEVLAEAND 257
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  321 ELTLDLlakvakaqvvrietlytndidCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERY 400
Cdd:PRK00405  258 EITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRY 316
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  401 DLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAV 480
Cdd:PRK00405  317 DLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAV 396
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  481 KERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 560
Cdd:PRK00405  397 RERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHY 476
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  561 GRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVA 640
Cdd:PRK00405  477 GRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVT 556
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  641 VRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 720
Cdd:PRK00405  557 ARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAV 636
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  721 VVARRGGVIDSVDASRVVVRVadDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELA 800
Cdd:PRK00405  637 VVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELA 714
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  801 LGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGA 880
Cdd:PRK00405  715 LGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA 794
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  881 EVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRdgverdsralsiekmqldq 960
Cdd:PRK00405  795 EVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------- 855
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  961 irkdlneefrivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrq 1040
Cdd:PRK00405      --------------------------------------------------------------------------------
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1041 llddkfedkkrkLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGV 1120
Cdd:PRK00405  856 ------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGV 923
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1121 PSRMNVGQILETHLGLAAKGLGEKinrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrggvpMATP 1200
Cdd:PRK00405  924 PSRMNIGQILETHLGWAAKGLGIK----------------------------------------------------FATP 951
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1201 VFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 1280
Cdd:PRK00405  952 VFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQF 1031
                        1290      1300      1310      1320      1330      1340      1350
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489205283 1281 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357
Cdd:PRK00405 1032 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
1-1357 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 2256.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    1 MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEqfrDVGLHAAFKSVFPIISYSGNAALEYVGYRLG 80
Cdd:PRK00405    1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   81 EPAFDVKECVLRGVTFAVPLRVKVRLIifdressNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVF 160
Cdd:PRK00405   78 EPKYDVEECKERGLTYSAPLRVKLRLI-------NKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVY 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  161 FDHDRGKThSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKget 240
Cdd:PRK00405  151 FDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKE--- 226
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  241 lnlelvpqrlrgevasidikdgsgkviveqgrritarhinqlekagvsqLEVPFDYLIGRTIAKAIVHPATGEIIAECNT 320
Cdd:PRK00405  227 -------------------------------------------------IEVPVEYLLGKVLAEDIVDEETGEVLAEAND 257
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  321 ELTLDLlakvakaqvvrietlytndidCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERY 400
Cdd:PRK00405  258 EITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRY 316
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  401 DLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAV 480
Cdd:PRK00405  317 DLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAV 396
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  481 KERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 560
Cdd:PRK00405  397 RERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHY 476
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  561 GRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVA 640
Cdd:PRK00405  477 GRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVT 556
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  641 VRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 720
Cdd:PRK00405  557 ARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAV 636
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  721 VVARRGGVIDSVDASRVVVRVadDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELA 800
Cdd:PRK00405  637 VVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELA 714
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  801 LGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGA 880
Cdd:PRK00405  715 LGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA 794
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  881 EVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRdgverdsralsiekmqldq 960
Cdd:PRK00405  795 EVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------- 855
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  961 irkdlneefrivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrq 1040
Cdd:PRK00405      --------------------------------------------------------------------------------
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1041 llddkfedkkrkLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGV 1120
Cdd:PRK00405  856 ------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGV 923
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1121 PSRMNVGQILETHLGLAAKGLGEKinrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrggvpMATP 1200
Cdd:PRK00405  924 PSRMNIGQILETHLGWAAKGLGIK----------------------------------------------------FATP 951
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1201 VFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 1280
Cdd:PRK00405  952 VFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQF 1031
                        1290      1300      1310      1320      1330      1340      1350
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489205283 1281 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357
Cdd:PRK00405 1032 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
8-1354 0e+00

