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Conserved domains on  [gi|16131817|ref|NP_418414|]
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RNA polymerase subunit beta [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-1342 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


:

Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 2281.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     1 MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405    1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    80 FDVQECQIRGVTYSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405   81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEirdnklqm 239
Cdd:PRK00405  154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   240 elvperlrgetasfdieangkvyvekgrritarhirqlekddvKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSL 319
Cdd:PRK00405  225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   320 DLlaklsqsghkrietlftndldHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405  262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   400 VGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405  321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405  401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSK 639
Cdd:PRK00405  481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405  561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   720 RGGVVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405  641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405  719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405  799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   960 lseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkITQG 1039
Cdd:PRK00405  856 ----------------------------------------------------------------------------IEQG 859

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1040 DDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405  860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1120 AAKGIGDKinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpIATPVFDGAKEAEIKELL 1199
Cdd:PRK00405  940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1200 KLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405  966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045

                        1290      1300      1310      1320      1330      1340
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16131817  1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:PRK00405 1046 AYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 972-1029 2.44e-04

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


The actual alignment was detected with superfamily member cd22011:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 75  Bit Score: 40.98  E-value: 2.44e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131817  972 FSRIRAVLVAGGVEAEK---LDKLPRDRWLelGLTDEEKQ---NQLEQLAEQYDELKHEFEKKL 1029
Cdd:cd22011   12 SQEIRKNLKSQGSPEEKvpeLSKRAAEQWR--SLTLAEKQpyyDEVEVLKKQYDVEKEEYEKEL 73
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-1342 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 2281.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     1 MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405    1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    80 FDVQECQIRGVTYSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405   81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEirdnklqm 239
Cdd:PRK00405  154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   240 elvperlrgetasfdieangkvyvekgrritarhirqlekddvKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSL 319
Cdd:PRK00405  225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   320 DLlaklsqsghkrietlftndldHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405  262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   400 VGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405  321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405  401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSK 639
Cdd:PRK00405  481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405  561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   720 RGGVVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405  641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405  719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405  799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   960 lseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkITQG 1039
Cdd:PRK00405  856 ----------------------------------------------------------------------------IEQG 859

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1040 DDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405  860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1120 AAKGIGDKinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpIATPVFDGAKEAEIKELL 1199
Cdd:PRK00405  940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1200 KLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405  966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045

                        1290      1300      1310      1320      1330      1340
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16131817  1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:PRK00405 1046 AYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 8-1339 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: 1943.69  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817      8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQ 83
Cdd:TIGR02013    1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     84 ECQIRGVTYSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013   81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffekvifeirdnklqmelvp 243
Cdd:TIGR02013  156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    244 erlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakdyidestgelicaanmelsldlla 323
Cdd:TIGR02013      --------------------------------------------------------------------------------

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    324 klsqsghkrIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013  209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    404 KFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013  280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013  360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    564 PEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGE 641
Cdd:TIGR02013  440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013  520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    722 GVVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013  600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013  679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdls 961
Cdd:TIGR02013  759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    962 eelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDD 1041
Cdd:TIGR02013  815 ----------------------------------------------------------------------------QGDE 818

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1042 LAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013  819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1122 KGIGdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKL 1201
Cdd:TIGR02013  899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1202 GDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013  928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007

                         1290      1300      1310      1320      1330
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 16131817   1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:TIGR02013 1008 GAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 12-1342 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: 1652.15  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   12 RKDFGKRPQVLDVPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVT 91
Cdd:COG0085    1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   92 YSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085   75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFEKVIFEIrdnklqmelvperlrget 250
Cdd:COG0085  145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  251 asfdIEANgkvyvekgrritarhirqLEKDDVKlievpveyiagkvvakdyidestgelicaanmelsldllaklsqsgh 330
Cdd:COG0085  207 ----ILAT------------------LEKDNTK----------------------------------------------- 217

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  331 krietlftndldhgpyisetlrvdptnDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085  218 ---------------------------TQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  411 REEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085  271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085  351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  571 LINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085  431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggvvqyvdas 730
Cdd:COG0085  511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085  560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085  622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileag 970
Cdd:COG0085  702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  971 lfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085  749 -------------------------------------------------------------------EGDELPPGVNKLV 761

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1051 KVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkina 1130
Cdd:COG0085  762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1131 mlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQI 1210
Cdd:COG0085  834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1211 RLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085  868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947