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: 1824.66  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283     8 KKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVK 87
Cdd:TIGR02013    1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    88 ECVLRGVTFAVPLRVKVRLIIFDRessnKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGk 167
Cdd:TIGR02013   81 ECKERGLTYSAPLKVKLRLINKEE----DGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   168 THSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSteeilnafyatnvfhikgetlnlelvp 247
Cdd:TIGR02013  156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   248 qrlrgevasidikdgsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakaivhpatgeiiaecnteltldll 327
Cdd:TIGR02013      --------------------------------------------------------------------------------
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   328 akvakaqvvrIETLYTNDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGR 407
Cdd:TIGR02013  209 ----------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGR 278
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   408 MKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMA 487
Cdd:TIGR02013  279 YKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQ 358
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   488 ESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIE 567
Cdd:TIGR02013  359 DTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIE 438
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   568 TPEGPNIGLINSLATYARTNKYGFLESPYRVVKD--SLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLN 645
Cdd:TIGR02013  439 TPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDgkVVVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRG 518
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   646 EFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARR 725
Cdd:TIGR02013  519 EITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKR 598
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   726 GGVIDSVDASRVVVRvADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNM 805
Cdd:TIGR02013  599 GGVVEYVDAKRIVIR-YDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNV 677
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   806 RVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAG 885
Cdd:TIGR02013  678 LVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAG 757
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   886 DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDgverdsralsiekmqldqirkdl 965
Cdd:TIGR02013  758 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE----------------------- 814
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   966 neefrivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddk 1045
Cdd:TIGR02013      --------------------------------------------------------------------------------
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1046 fedkkrklqQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMN 1125
Cdd:TIGR02013  815 ---------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMN 885
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1126 VGQILETHLGLAAKGLGEKinrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrgGVPMATPVFDGA 1205
Cdd:TIGR02013  886 IGQILETHLGWAGKRLGRK-------------------------------------------------GVPIATPVFDGA 916
                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1206 KEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRF 1285
Cdd:TIGR02013  917 SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 996
                         1290      1300      1310      1320      1330      1340
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489205283  1286 GEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIEL 1354
Cdd:TIGR02013  997 GEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
12-1357 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: 1630.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   12 RKDFSKLPDVMDVPYLLAIQLDSYREFLqagatkeqfrDVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKECVL 91
Cdd:COG0085     1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   92 RGVTFAVPLRVKVRLIifdressNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKthsS 171
Cdd:COG0085    71 RDLTYAAPLYVKVRLV-------NKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---S 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  172 GKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYST-EEILNAFYatnvfhikgetlnlelvpqrl 250
Cdd:COG0085   141 GKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFG--------------------- 199
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  251 rgevasidikdgsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakaivhpatgeiiaecnteltldllakv 330
Cdd:COG0085       --------------------------------------------------------------------------------
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  331 akaqvvrietlytnDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKF 410
Cdd:COG0085   200 --------------DDPIQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKI 265
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  411 NRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESE 490
Cdd:COG0085   266 NKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVE 345
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  491 GLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 570
Cdd:COG0085   346 AITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPE 425
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  571 GPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVK 650
Cdd:COG0085   426 GPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLV 505
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  651 APEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLvgtgmernvardsgvcvvarrggvid 730
Cdd:COG0085   506 PPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL-------------------------- 559
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  731 svdasrvvvrvaddevetgeagvDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNMRVAFM 810
Cdd:COG0085   560 -----------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFM 616
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  811 PWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVG 890
Cdd:COG0085   617 PWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVG 696
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  891 KVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDgverdsralsiekmqldqirkdlneefr 970
Cdd:COG0085   697 KVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE---------------------------- 748
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  971 ivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddkfedkk 1050
Cdd:COG0085       --------------------------------------------------------------------------------
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1051 rklqQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQIL 1130
Cdd:COG0085   749 ----EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVL 824
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1131 ETHLGLAAKGLGEKInrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrggvpmATPVFDGAKEREI 1210
Cdd:COG0085   825 ETHLGWAAALLGRRV----------------------------------------------------ATPVFDGAPEEEI 852
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1211 KAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV 1290
Cdd:COG0085   853 RELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEV 932
                        1290      1300      1310      1320      1330      1340
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489205283 1291 WALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357
Cdd:COG0085   933 WALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
27-1355 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: 874.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   27 LLAIQLDSYREFLQagatkeqfrdVGLHAAFKSVFPIISYS--GNAALEYVGYRLGEP---------AFDVKECVLRGVT 95
Cdd:cd00653     1 LVKQQIDSFNYFLN----------VGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   96 FAVPLRVKVRLIIFDREssnkaikDIKEQEVYMGEIPLMTE------------------------NGTFIINGTERVIVS 151
Cdd:cd00653    71 YSAPLYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIIN 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  152 QLHRSPGVFFDHDrgkthSSGKLLYSARIIP----YRGSWLDFEFDPKDCV-FVRIDRRrklpasvllralgysteeiln 226
Cdd:cd00653   144 QEQRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDRiYVRIDLK--------------------- 197
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  227 afyatnvfhikgetlnlelvpqrlrgevasidikdgsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakai 306
Cdd:cd00653       --------------------------------------------------------------------------------
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  307 vhpatgeiiaecnteltldllakvakaqvvrietlytndidcgpfisdtlkidntsNQLEALVEIYRmmrpgepptkeaa 386
Cdd:cd00653   198 --------------------------------------------------------RQEEALKYIGK------------- 208
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  387 etlfgnlffsaerydlsavgrmKFnrrigrteiegpgvlskEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAE 466
Cdd:cd00653   209 ----------------------RF-----------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQ 249
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  467 NQFRVGLVRVERAVKERLSMAESEG--LMPQDLINAKPVAAAIKEFFGSSQ------------LSQFMDQNNPLSEITHK 532
Cdd:cd00653   250 NLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHK 329
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  533 RRVSAlgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNkyGFLESPYRVVKdslvtdeivfls 612
Cdd:cd00653   330 RRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------ 392
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  613 aieeadhviaqasatlnekgqlvdelvavrhlneftvkapEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQR 692
Cdd:cd00653   393 ----------------------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQK 432
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  693 QAVPT----------------LRADKPLVGTGMERNVARDsgvcvvarrggvidsvdasrvvvrvaddevetgeagvdiy 756
Cdd:cd00653   433 QAVGTpalnqqyrmdtklyllLYPQKPLVGTGIEEYIAFG---------------------------------------- 472
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  757 nltkytrsnqntcinqrplvskgdvvargdiladgpstdmgELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836
Cdd:cd00653   473 -----------------------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSI 511
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  837 HIQELTCVARDTKLGPEEIT-ADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGETQLTPeekllraIFGEKA 915
Cdd:cd00653   512 HYKKYEIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKA 584
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  916 SDVKDTSLRVPTGTKGTVIDVQVFTRDgverdsralsiekmqldqirkdlneefrivegatferlraalvgakaeggpal 995
Cdd:cd00653   585 RDVRDTSLKYPGGEKGIVDDVKIFSRE----------------------------------------------------- 611
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  996 kkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddkfedkkrklqqgddLAPGVLKIVKVYLAIKR 1075
Cdd:cd00653   612 ---------------------------------------------------------------LNDGGNKLVKVYIRQKR 628
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINrmleeqrkv 1155
Cdd:cd00653   629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGD--------- 699
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1156 aelrkflheiyneiggreenldelgdneilalaknlrggvpmATPvFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQ 1235
Cdd:cd00653   700 ------------------------------------------ATP-FDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEP 736
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1236 FERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNG 1315
Cdd:cd00653   737 LEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVA 816
                        1370      1380      1390      1400      1410
                  ....*....|....*....|....*....|....*....|....*....|
gi 489205283 1316 RTKMYKNIV----------DGDHRMEAGMPESFNVLIKEIRSLGIDIELE 1355
Cdd:cd00653   817 RVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
722-1279 1.24e-165

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: 499.36  E-value: 1.24e-165
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   722 VARRGGVIDSVDASRVVVRVADdevetGEAGVDIYNLTKYTRSNQNT---CINQRPLVSKGDVVArgdiladgpsTDMGE 798
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEA----------GGFGE 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   799 LALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQEltCVARDTKLGP-EEITADIPNVGEAALNKLDEAGIVY 877
Cdd:pfam00562   66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   878 VGAEVQAGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFtrdgverdsralsiekmq 957
Cdd:pfam00562  144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   958 ldqirkdlneefrivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisd 1037
Cdd:pfam00562      --------------------------------------------------------------------------------
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1038 rrqllddkfedkkrklqqgdDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNP 1117
Cdd:pfam00562  200 --------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1118 LGVPSRMNVGQILETHLGLAAKGLgekinrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrgGVPM 1197
Cdd:pfam00562  260 HGVPSRMTIGQLLETHLGKAAALL----------------------------------------------------GVFV 287
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1198 ATPVFDGAKER--EIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG 1275
Cdd:pfam00562  288 DATPFDGASTEveDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLG 367