                       1290      1300      1310      1320      1330
                 ....*....|....*....|....*....|....*....|....*....|..
gi 16131817 1291 LTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:COG0085  948 LTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 27-1340 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: 893.08  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVQECQIRGVTYSAP 95
Cdd:cd00653    1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653   75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffe 226
Cdd:cd00653  148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  227 kvifeirdnklqmelvperlrgetasfdieangkvyvekgrritarhIRQLEkddvklievpveyiagkvvAKDYIDest 306
Cdd:cd00653  197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  307 gelicaanmelsldllaklsqsghKRIEtlftndldhgpyisetlrvdptndrlsalveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653  208 ------------------------KRFE---------------------------------------------------- 211

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  387 nlffsedrydlsavgrmkfnrsllreeiegsgilskdDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653  212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653  255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieeg 612
Cdd:cd00653  335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV------------------ 391

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  613 nyviaqansnldeeghfvedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653  392 ----------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggvvqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653  438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  757 trsnqntcinqmpcvslgepvergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653  471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653  517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriravlvaggveaekldklprd 995
Cdd:cd00653  590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  996 rwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075
Cdd:cd00653  612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1076 ISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinamlkqqqevaklrefiqraydlgadv 1155
Cdd:cd00653  646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1156 rqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKL 1235
Cdd:cd00653  693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751

                       1290      1300      1310      1320      1330      1340      1350      1360
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653  752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831

                       1370      1380      1390
                 ....*....|....*....|....*....|....*
gi 16131817 1310 ----DGNHQMEPGMPESFNVLLKEIRSLGINIELE 1340
Cdd:cd00653  832 rlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 717-1264 9.20e-167

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: 502.06  E-value: 9.20e-167
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    717 VAKRGGVVQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVSLGEpVERGDvladgpstdLGE 793
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562   66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562  144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    953 lkqakkdlseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:pfam00562      --------------------------------------------------------------------------------

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1033 rrkitqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562  200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1113 LETHLGMAAKGigdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrKGMPIATPVFDGAKE 1192
Cdd:pfam00562  272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131817   1193 --AEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562  298 evEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 972-1029 2.44e-04

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 40.98  E-value: 2.44e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131817  972 FSRIRAVLVAGGVEAEK---LDKLPRDRWLelGLTDEEKQ---NQLEQLAEQYDELKHEFEKKL 1029
Cdd:cd22011   12 SQEIRKNLKSQGSPEEKvpeLSKRAAEQWR--SLTLAEKQpyyDEVEVLKKQYDVEKEEYEKEL 73
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-1342 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 2281.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     1 MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405    1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    80 FDVQECQIRGVTYSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405   81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEirdnklqm 239
Cdd:PRK00405  154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   240 elvperlrgetasfdieangkvyvekgrritarhirqlekddvKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSL 319
Cdd:PRK00405  225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   320 DLlaklsqsghkrietlftndldHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405  262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   400 VGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405  321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405  401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSK 639
Cdd:PRK00405  481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405  561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   720 RGGVVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405  641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405  719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405  799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   960 lseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkITQG 1039
Cdd:PRK00405  856 ----------------------------------------------------------------------------IEQG 859

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1040 DDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405  860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1120 AAKGIGDKinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpIATPVFDGAKEAEIKELL 1199
Cdd:PRK00405  940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1200 KLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405  966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045

                        1290      1300      1310      1320      1330      1340
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16131817  1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:PRK00405 1046 AYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 8-1339 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: 1943.69  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817      8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQ 83
Cdd:TIGR02013    1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     84 ECQIRGVTYSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013   81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffekvifeirdnklqmelvp 243
Cdd:TIGR02013  156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    244 erlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakdyidestgelicaanmelsldlla 323
Cdd:TIGR02013      --------------------------------------------------------------------------------

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    324 klsqsghkrIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013  209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    404 KFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013  280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013  360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    564 PEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGE 641
Cdd:TIGR02013  440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013  520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    722 GVVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013  600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013  679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdls 961
Cdd:TIGR02013  759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    962 eelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDD 1041
Cdd:TIGR02013  815 ----------------------------------------------------------------------------QGDE 818

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1042 LAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013  819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1122 KGIGdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKL 1201
Cdd:TIGR02013  899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927

                         1210      1220      1230      1240      1250      1260      1270      1280
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1202 GDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013  928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007

                         1290      1300      1310      1320      1330
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 16131817   1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:TIGR02013 1008 GAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 12-1342 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: 1652.15  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   12 RKDFGKRPQVLDVPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVT 91
Cdd:COG0085    1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   92 YSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085   75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFEKVIFEIrdnklqmelvperlrget 250
Cdd:COG0085  145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  251 asfdIEANgkvyvekgrritarhirqLEKDDVKlievpveyiagkvvakdyidestgelicaanmelsldllaklsqsgh 330
Cdd:COG0085  207 ----ILAT------------------LEKDNTK----------------------------------------------- 217

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  331 krietlftndldhgpyisetlrvdptnDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085  218 ---------------------------TQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  411 REEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085  271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085  351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  571 LINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085  431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggvvqyvdas 730
Cdd:COG0085  511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085  560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085  622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileag 970
Cdd:COG0085  702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  971 lfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085  749 -------------------------------------------------------------------EGDELPPGVNKLV 761

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1051 KVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkina 1130
Cdd:COG0085  762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1131 mlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQI 1210
Cdd:COG0085  834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1211 RLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085  868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947

                       1290      1300      1310      1320      1330
                 ....*....|....*....|....*....|....*....|....*....|..
gi 16131817 1291 LTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:COG0085  948 LTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
27-1340 0e+00

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 1434.80  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    27 LLSIQLDSFQKFIEQDpEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVI-- 104
Cdd:PRK14844   32 LVKVQKESYDSFTPKN-KGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRLVImq 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   105 -------YEREAPEG-------TVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKV 170
Cdd:PRK14844  111 dgisldeYKSIKESGdhsklatVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   171 LYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGET 250
Cdd:PRK14844  191 IYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVR 270

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   251 ASFDI-EANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSG 329
Cdd:PRK14844  271 LPFDLmDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLS 350

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   330 HKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSL 409
Cdd:PRK14844  351 IDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYL 430

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   410 LREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMP 489
Cdd:PRK14844  431 GLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSP 510

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   490 QDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 569
Cdd:PRK14844  511 SDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNI 590

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   570 GLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQ 649
Cdd:PRK14844  591 GLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQ 670

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   650 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDA 729
Cdd:PRK14844  671 VSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDS 750

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   730 SRIVIKVNEDEMYpGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNG 809
Cdd:PRK14844  751 NSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQG 829

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   810 YNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Cdd:PRK14844  830 YNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTP 909

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   890 KGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEA 969
Cdd:PRK14844  910 KPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSE 989

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   970 GLFSRIRAVLV-AGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLK 1048
Cdd:PRK14844  990 YFYDELKKLLInSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSM 1069

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKI 1128
Cdd:PRK14844 1070 SVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKV 1149

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1129 NAML--------------------------------KQQQEV-------------------------------------A 1139
Cdd:PRK14844 1150 GNILdeinkiksafckgirslnddnftkfaaayldnKKIENIdddeitasvlntpnknalndelnelvenylnscksayS 1229

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1140 KLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGE 1219
Cdd:PRK14844 1230 NLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGE 1309

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1220 QFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:PRK14844 1310 KFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIN 1389

                        1370      1380      1390      1400
                  ....*....|....*....|....*....|....*....|.
gi 16131817  1300 GRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELE 1340
Cdd:PRK14844 1390 GRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLK 1430
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
8-1339 0e+00

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 1415.45  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQI 87
Cdd:PRK09603    8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAME 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    88 RGVTYSAPLRVKLRLVIYEREAPEG---TVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKT 164
Cdd:PRK09603   88 RGITYSIPLKIKVRLILWEKDTKSGeknGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   165 hSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPE 244
Cdd:PRK09603  168 -SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASL 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   245 RLRGEtASFDI-EANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDEStgelicaanmELSLDLLA 323
Cdd:PRK09603  247 DANQR-MEFDLkDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGK----------EVLLDMLT 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   324 KLSQSGHKRI------ETLFTNDLDHG----------------PYISETLRVDPTNDRlsALVEIYRMMRPGEPPTREAA 381
Cdd:PRK09603  316 QLDKNKLEKIhdlgvqEFVIINDLALGhdasiihsfsadseslKLLKQTEKIDDENAL--AAIRIHKVMKPGDPVTTEVA 393

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   382 ESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:PRK09603  394 KQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLA 473

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   462 NQFRVGLVRVERAVKERLSL--GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLT 539
Cdd:PRK09603  474 NELHSGLVKMQKTIKDKLTTmsGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLV 553

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   540 RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 619
Cdd:PRK09603  554 KDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPA 633

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   620 NSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPL 699
Cdd:PRK09603  634 STPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPI 713

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   700 VGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIkVNEDEmypGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVER 779
Cdd:PRK09603  714 VGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI-LGEGK---EEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEA 789

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   780 GDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGE 859
Cdd:PRK09603  790 GQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKE 869