                   ....
gi 489205283  1276 GKAQ 1279
Cdd:pfam00562  368 GRAR 371
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
1-1357 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 2256.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    1 MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEqfrDVGLHAAFKSVFPIISYSGNAALEYVGYRLG 80
Cdd:PRK00405    1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   81 EPAFDVKECVLRGVTFAVPLRVKVRLIifdressNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVF 160
Cdd:PRK00405   78 EPKYDVEECKERGLTYSAPLRVKLRLI-------NKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVY 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  161 FDHDRGKThSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIKget 240
Cdd:PRK00405  151 FDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKE--- 226
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  241 lnlelvpqrlrgevasidikdgsgkviveqgrritarhinqlekagvsqLEVPFDYLIGRTIAKAIVHPATGEIIAECNT 320
Cdd:PRK00405  227 -------------------------------------------------IEVPVEYLLGKVLAEDIVDEETGEVLAEAND 257
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  321 ELTLDLlakvakaqvvrietlytndidCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERY 400
Cdd:PRK00405  258 EITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRY 316
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  401 DLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAV 480
Cdd:PRK00405  317 DLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAV 396
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  481 KERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 560
Cdd:PRK00405  397 RERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHY 476
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  561 GRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVA 640
Cdd:PRK00405  477 GRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVT 556
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  641 VRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVC 720
Cdd:PRK00405  557 ARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAV 636
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  721 VVARRGGVIDSVDASRVVVRVadDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELA 800
Cdd:PRK00405  637 VVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELA 714
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  801 LGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGA 880
Cdd:PRK00405  715 LGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGA 794
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  881 EVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRdgverdsralsiekmqldq 960
Cdd:PRK00405  795 EVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------- 855
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  961 irkdlneefrivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrq 1040
Cdd:PRK00405      --------------------------------------------------------------------------------
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1041 llddkfedkkrkLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGV 1120
Cdd:PRK00405  856 ------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGV 923
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1121 PSRMNVGQILETHLGLAAKGLGEKinrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrggvpMATP 1200
Cdd:PRK00405  924 PSRMNIGQILETHLGWAAKGLGIK----------------------------------------------------FATP 951
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1201 VFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQF 1280
Cdd:PRK00405  952 VFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQF 1031
                        1290      1300      1310      1320      1330      1340      1350
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489205283 1281 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357
Cdd:PRK00405 1032 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
8-1354 0e+00

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: 1824.66  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283     8 KKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQFRDVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVK 87
Cdd:TIGR02013    1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    88 ECVLRGVTFAVPLRVKVRLIIFDRessnKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGk 167
Cdd:TIGR02013   81 ECKERGLTYSAPLKVKLRLINKEE----DGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   168 THSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSteeilnafyatnvfhikgetlnlelvp 247
Cdd:TIGR02013  156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   248 qrlrgevasidikdgsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakaivhpatgeiiaecnteltldll 327
Cdd:TIGR02013      --------------------------------------------------------------------------------
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   328 akvakaqvvrIETLYTNDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGR 407
Cdd:TIGR02013  209 ----------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGR 278
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   408 MKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMA 487
Cdd:TIGR02013  279 YKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQ 358
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   488 ESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIE 567
Cdd:TIGR02013  359 DTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIE 438
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   568 TPEGPNIGLINSLATYARTNKYGFLESPYRVVKD--SLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLN 645
Cdd:TIGR02013  439 TPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDgkVVVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRG 518
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   646 EFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARR 725
Cdd:TIGR02013  519 EITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKR 598
                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   726 GGVIDSVDASRVVVRvADDEVETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNM 805
Cdd:TIGR02013  599 GGVVEYVDAKRIVIR-YDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNV 677
                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   806 RVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAG 885
Cdd:TIGR02013  678 LVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAG 757
                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   886 DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDgverdsralsiekmqldqirkdl 965
Cdd:TIGR02013  758 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE----------------------- 814
                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   966 neefrivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddk 1045
Cdd:TIGR02013      --------------------------------------------------------------------------------
                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1046 fedkkrklqQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMN 1125
Cdd:TIGR02013  815 ---------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMN 885
                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1126 VGQILETHLGLAAKGLGEKinrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrgGVPMATPVFDGA 1205
Cdd:TIGR02013  886 IGQILETHLGWAGKRLGRK-------------------------------------------------GVPIATPVFDGA 916
                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1206 KEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRF 1285
Cdd:TIGR02013  917 SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRF 996
                         1290      1300      1310      1320      1330      1340
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489205283  1286 GEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIEL 1354
Cdd:TIGR02013  997 GEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
12-1357 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: 1630.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   12 RKDFSKLPDVMDVPYLLAIQLDSYREFLqagatkeqfrDVGLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKECVL 91
Cdd:COG0085     1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   92 RGVTFAVPLRVKVRLIifdressNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKthsS 171
Cdd:COG0085    71 RDLTYAAPLYVKVRLV-------NKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---S 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  172 GKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYST-EEILNAFYatnvfhikgetlnlelvpqrl 250
Cdd:COG0085   141 GKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFG--------------------- 199
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  251 rgevasidikdgsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakaivhpatgeiiaecnteltldllakv 330
Cdd:COG0085       --------------------------------------------------------------------------------
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  331 akaqvvrietlytnDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKF 410
Cdd:COG0085   200 --------------DDPIQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKI 265
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  411 NRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESE 490
Cdd:COG0085   266 NKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVE 345
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  491 GLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 570
Cdd:COG0085   346 AITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPE 425
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  571 GPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVK 650
Cdd:COG0085   426 GPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLV 505
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  651 APEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLvgtgmernvardsgvcvvarrggvid 730
Cdd:COG0085   506 PPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL-------------------------- 559
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  731 svdasrvvvrvaddevetgeagvDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNMRVAFM 810
Cdd:COG0085   560 -----------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFM 616
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  811 PWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVG 890
Cdd:COG0085   617 PWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVG 696
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  891 KVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDgverdsralsiekmqldqirkdlneefr 970
Cdd:COG0085   697 KVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE---------------------------- 748
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  971 ivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddkfedkk 1050
Cdd:COG0085       --------------------------------------------------------------------------------
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1051 rklqQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQIL 1130
Cdd:COG0085   749 ----EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVL 824
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1131 ETHLGLAAKGLGEKInrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrggvpmATPVFDGAKEREI 1210
Cdd:COG0085   825 ETHLGWAAALLGRRV----------------------------------------------------ATPVFDGAPEEEI 852
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1211 KAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV 1290
Cdd:COG0085   853 RELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEV 932
                        1290      1300      1310      1320      1330      1340
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489205283 1291 WALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELETE 1357
Cdd:COG0085   933 WALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-1354 0e+00