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   860 AALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGV 939
Cdd:PRK09603  870 EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGY 949

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   940 EKDKRALEIEEMQlkQAKKDLS--EELQILEAGLFSRIRAVL---------VAGGVEAEKLDKLPR------DRWLELGL 1002
Cdd:PRK09603  950 EKDARVLSAYEEE--KAKLDMEhfDRLTMLNREELLRVSSLLsqaileepfSHNGKDYKEGDQIPKeeiasiNRFTLASL 1027

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1003 TD---EEKQNQLEQLA----EQYDELKHEFEKKLEakrrkITQGDDLAP-GVLKIVKVYLAVKRRIQPGDKMAGRHGNKG 1074
Cdd:PRK09603 1028 VKkysKEVQNHYEITKnnflEQKKVLGEEHEEKLS-----ILEKDDILPnGVIKKVKLYIATKRKLKVGDKMAGRHGNKG 1102

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1075 VISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQE------VAKLREFIQRA 1148
Cdd:PRK09603 1103 IVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKdfakelRAKMLEIANAI 1182

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1149 YDLGADVRQKvdLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVG 1228
Cdd:PRK09603 1183 NEKDPLTIHA--LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVG 1260

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNI 1308
Cdd:PRK09603 1261 YMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAI 1340

                        1370      1380      1390
                  ....*....|....*....|....*....|.
gi 16131817  1309 VDGNHQMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:PRK09603 1341 AKGEQVGESEIPETFYVLTKELQSLALDINI 1371
rpoB CHL00001
RNA polymerase beta subunit
 25-1338 0e+00

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 1067.98  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    25 PYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVQECQIRGVTYSAPLRVKLRL 102
Cdd:CHL00001   13 PGFNQIQFEGFCRFIDQ------GLTEELSKFPKIEDTDQEIEFQLFVetYQLVEPLIKERDAVYESLTYSSELYVPAGL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   103 vIYEREapegtvKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVLYNARIIPYRGS 182
Cdd:CHL00001   87 -IWKKS------RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDH---NGISVYTGTIISDWGG 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   183 WLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKlqmelvperlrgetasfdieangkvy 262
Cdd:CHL00001  157 RLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLND-------------------------- 210

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   263 vekgrritarhirqleKDDVKLievpveyiagkvvakdyidESTGElicaanmelsldllaklsqsghkrietlftndld 342
Cdd:CHL00001  211 ----------------KEKKKI-------------------GSKEN---------------------------------- 221

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   343 hgpyisetlrvdptndrlsALVEIYRMM--RPGEPPTREAAESLFENLFFSEdRYDLSAVGRMKFNRSLLREEIEGSGIL 420
Cdd:CHL00001  222 -------------------AILEFYQQFacVGGDPVFSESLCKELQKKFFQQ-RCELGRIGRRNMNRKLNLDIPENNTFL 281

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   421 SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLM--PQDMINAKPI 498
Cdd:CHL00001  282 LPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIptPQNLVTSTPL 361

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   499 SAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVY 578
Cdd:CHL00001  362 TTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIH 441

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   579 AQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQ 658
Cdd:CHL00001  442 ARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPF 521

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   659 QVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNE 738
Cdd:CHL00001  522 QYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNG 601

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   739 DEMYpgeagidiYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILV 818
Cdd:CHL00001  602 DTLS--------IPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   819 SERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK--GETQLT 896
Cdd:CHL00001  674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYA 753

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   897 PEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVqvftrdgvekdkraleieemqlkqakkdlseelqileaglfsrir 976
Cdd:CHL00001  754 PEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDV--------------------------------------------- 788

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   977 avlvaggveaekldklprdRWLelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIVKVYLAV 1056
Cdd:CHL00001  789 -------------------RWI---------------------------------------QKKGGSSYNPETIHVYILQ 810

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1057 KRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinaMLKQQQ 1136
Cdd:CHL00001  811 KREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGD--------LLNRHY 882

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1137 EVAKLrefiqraydlgadvrqkvdlstfsDEevMRLAENLRKgmpiatPVFdgakeaeiKELLK---------LGDLPTS 1207
Cdd:CHL00001  883 RIAPF------------------------DE--RYEQEASRK------LVF--------SELYEaskqtanpwVFEPEYP 922

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1208 GQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1287
Cdd:CHL00001  923 GKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYIL 1002

                        1290      1300      1310      1320      1330
                  ....*....|....*....|....*....|....*....|....*....|..
gi 16131817  1288 QEMLTVKSDDVNGRTKMYKNIVDGNHQMEP-GMPESFNVLLKEIRSLGINIE 1338
Cdd:CHL00001 1003 QEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLALELN 1054
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 24-1339 0e+00

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 1063.55  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    24 VPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVQECQIRGVTYSAPLRVKLR 101
Cdd:CHL00207    7 LPDFLEIQRTSFCWFLNE------GLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIYLPLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   102 LViyereapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHssgKVLYNARIIPYRG 181
Cdd:CHL00207   81 FI-------NLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSATLIPNRG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   182 SWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQmelvperlrgetasfdieangkv 261
Cdd:CHL00207  151 SWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYSRLTKSEFLKKLKPILL----------------------- 207

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   262 yvekgrritarhirqlekddvklievpveyiagkvvakdyidestgelicaanmelsldllaklsqsghkrietlftndl 341
Cdd:CHL00207      --------------------------------------------------------------------------------

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   342 DHGPYISETlrvdptndrlsALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILS 421
Cdd:CHL00207  208 NSNSYTNEE-----------ILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLT 276

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   422 KDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAA 501
Cdd:CHL00207  277 YEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIAL 356

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   502 VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQT 581
Cdd:CHL00207  357 IREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARI 436

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   582 NEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQ 659
Cdd:CHL00207  437 NKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQ 516

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   660 VVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNED 739
Cdd:CHL00207  517 VFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNN 596

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   740 EMYpgeagidIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVS 819
Cdd:CHL00207  597 RYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILIN 669

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   820 ERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEE 899
Cdd:CHL00207  670 KRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEG 749

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   900 KLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriravl 979
Cdd:CHL00207  750 KLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS------------------------------------------ 787

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   980 vaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIVKVYLAVKRR 1059
Cdd:CHL00207  788 ----------------------------------------------------------KGDELKFGYYLKIRVFIAQIRK 809

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1060 IQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAakgiGDKINAMLKQqqeva 1139
Cdd:CHL00207  810 IQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLA----GDNLNKRFKI----- 880

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1140 klrefiqraydlgadvrqkVDLSTFSDEEVMRLAENlRKGMPIATpvfdgakeaeIKELLKLGDLPTSGQIRLYDGRTGE 1219
Cdd:CHL00207  881 -------------------LPFDEMYGSEYSRILIN-NKLNQASI----------KNNEYWLFNSYHPGKMVLRDGRTGY 930

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1220 QFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:CHL00207  931 KFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQ 1010

                        1290      1300      1310      1320
                  ....*....|....*....|....*....|....*....|
gi 16131817  1300 GRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:CHL00207 1011 GRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 27-1340 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: 893.08  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVQECQIRGVTYSAP 95
Cdd:cd00653    1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653   75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffe 226
Cdd:cd00653  148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  227 kvifeirdnklqmelvperlrgetasfdieangkvyvekgrritarhIRQLEkddvklievpveyiagkvvAKDYIDest 306
Cdd:cd00653  197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  307 gelicaanmelsldllaklsqsghKRIEtlftndldhgpyisetlrvdptndrlsalveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653  208 ------------------------KRFE---------------------------------------------------- 211

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  387 nlffsedrydlsavgrmkfnrsllreeiegsgilskdDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653  212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653  255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieeg 612
Cdd:cd00653  335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV------------------ 391

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  613 nyviaqansnldeeghfvedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653  392 ----------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggvvqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653  438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  757 trsnqntcinqmpcvslgepvergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653  471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653  517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589

                        970       980       990      1000      1010      1020      1030      1040
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriravlvaggveaekldklprd 995
Cdd:cd00653  590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611

                       1050      1060      1070      1080      1090      1100      1110      1120
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  996 rwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075
Cdd:cd00653  612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645

                       1130      1140      1150      1160      1170      1180      1190      1200
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1076 ISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinamlkqqqevaklrefiqraydlgadv 1155
Cdd:cd00653  646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692

                       1210      1220      1230      1240      1250      1260      1270      1280
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1156 rqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKL 1235
Cdd:cd00653  693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751

                       1290      1300      1310      1320      1330      1340      1350      1360
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653  752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831

                       1370      1380      1390
                 ....*....|....*....|....*....|....*
gi 16131817 1310 ----DGNHQMEPGMPESFNVLLKEIRSLGINIELE 1340
Cdd:cd00653  832 rlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 717-1264 9.20e-167

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: 502.06  E-value: 9.20e-167
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    717 VAKRGGVVQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVSLGEpVERGDvladgpstdLGE 793
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562   66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562  144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    953 lkqakkdlseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:pfam00562      --------------------------------------------------------------------------------