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 1435.87  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    1 MAYSYTEKKRIRKDFSKLPDVMDVPYLLAIQLDSYREFLQAGATKEQfrdvGLHAAFKSVFPIISYSGNAALEYVGYRLG 80
Cdd:PRK09603    1 MSKKIPLKNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKES----GIEKVFKSIFPIQDEHNRITLEYAGCEFG 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   81 EPAFDVKECVLRGVTFAVPLRVKVRLIIFDRESSNK---AIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSP 157
Cdd:PRK09603   77 KSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGeknGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSP 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  158 GVFFDHDRGKThSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVFHIK 237
Cdd:PRK09603  157 GVIFKEEESST-SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYE 235
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  238 GETLNLELVPQRLRGEVaSIDIKDGSGKVIVEQGRRITARHINQLEKAGVSQLEVPFDYLIGRTIAKAIVHPatgeiiae 317
Cdd:PRK09603  236 NDKYLIPFASLDANQRM-EFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVG-------- 306
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  318 cnTELTLDLLAKVAKAQVVRI------ETLYTNDIDCG-------PFISD---------TLKIDNtSNQLEAlVEIYRMM 375
Cdd:PRK09603  307 --KEVLLDMLTQLDKNKLEKIhdlgvqEFVIINDLALGhdasiihSFSADseslkllkqTEKIDD-ENALAA-IRIHKVM 382
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  376 RPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGrteIEGPG---VLSKEDIIDVLKTLVDIRNGKGIVDDIDH 452
Cdd:PRK09603  383 KPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLG---LHVPDyitTLTHEDIITTVKYLMKIKNNQGKIDDRDH 459
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  453 LGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAES--EGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEIT 530
Cdd:PRK09603  460 LGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVT 539
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  531 HKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVF 610
Cdd:PRK09603  540 HKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIY 619
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  611 LSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNM 690
Cdd:PRK09603  620 LTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNM 699
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  691 QRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRVVVRVADDEvetgEAGVDIYNLTKYTRSNQNTCI 770
Cdd:PRK09603  700 QRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKE----EAYIDAYSLQKNLRTNQNTSF 775
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  771 NQRPLVSKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKL 850
Cdd:PRK09603  776 NQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKH 855
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  851 GPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTK 930
Cdd:PRK09603  856 GVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLE 935
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  931 GTVIDVQVFTRDGVERDSRALSI---EKMQLDQIRKD----LNEEfrivegatfERLRAALVGAKAE-------GGPALK 996
Cdd:PRK09603  936 GTVIDVKVFTKKGYEKDARVLSAyeeEKAKLDMEHFDrltmLNRE---------ELLRVSSLLSQAIleepfshNGKDYK 1006
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  997 KGTEITDDYLDGLERGQWFKL-RMADDALNEQLEKAQAYISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKR 1075
Cdd:PRK09603 1007 EGDQIPKEEIASINRFTLASLvKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKR 1086
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQRK- 1154
Cdd:PRK09603 1087 KLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKd 1166
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1155 -VAELRKFLHEIYNEIGGREENLDE----LGDNEILALAKNLRGGVPMATPVFDGAKEREIKAMLKLADLPESGQMRLFD 1229
Cdd:PRK09603 1167 fAKELRAKMLEIANAINEKDPLTIHalenCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYD 1246
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1230 GRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVK 1309
Cdd:PRK09603 1247 GRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIK 1326
                        1370      1380      1390      1400
                  ....*....|....*....|....*....|....*....|....*
gi 489205283 1310 SDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIEL 1354
Cdd:PRK09603 1327 SDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINI 1371
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
12-1355 0e+00

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 1417.85  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   12 RKDFSKLPDVMD-VPYLLAIQLDSYREFLQAGATKEQfrdvgLHAAFKSVFPIISYSGNAALEYVGYRLGEPAFDVKECV 90
Cdd:PRK14844   16 RVSYSRSIDLKDsLLDLVKVQKESYDSFTPKNKGNER-----LEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECI 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   91 LRGVTFAVPLRVKVRLIIF----------------DRESSNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLH 154
Cdd:PRK14844   91 KRGITFSAQVIASIRLVIMqdgisldeyksikesgDHSKLATVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMH 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  155 RSPGVFFDHDRGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNAFYATNVF 234
Cdd:PRK14844  171 RSPGVFFDSDKGKTYNSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKY 250
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  235 HIKGETLNLELVPQRLRGEVASIDIKDGSGKVIVEQGRRITARHINQLEKAGVSQLEVPFDYLIGRTIAKAIVHPATGEI 314
Cdd:PRK14844  251 IKHKDGWKVPFVPDKFKGVRLPFDLMDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTK 330
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  315 IAECNTELTLDLLAKVAKAQVVRIETLYTNDIDCGPFISDTLKIDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLF 394
Cdd:PRK14844  331 ILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLF 410
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  395 FSAERYDLSAVGRMKFNRRIGRTEIEGPGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLV 474
Cdd:PRK14844  411 FSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLL 490
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  475 RVERAVKERLSMAESEGLMPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRD 554
Cdd:PRK14844  491 KLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRD 570
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  555 VHPTHYGRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQL 634
Cdd:PRK14844  571 VHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCF 650
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  635 VDELVAVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVA 714
Cdd:PRK14844  651 VDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVA 730
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  715 RDSGVCVVARRGGVIDSVDASRVVVRVADDEvETGEAGVDIYNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPST 794
Cdd:PRK14844  731 SGSGAVVLAKRDGIVDSSDSNSIVIRAFDKE-RVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAI 809
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  795 DMGELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAG 874
Cdd:PRK14844  810 NSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSG 889
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  875 IVYVGAEVQAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRDGVERDSRALSIE 954
Cdd:PRK14844  890 IVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIK 969
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  955 KMQLDQIRKDLNEEFRIVEGATFERLRAALVGAKAEggpalkkgteiTDDYLDGLERGQWFKLRMADDALNEQLEKAQAY 1034
Cdd:PRK14844  970 QKEINDFEKERDYIINVTSEYFYDELKKLLINSGSQ-----------DREKFDSIEREQWWGIGLKNQSISEQVKSLKKD 1038
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1035 ISDRRQLLDDKFEDKKRKLQQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIV 1114
Cdd:PRK14844 1039 FDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDII 1118
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1115 LNPLGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQRKV--------------------------------------- 1155
Cdd:PRK14844 1119 LNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEINKIksafckgirslnddnftkfaaayldnkkienidddeita 1198
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1156 ------------------------------AELRKFLHEIYNEIGGRE--ENLDELGDNEILALAKNLRGGVPMATPVFD 1203
Cdd:PRK14844 1199 svlntpnknalndelnelvenylnscksaySNLRNFLIEVYSCGSNVSicNNIRDISDNNLIEFARKLRDGIPVAAPVFE 1278
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1204 GAKEREIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQ 1283
Cdd:PRK14844 1279 GPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQ 1358
                        1370      1380      1390      1400      1410      1420      1430
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489205283 1284 RFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIELE 1355
Cdd:PRK14844 1359 RFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLK 1430
rpoB CHL00001
RNA polymerase beta subunit
13-1353 0e+00