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1033 rrkitqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562  200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1113 LETHLGMAAKGigdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrKGMPIATPVFDGAKE 1192
Cdd:pfam00562  272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131817   1193 --AEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562  298 evEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 26-500 2.23e-110

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: 353.22  E-value: 2.23e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     26 YLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGN---SELQYVSYRLGEPVFDV----------QECQIRGVTY 92
Cdd:pfam04563    1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENgdkLSLKFGQIRLGKPMFDEtdgstreiypQECRLRNLTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817     93 SAPLRVKLRLVIYereapegTVKDIKEQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQ 148
Cdd:pfam04563   81 SAPLYVDLELSVY-------NGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQ 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    149 LHRS---PGVFFDSDKGKTHSSGKVLYNARI--IPYRGSWLDF-EFDPKDNLFVRIDRRRK-LPATIILRALNYTTEQIL 221
Cdd:pfam04563  154 EHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDREI 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    222 dlfFEKVIFEIRDNKLQMELVPErlrgetasfdieangkvyVEKGRRITarhirqlekddVKLIEVPVEYIAGKVVAkdy 301
Cdd:pfam04563  234 ---FELICYDVNDQQLQEELLPS------------------LEEGFKIR-----------IQTQEQALDYIGGRGRA--- 278

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    302 idestgelicaanmelsldllaklsqsghkrietlftndldhgpyisetlrvdptndrlsalveIYRMMRPGEPPTREAA 381
Cdd:pfam04563  279 ----------------------------------------------------------------IFRMGRPREPRIKYAE 294

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    382 ESLFENLFFSEDRYDLSAVGRMKFnrsllreeiegsgilskddIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:pfam04563  295 EILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLA 355

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|.
gi 16131817    462 NQFRVGLVRVERAVKERL--SLGDLDTLMPQDMINAKPISA 500
Cdd:pfam04563  356 SLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 31-1340 1.65e-88

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 312.28  E-value: 1.65e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    31 QLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDV----------QECQIRGVTYSAPLRVKL 100
Cdd:PRK08565   18 HLDSYNDFIER------GLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEadgserpitpMEARLRNLTYAAPLYLTM 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   101 RLVIYEREapegtvkdIKEQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQLHRSPG-V 155
Cdd:PRK08565   92 IPVENGIE--------YEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNrV 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   156 FFDSDKgkthSSGKVLYNARIIPYRG---SWLDFEFDPKDNLFVRIDR-RRKLPATIILRALNYTTEQ-ILDLFFEkvif 230
Cdd:PRK08565  164 LVDKGE----AGSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRALGLETDRdIVYAVSL---- 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   231 eirDNKLQMELVPerlrgetaSFdieangkvyvEKGRRItarhirqlekddvklievpveyiagkvvakdyidestgeli 310
Cdd:PRK08565  236 ---DPEIQQELLP--------SL----------EQASSI----------------------------------------- 253

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   311 cAANMELSLDLLAKLSQSGHKRietlftndldhgpyisetlrvdptNDRLsalveiyrmmrpgepptREAAESLfenlff 390
Cdd:PRK08565  254 -AATVEDALDYIGKRVAIGQPR------------------------EYRI-----------------ERAEQIL------ 285

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   391 seDRYDLSAVGRMKFNRsllreeiegsgiLSKDDIIDVM-KKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLV 469
Cdd:PRK08565  286 --DKYLLPHLGTSPEDR------------IKKAYFLGQMaSKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFK 351

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   470 RVERAVKERL----SLG---DLDTLMPQDMINAKPISA-AVKEFFGS-SQLSQFMDQNNPLSEITHKRRIsaLGPggLTR 540
Cdd:PRK08565  352 QLVKDLKYQLeksyARGrklDLRAIVRPDIITERIRHAlATGNWVGGrTGVSQLLDRTNYLSTLSHLRRV--VSP--LSR 427

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   541 ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ----TNEYGFLETPYRKvtdGVVtdeiHYLSAIEEGNYVI 616
Cdd:PRK08565  428 GQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQisvgVDEEEVEEILYEL---GVV----PVEEAREEEYISW 500

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   617 AQA--NSNL---DEEGH-FVEDLVTCRSKGESSlfsrdqvdymdvstqQVVSVGaslipFLEHDDANRALMGANMQRQAV 690
Cdd:PRK08565  501 SRVylNGRLigyHPDGEeLAEKIRELRRSGKIS---------------DEVNVA-----YIETGEINEVYVNCDSGRVRR 560