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 1083.01  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   13 KDFSKLPDvmdvpyLLAIQLDSYREFLQAGATKEQFRdvglhaafksvFPIIsYSGNAALEYV----GYRLGEPAFDVKE 88
Cdd:CHL00001    7 EGMSTIPG------FNQIQFEGFCRFIDQGLTEELSK-----------FPKI-EDTDQEIEFQlfveTYQLVEPLIKERD 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   89 CVLRGVTFAVPLRVKVRLIifdressNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFdhdRGKT 168
Cdd:CHL00001   69 AVYESLTYSSELYVPAGLI-------WKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYY---RSEL 138
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  169 HSSGKLLYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNafyatNVfhikgetlnlelvpq 248
Cdd:CHL00001  139 DHNGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILD-----NV--------------- 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  249 rlrgevasidikdgsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakaivhpatgeiiaeCNTELTLDLLA 328
Cdd:CHL00001  199 ---------------------------------------------------------------------CYPEIFLSFLN 209
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  329 KVAKaqvvrietlytndidcgpfisdtLKIDNTSNqleALVEIYRMM--RPGEPPTKEAAETLFGNLFFSAeRYDLSAVG 406
Cdd:CHL00001  210 DKEK-----------------------KKIGSKEN---AILEFYQQFacVGGDPVFSESLCKELQKKFFQQ-RCELGRIG 262
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  407 RMKFNRR----IGRTEIegpgVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKE 482
Cdd:CHL00001  263 RRNMNRKlnldIPENNT----FLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRG 338
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  483 RLSMAESEGLM--PQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHY 560
Cdd:CHL00001  339 TICGAIRRKLIptPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHY 418
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  561 GRVCPIETPEGPNIGLINSLATYARTNKYGFLESPYRVVKDSLVTDEIVFLSAIEEADHVIA-QASATLNEKGQlVDELV 639
Cdd:CHL00001  419 GRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAaGNSLALNQGIQ-EEQVV 497
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  640 AVRHLNEFTVKAPEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGV 719
Cdd:CHL00001  498 PARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGV 577
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  720 CVVARRGGVIDSVDASRVVVRVADDEVETgeagvdiyNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGEL 799
Cdd:CHL00001  578 VAIAEHEGKIIYTDTDKIILSGNGDTLSI--------PLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGEL 649
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  800 ALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVG 879
Cdd:CHL00001  650 ALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLG 729
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  880 AEVQAGDILVGKVTPK--GETQLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVqvftrdgverdsralsiekmq 957
Cdd:CHL00001  730 SWVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDV--------------------- 788
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  958 ldqirkdlneefrivegatferlraalvgakaeggpalkkgteitddyldglergQWFklrmaddalneqlekaqayisd 1037
Cdd:CHL00001  789 -------------------------------------------------------RWI---------------------- 791
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1038 rrqllddkfedkkrklqQGDDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNP 1117
Cdd:CHL00001  792 -----------------QKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNP 854
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1118 LGVPSRMNVGQILETHLGLAAKGLGEKINRMLEEQRKVAEL-RKF-LHEIYneiggreenldelgdneilalaknlRGGV 1195
Cdd:CHL00001  855 LGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEAsRKLvFSELY-------------------------EASK 909
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1196 PMATP-VFDgakereikamlkladlPES-GQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQP 1273
Cdd:CHL00001  910 QTANPwVFE----------------PEYpGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQP 973
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1274 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGD--HRMEaGMPESFNVLIKEIRSLGID 1351
Cdd:CHL00001  974 LRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGtiPKPE-DAPESFRLLVRELRSLALE 1052

                  ..
gi 489205283 1352 IE 1353
Cdd:CHL00001 1053 LN 1054
rpoB CHL00207
RNA polymerase beta subunit; Provisional
24-1354 0e+00