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   691 PTL--RADKPLVGtgMERAVAVDSGVTAVAK--RGGVVQYVDASR---IVIKVNEDEMYPGEAGIDIY---------NLT 754
Cdd:PRK08565  561 PLIvvENGKPKLT--REHVEKLKKGELTFDDlvKMGVIEYLDAEEeenAYVALDPEDLTPEHTHLEIWppailgitaSII 638

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   755 KYTRSNQ---NTCINQMPCVSLGEPV--------ERGDVL------------------ADGPStdlgelalGQNMRVAFM 805
Cdd:PRK08565  639 PYPEHNQsprNTYQAAMAKQSLGLYAanfrirtdTRGHLLhypqrplvqtraleiigyNDRPA--------GQNAVVAVL 710

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   806 PWNGYNFEDSILVSERVVqeDR-------FTTIHIQELacvsrdTKLGPEEITADIP--NV----GEAALSKLDESGIVY 872
Cdd:PRK08565  711 SYTGYNIEDAIIMNKASI--ERglarstfFRTYETEER------KYPGGQEDKIEIPepNVrgyrGEEYYRKLDEDGIVS 782

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   873 IGAEVTGGDILVGKVTPKgetQLTPEEKLLRAIFGEKasdvKDSSLRVPNGVSGTVidvqvftrdgvekDKraleieemq 952
Cdd:PRK08565  783 PEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER----RDTSVTVRHGEKGIV-------------DT--------- 833

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   953 lkqakkdlseelqileaglfsriraVLVAGGVEAEKLdklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:PRK08565  834 -------------------------VLITESPEGNKL------------------------------------------- 845

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1033 rrkitqgddlapgvlkiVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:PRK08565  846 -----------------VKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQL 908

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1113 LEThlgmaakgIGDKINAMlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrKGMPI-ATPvFDGAK 1191
Cdd:PRK08565  909 LES--------IAGKVAAL----------------------------------------------EGRFVdATP-FYGEP 933

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1192 EAEI-KELLKLGDLPTSGQIrLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRF 1270
Cdd:PRK08565  934 EEELrKELLKLGYKPDGTEV-MYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012

                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1271 GEMEVWALEAYGAAYTLQEMLTVKSDdvngRTKMY--------------KNI----VDGN----HQMEpgMPESFNVLLK 1328
Cdd:PRK08565 1013 GEMERDCLIGHGAAMLLKERLLDSSD----KTTIYvcelcghiawydrrKNKyvcpIHGDkgniSPVE--VSYAFKLLLQ 1086

                        1450
                  ....*....|..
gi 16131817  1329 EIRSLGINIELE 1340
Cdd:PRK08565 1087 ELMSMGISPRLK 1098
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 603-1341 7.31e-61

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: 220.28  E-value: 7.31e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    603 IHYLSAIEEGNYVIAQansnldeeghFVEDLvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMG 682
Cdd:TIGR03670   92 IEYLDAEEEENAYIAL----------DPEEL-------------TPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMG 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    683 ANMQRQAVPTLRADKPLvgtgmeravAVDSgvtavakRGGVVQYvdasrivikvnedemyPgeagidiynltkytrsnqn 762
Cdd:TIGR03670  149 AAMAKQSLGLYAANYRI---------RLDT-------RGHLLHY----------------P------------------- 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    763 tcinQMPCVSlgepvERGDVLadgpsTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRD 842
Cdd:TIGR03670  178 ----QKPLVK-----TRVLEL-----IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERR 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    843 TKLGPE-EITADIPNV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTPkgetqltP---EEkllRAIFGEKASDVK 914
Cdd:TIGR03670  244 YPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LREFGLVTERRR 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    915 DSSLRVPNGVSGTVidvqvftrdgvekDKraleieemqlkqakkdlseelqileaglfsriraVLVAGGVEAEKLdklpr 994
Cdd:TIGR03670  314 DTSVTVRHGEKGIV-------------DK----------------------------------VIITETEEGNKL----- 341

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    995 drwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddlapgvlkiVKVYLAVKRRIQPGDKMAGRHGNKG 1074
Cdd:TIGR03670  342 -------------------------------------------------------VKVRVRDLRIPELGDKFASRHGQKG 366

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1075 VISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILEThlgmaakgIGDKINAMlkqqqevaklrefiqraydlgad 1154
Cdd:TIGR03670  367 VIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM--------IAGKVAAL----------------------- 415