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 1070.10  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   24 VPYLLAIQLDSYREFLQAGATKEqfrdvglhaaFKSVFPIISYSGNAALEYVG--YRLGEPAFDVKECVLRGVTFAVPLR 101
Cdd:CHL00207    7 LPDFLEIQRTSFCWFLNEGLNEE----------LNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIY 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  102 VKVRLIifdressNKAIKDIKEQEVYMGEIPLMTENGTFIINGTERVIVSQLHRSPGVFFDHDRGKTHssgKLLYSARII 181
Cdd:CHL00207   77 LPLKFI-------NLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSATLI 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  182 PYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALGYSTEEILNafYATNVFHIKGETLNLELvpqrlrgevasidikd 261
Cdd:CHL00207  147 PNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYS--RLTKSEFLKKLKPILLN---------------- 208
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  262 gsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakaivhpatgeiiaecnteltldllakvakaqvvrietl 341
Cdd:CHL00207      --------------------------------------------------------------------------------
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  342 ytndidcgpfisdtlkiDNTSNQLEALVEIYRMMRPGEPPTKEAAETLFGNLFFSAERYDLSAVGRMKFNRRIGRTEIEG 421
Cdd:CHL00207  209 -----------------SNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPER 271
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  422 PGVLSKEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMPQDLINAK 501
Cdd:CHL00207  272 VRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPK 351
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  502 PVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLA 581
Cdd:CHL00207  352 PLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  582 TYARTNKYGFLESPYRVVKDSLV--TDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMD 659
Cdd:CHL00207  432 TNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIA 511
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  660 VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMERNVARDSGVCVVARRGGVIDSVDASRVVV 739
Cdd:CHL00207  512 ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIII 591
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  740 RvaDDEvetgeaGVDI-YNLTKYTRSNQNTCINQRPLVSKGDVVARGDILADGPSTDMGELALGQNMRVAFMPWNGFNFE 818
Cdd:CHL00207  592 Q--DDN------NRYIhYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFE 663
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  819 DSICLSERVVQEDRFTTIHIQELTCVARDTKLGPEEITADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGET 898
Cdd:CHL00207  664 DAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGES 743
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  899 QLTPEEKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFTRdgverdsralsiekmqldqirkdlneefrivegatfe 978
Cdd:CHL00207  744 DQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSR------------------------------------- 786
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  979 rlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddkfedkkrklQQGDD 1058
Cdd:CHL00207  787 ---------------------------------------------------------------------------SKGDE 791
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1059 LAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAa 1138
Cdd:CHL00207  792 LKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLA- 870
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1139 kglGEKINRMLeeqrkvaelrKFLHeiYNEIGGREENLDELgdNEILALAKNLRGgvpmatpvfdgakereikaMLKLAD 1218
Cdd:CHL00207  871 ---GDNLNKRF----------KILP--FDEMYGSEYSRILI--NNKLNQASIKNN-------------------EYWLFN 914
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1219 LPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGA 1298
Cdd:CHL00207  915 SYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGA 994
                        1290      1300      1310      1320      1330
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489205283 1299 AYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEAGMPESFNVLIKEIRSLGIDIEL 1354
Cdd:CHL00207  995 AYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
27-1355 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: 874.97  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   27 LLAIQLDSYREFLQagatkeqfrdVGLHAAFKSVFPIISYS--GNAALEYVGYRLGEP---------AFDVKECVLRGVT 95
Cdd:cd00653     1 LVKQQIDSFNYFLN----------VGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   96 FAVPLRVKVRLIIFDREssnkaikDIKEQEVYMGEIPLMTE------------------------NGTFIINGTERVIVS 151
Cdd:cd00653    71 YSAPLYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIIN 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  152 QLHRSPGVFFDHDrgkthSSGKLLYSARIIP----YRGSWLDFEFDPKDCV-FVRIDRRrklpasvllralgysteeiln 226
Cdd:cd00653   144 QEQRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDRiYVRIDLK--------------------- 197
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  227 afyatnvfhikgetlnlelvpqrlrgevasidikdgsgkviveqgrritarhinqlekagvsqlevpfdyligrtiakai 306
Cdd:cd00653       --------------------------------------------------------------------------------
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  307 vhpatgeiiaecnteltldllakvakaqvvrietlytndidcgpfisdtlkidntsNQLEALVEIYRmmrpgepptkeaa 386
Cdd:cd00653   198 --------------------------------------------------------RQEEALKYIGK------------- 208
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  387 etlfgnlffsaerydlsavgrmKFnrrigrteiegpgvlskEDIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRCVGEMAE 466
Cdd:cd00653   209 ----------------------RF-----------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQ 249
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  467 NQFRVGLVRVERAVKERLSMAESEG--LMPQDLINAKPVAAAIKEFFGSSQ------------LSQFMDQNNPLSEITHK 532
Cdd:cd00653   250 NLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHK 329
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  533 RRVSAlgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNkyGFLESPYRVVKdslvtdeivfls 612
Cdd:cd00653   330 RRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------ 392
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  613 aieeadhviaqasatlnekgqlvdelvavrhlneftvkapEDVTLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQR 692
Cdd:cd00653   393 ----------------------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQK 432
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  693 QAVPT----------------LRADKPLVGTGMERNVARDsgvcvvarrggvidsvdasrvvvrvaddevetgeagvdiy 756
Cdd:cd00653   433 QAVGTpalnqqyrmdtklyllLYPQKPLVGTGIEEYIAFG---------------------------------------- 472
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  757 nltkytrsnqntcinqrplvskgdvvargdiladgpstdmgELALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836
Cdd:cd00653   473 -----------------------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSI 511
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  837 HIQELTCVARDTKLGPEEIT-ADIPNVGEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKGETQLTPeekllraIFGEKA 915
Cdd:cd00653   512 HYKKYEIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKA 584
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  916 SDVKDTSLRVPTGTKGTVIDVQVFTRDgverdsralsiekmqldqirkdlneefrivegatferlraalvgakaeggpal 995
Cdd:cd00653   585 RDVRDTSLKYPGGEKGIVDDVKIFSRE----------------------------------------------------- 611
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  996 kkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddkfedkkrklqqgddLAPGVLKIVKVYLAIKR 1075
Cdd:cd00653   612 ---------------------------------------------------------------LNDGGNKLVKVYIRQKR 628
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1076 RIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINrmleeqrkv 1155
Cdd:cd00653   629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGD--------- 699
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1156 aelrkflheiyneiggreenldelgdneilalaknlrggvpmATPvFDGAKEREIKAMLKLADLPESGQMRLFDGRTGNQ 1235
Cdd:cd00653   700 ------------------------------------------ATP-FDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEP 736
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1236 FERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNG 1315
Cdd:cd00653   737 LEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVA 816
                        1370      1380      1390      1400      1410
                  ....*....|....*....|....*....|....*....|....*....|
gi 489205283 1316 RTKMYKNIV----------DGDHRMEAGMPESFNVLIKEIRSLGIDIELE 1355
Cdd:cd00653   817 RVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
722-1279 1.24e-165

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: 499.36  E-value: 1.24e-165
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   722 VARRGGVIDSVDASRVVVRVADdevetGEAGVDIYNLTKYTRSNQNT---CINQRPLVSKGDVVArgdiladgpsTDMGE 798
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEA----------GGFGE 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   799 LALGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHIQEltCVARDTKLGP-EEITADIPNVGEAALNKLDEAGIVY 877
Cdd:pfam00562   66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   878 VGAEVQAGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDTSLRVPTGTKGTVIDVQVFtrdgverdsralsiekmq 957
Cdd:pfam00562  144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   958 ldqirkdlneefrivegatferlraalvgakaeggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisd 1037
Cdd:pfam00562      --------------------------------------------------------------------------------
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1038 rrqllddkfedkkrklqqgdDLAPGVLKIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNP 1117
Cdd:pfam00562  200 --------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1118 LGVPSRMNVGQILETHLGLAAKGLgekinrmleeqrkvaelrkflheiyneiggreenldelgdneilalaknlrgGVPM 1197
Cdd:pfam00562  260 HGVPSRMTIGQLLETHLGKAAALL----------------------------------------------------GVFV 287
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1198 ATPVFDGAKER--EIKAMLKLADLPESGQMRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG 1275
Cdd:pfam00562  288 DATPFDGASTEveDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLG 367

                   ....
gi 489205283  1276 GKAQ 1279
Cdd:pfam00562  368 GRAR 371
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
31-1355 4.15e-82

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 293.40  E-value: 4.15e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   31 QLDSYREFLQAGATKeqfrdvgLHAAFKSVFPIIsysGNAALEYVGYRLGEPAFDVK----------ECVLRGVTFAVPL 100
Cdd:PRK08565   18 HLDSYNDFIERGLQE-------IVDEFGEIKTEI---PGLKIVLGKIRVGEPEIKEAdgserpitpmEARLRNLTYAAPL 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  101 RVKVRLIIFDREssnkaikdIKEQEVYMGEIPLMTEN------------------------GTFIINGTERVIVSQLHRS 156
Cdd:PRK08565   88 YLTMIPVENGIE--------YEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLA 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  157 PG---VffdhDRGKTHSSGKllYSARIIPYRG---SWLDFEFDpKDCVF-VRIDR-RRKLPASVLLRALGYST-EEILNA 227
Cdd:PRK08565  160 PNrvlV----DKGEAGSSIT--HTAKVISSRAgyrAQVTVERR-KDGTIyVSFPAvPGKIPFVILMRALGLETdRDIVYA 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  228 fyatnvfhikgetlnLELVPQRLRGEVASIdikdgsgkvivEQGRRItarhINQLEKAgvsqlevpFDYlIGRTIAkaiv 307
Cdd:PRK08565  233 ---------------VSLDPEIQQELLPSL-----------EQASSI----AATVEDA--------LDY-IGKRVA---- 269
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  308 hpatgeiiaecnteltldllakVAKAQVVRIEtlytndidcgpfisdtlkidntsnQLEALVEIYRMMRPGEPPTKEAAE 387
Cdd:PRK08565  270 ----------------------IGQPREYRIE------------------------RAEQILDKYLLPHLGTSPEDRIKK 303
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  388 TLFgnlffsaerydlsaVGRMkfnrrigrteiegpgvlskediidVLKtLVDIRNGKGIVDDIDHLGNRRVRCVGEMAEN 467
Cdd:PRK08565  304 AYF--------------LGQM------------------------ASK-LLELYLGRREPDDKDHYANKRLRLAGDLLAE 344
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  468 QFRVGLVRVERAVKERL--SMAESEGLMPQDLINAKPVAAAIKEFF-------GSSQLSQFMDQNNPLSEITHKRRVsaL 538
Cdd:PRK08565  345 LFRVAFKQLVKDLKYQLekSYARGRKLDLRAIVRPDIITERIRHALatgnwvgGRTGVSQLLDRTNYLSTLSHLRRV--V 422
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  539 GPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYARTNkYGFLESP-----YRV----VKDSLVTDEI- 608
Cdd:PRK08565  423 SP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQIS-VGVDEEEveeilYELgvvpVEEAREEEYIs 499
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  609 ---VFLS----AIEEADHVIAQASATLNEKGQLVDElVAVRHLNEFTVKA------------------------------ 651
Cdd:PRK08565  500 wsrVYLNgrliGYHPDGEELAEKIRELRRSGKISDE-VNVAYIETGEINEvyvncdsgrvrrplivvengkpkltrehve 578
                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  652 ----------------------------------PEDV----TLMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQ 693
Cdd:PRK08565  579 klkkgeltfddlvkmgvieyldaeeeenayvaldPEDLtpehTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQ 658
                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  694 A--VPT----LRAD----------KPLVGT-GMErnvardsgvcvvarrggvidsvdasrvvvrvaddevetgeagvdiy 756
Cdd:PRK08565  659 SlgLYAanfrIRTDtrghllhypqRPLVQTrALE---------------------------------------------- 692
                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  757 nLTKYtrsnqntciNQRPLvskgdvvargdiladgpstdmgelalGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTI 836
Cdd:PRK08565  693 -IIGY---------NDRPA--------------------------GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARST 736
                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  837 HIQELTCVARDTKLGPE-EITADIPNV----GEAALNKLDEAGIVYVGAEVQAGDILVGKVTPKgetQLTPEEKLLRAIF 911
Cdd:PRK08565  737 FFRTYETEERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGL 813
                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  912 GEKasdvKDTSLRVPTGTKGTVIDVqvftrdgverdsralsiekmqldqirkdlneefrivegatferlraaLVGAKAEG 991
Cdd:PRK08565  814 QER----RDTSVTVRHGEKGIVDTV-----------------------------------------------LITESPEG 842
                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  992 GpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddkfedkkrklqqgddlapgvlKIVKVYL 1071
Cdd:PRK08565  843 N------------------------------------------------------------------------KLVKVRV 850
                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1072 AIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGlaakglgekinrmlee 1151
Cdd:PRK08565  851 RDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAG---------------- 914
                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1152 qrKVAELRkflheiyneigGReeNLDelgdneilalaknlrggvpmATPvFDGAKEREIKAMLKLADLPESGQMRLFDGR 1231
Cdd:PRK08565  915 --KVAALE-----------GR--FVD--------------------ATP-FYGEPEEELRKELLKLGYKPDGTEVMYDGR 958
                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1232 TGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1311
Cdd:PRK08565  959 TGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD 1038
                        1450      1460      1470      1480      1490      1500
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489205283 1312 dvngRTKMY--------------KNI----VDGD----HRMEagMPESFNVLIKEIRSLGIDIELE 1355
Cdd:PRK08565 1039 ----KTTIYvcelcghiawydrrKNKyvcpIHGDkgniSPVE--VSYAFKLLLQELMSMGISPRLK 1098
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
26-505 2.55e-75

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: 255.77  E-value: 2.55e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    26 YLLAIQLDSYREFLQAGATKEqfrdVGLHAAFKSVFPIISYSGNAA---LEYVGYRLGEPAFDVK----------ECVLR 92
Cdd:pfam04563    1 GLVRQQLDSFNEFVDNDLQKI----IDENALIESEFEIQHPGENGDklsLKFGQIRLGKPMFDETdgstreiypqECRLR 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283    93 GVTFAVPLRVKVRLIIFDREssnkaikDIKEQEVYMGEIPLMTEN------------------------GTFIINGTERV 148
Cdd:pfam04563   77 NLTYSAPLYVDLELSVYNGE-------DIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKV 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   149 IVSQLHRS---PGVFFDHDRGKTHSSGKLLYSARI--IPYRGSWLDF-EFDPKDCVFVRIDRRRK-LPASVLLRALGYST 221
Cdd:pfam04563  150 IVAQEHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTS 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   222 E-EILNAFyatnVFHIKGETLNLELVPQrlrgevasidikdgsgkviVEQGRRITARHInqlekagvsqlEVPFDYLIGR 300
Cdd:pfam04563  230 DrEIFELI----CYDVNDQQLQEELLPS-------------------LEEGFKIRIQTQ-----------EQALDYIGGR 275
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   301 tiakaivhpatgeiiaecnteltldllakvakaqvvrietlytndidcgpfisdtlkidntsnqleaLVEIYRMMRPGEP 380
Cdd:pfam04563  276 -------------------------------------------------------------------GRAIFRMGRPREP 288
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   381 PTKEAAETLFGNLFFSAERYDLSAVGRMKFnrrigrteiegpgvlskedIIDVLKTLVDIRNGKGIVDDIDHLGNRRVRC 460
Cdd:pfam04563  289 RIKYAEEILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRL 349
                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*..
gi 489205283   461 VGEMAENQFRVGLVRVERAVKERL--SMAESEGLMPQDLINAKPVAA 505
Cdd:pfam04563  350 AGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
601-1357 2.49e-53

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: 197.94  E-value: 2.49e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   601 DSLVTDEIV-FLSAIEEADHVIAQASATLNEKgqlvdelvavrHlneftvkapedvTLMDVSPKQVVSVAASLIPFLEHD 679
Cdd:TIGR03670   84 DDLVKQGVIeYLDAEEEENAYIALDPEELTPE-----------H------------THLEIDPSAILGIIASTIPYPEHN 140
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   680 DANRALMGSNMQRQAVPTLRADKPLvgtgmernvardsgvcvvarrggvidsvdasRVVVRVaddevetgeagvdiyNLT 759
Cdd:TIGR03670  141 QSPRNTMGAAMAKQSLGLYAANYRI-------------------------------RLDTRG---------------HLL 174
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   760 KYTrsnqntcinQRPLV-SKGDVVARGDilaDGPStdmgelalGQNMRVAFMPWNGFNFEDSICLSERVVQEDRFTTIHI 838
Cdd:TIGR03670  175 HYP---------QKPLVkTRVLELIGYD---DRPA--------GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFF 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   839 QELTCVARDTKLGPE-EITADIPNV----GEAALNKLDEAGIVYVGAEVQAGDILVGKVTPkgetqltP---EEkllRAI 910
Cdd:TIGR03670  235 RTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LRE 304
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   911 FGEKASDVKDTSLRVPTGTKGtVIDvQVFTRDGVERDsralsiekmqldqirkdlneefrivegatferlraalvgakae 990
Cdd:TIGR03670  305 FGLVTERRRDTSVTVRHGEKG-IVD-KVIITETEEGN------------------------------------------- 339
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283   991 ggpalkkgteitddyldglergqwfklrmaddalneqlekaqayisdrrqllddkfedkkrklqqgddlapgvlKIVKVY 1070
Cdd:TIGR03670  340 --------------------------------------------------------------------------KLVKVR 345
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1071 LAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGLAAKGLGEKINrmle 1150
Cdd:TIGR03670  346 VRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVD---- 421
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1151 eqrkvaelrkflheiyneiggreenldelgdneilalaknlrggvpmATPvFDGAKEREIKAMLKLADLPESGQMRLFDG 1230
Cdd:TIGR03670  422 -----------------------------------------------GTP-FEGEPEEELRKELLKLGFKPDGKEVMYDG 453
                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1231 RTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1310
Cdd:TIGR03670  454 ITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDES 533
                          730       740       750       760       770       780
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489205283  1311 DDV--------------NGRTKMYKNIVDGD----HRMEagMPESFNVLIKEIRSLGIDIELETE 1357
Cdd:TIGR03670  534 DKYvvyvcencghiaweDKRKGTAYCPVCGEtgdiSPVE--MSYAFKLLLDELKSLGISPRLELG 596
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
1065-1357 6.18e-44

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 170.14  E-value: 6.18e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1065 KIVKVYLAIKRRIQPGDKMAGRHGNKGVVSVIMPVEDMPHDANGTPVDIVLNPLGVPSRMNVGQILETHLGlaakglgek 1144
Cdd:PRK07225  346 RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGG--------- 416
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1145 inrmleeqrKVAELRkflheiyneigGREENldelgdneilalaknlrggvpmATPvFDGAKEREIKAMLKLADLPESGQ 1224
Cdd:PRK07225  417 ---------KVGSLE-----------GRRVD----------------------GTA-FSGEDEEDLREALEKLGFEHTGK 453
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283 1225 MRLFDGRTGNQFERPTTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQE 1304
Cdd:PRK07225  454 EVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKE 533
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489205283 1305 MLTVKSDDVN-------GRTKMY---KNIV--------DGDHRMEagMPESFNVLIKEIRSLGIDIELETE 1357
Cdd:PRK07225  534 RLLDESDKVEiyvcakcGMIAIYdkkRNRKycpicgeeTDIYPVE--MSYAFKLLLDELKSLGIAPRLELE 602
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
518-585 4.76e-37

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: 133.42  E-value: 4.76e-37
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489205283   518 QFMDQNNPLSEITHKRRVSAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYAR 585
Cdd:pfam04565    1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
1281-1357 7.44e-34

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: 125.39  E-value: 7.44e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  1281 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVNGRTKMYKN-----IVDGDHRMEAG-MPESFNVLIKEIRSLGI 1350
Cdd:pfam04560    1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80

                   ....*..
gi 489205283  1351 DIELETE 1357
Cdd:pfam04560   81 DPRLLLE 87
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
596-661 1.42e-27

RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.


Pssm-ID: 463067 [Multi-domain]  Cd Length: 66  Bit Score: 106.68  E-value: 1.42e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489205283   596 YRVVKDSLVTDEIVFLSAIEEADHVIAQASATLNEKGQLVDELVAVRHLNEFTVKAPEDVTLMDVS 661
Cdd:pfam10385    1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
443-584 3.82e-21

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 98.87  E-value: 3.82e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489205283  443 GKGIVDDIDHLGNRRVRCVGEMAENQFRVGLVRVERAVKERLSMAESEGLMP--QDLINAKPVAAAIKEFF-------GS 513
Cdd:PRK09606  323 GRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELsiKTAVRSDVLTERLEHAMatgnwvgGR 402
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489205283  514 SQLSQFMDQNNPLSEITHKRRVSAlgpgGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLATYA 584
Cdd:PRK09606  403 TGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMV 469
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
155-227 2.12e-09

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: 58.51  E-value: 2.12e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489205283   155 RSPGVFF--DHDRGKTHSSgkllYSARIIPYRGSWLDFEFDPKDCVFVRIDRRRKLPASVLLRALG-YSTEEILNA 227
Cdd:pfam04561    1 RSNGIYVekELDKNGIIAT----YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGlVSDREILDR 72
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
261-335 1.81e-04

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 46.14  E-value: 1.81e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489205283  261 DGSGKVIVEQGRRITARHINQLEKAGVSQLEVPF-DYLIGRTIAKAIVHPAtGEIIAECNTELTLDLLAKVAKAQV 335
Cdd:PRK02597  202 DVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIPLgDRLLGRVLAEDVVDPE-GEVIAERNTAIDPDLAKKIEKAGV 276
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
295-339 2.65e-04

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 45.44  E-value: 2.65e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 489205283  295 DYLIGRTIAKAIVHPATGEIIAECNTELTLDLLAKVAKAQVVRIE 339
Cdd:PRK00566  804 ERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVK 848
 
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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