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1155 vrqkvdlstfsdeevmrlaenlrKGMPI-ATPvFDGAKEAEI-KELLKLGDLPTSGQIrLYDGRTGEQFERPVTVGYMYM 1232
Cdd:TIGR03670  416 -----------------------EGRRVdGTP-FEGEPEEELrKELLKLGFKPDGKEV-MYDGITGEKLEAEIFIGVIYY 470

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1233 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV-------------- 1298
Cdd:TIGR03670  471 QKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYvvyvcencghiawe 550

                          730       740       750       760
                   ....*....|....*....|....*....|....*....|....*....
gi 16131817   1299 NGRTKMYKNIVDGN----HQMEpgMPESFNVLLKEIRSLGI--NIELED 1341
Cdd:TIGR03670  551 DKRKGTAYCPVCGEtgdiSPVE--MSYAFKLLLDELKSLGIspRLELGD 597
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 603-1341 2.51e-50

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 189.02  E-value: 2.51e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   603 IHYLSAIEEGNYVIAQANSNLDEEgHfvedlvtcrskgesslfsrdqvDYMDVSTQQVVSVGASLIPFLEHDDANRALMG 682
Cdd:PRK07225   98 IEYLDAEEEENAYIAVYEEDLTEE-H----------------------THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   683 ANMQRQA--VPT----LRADKplvgtgmeravavdsgvtavakRGGVVQYVDASRIVIKVNEdemypgEAGIDiynltky 756
Cdd:PRK07225  155 AGMIKQSlgLPAanykLRPDT----------------------RGHLLHYPQVPLVKTQTQE------IIGFD------- 199

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   757 trsnqntcinqmpcvslgepvERgdvladgPStdlgelalGQNMRVAFMPWNGYNFEDSILVSERVV------------- 823
Cdd:PRK07225  200 ---------------------ER-------PA--------GQNFVVAVMSYEGYNIEDALIMNKASIerglgrshffrty 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   824 ----------QEDRFTTihiqelacvsrdtklgPEEitadipNV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Cdd:PRK07225  244 egeerrypggQEDRFEI----------------PDK------DVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSP 301

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   890 kgetqltP---EEKllrAIFGEKASDVKDSSLRVPNGVSGTVidvqvftrdgvekdkraleieemqlkqakkdlseelqi 966
Cdd:PRK07225  302 -------PrflEEP---DDFGISPEKRRETSVTMRSGEEGIV-------------------------------------- 333

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   967 leaglfsriRAVLVAGGVEAEKLDKLpRDRwlelgltdeekqnqleqlaeqyDELKHEFekkleakrrkitqgddlapgv 1046
Cdd:PRK07225  334 ---------DTVILTETEEGSRLVKV-RVR----------------------DLRIPEL--------------------- 360

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1047 lkivkvylavkrriqpGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILEThlgmaakgIGD 1126
Cdd:PRK07225  361 ----------------GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM--------IGG 416

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1127 KINAMLKQqqevaklrefiqraydlgadvrqKVDlstfsdeevmrlaenlrkgmpiATPvFDGAKEAEIKELLKLGDLPT 1206
Cdd:PRK07225  417 KVGSLEGR-----------------------RVD----------------------GTA-FSGEDEEDLREALEKLGFEH 450

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817  1207 SGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Cdd:PRK07225  451 TGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAML 530

                         730       740       750       760       770       780       790
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131817  1287 LQEMLTVKSDDVN-------GRTKMY---KNIV--------DGNHQMEpgMPESFNVLLKEIRSLGI--NIELED 1341
Cdd:PRK07225  531 LKERLLDESDKVEiyvcakcGMIAIYdkkRNRKycpicgeeTDIYPVE--MSYAFKLLLDELKSLGIapRLELED 603
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 513-580 2.63e-36

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: 131.49  E-value: 2.63e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16131817    513 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Cdd:pfam04565    1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 591-656 9.90e-35

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: 126.71  E-value: 9.90e-35
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16131817    591 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVS 656
Cdd:pfam10385    1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 1266-1342 2.65e-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: 126.55  E-value: 2.65e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   1266 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVNGRTKMYKN-----IVDGNHQMEPG-MPESFNVLLKEIRSLGI 1335
Cdd:pfam04560    1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80


                   ....*..
gi 16131817   1336 NIELEDE 1342
Cdd:pfam04560   81 DPRLLLE 87
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 31-580 1.41e-26

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 115.43  E-value: 1.41e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    31 QLDSFQKFIEqdpegqYGLEAAFRSVFPIQSYSGNSE-LQYVSYRLGEPV----------FDVQECQIRGVTYSAPLRvk 99
Cdd:PRK09606   22 HIDSYNDFVD------NGLQKIIDEQGPIETEIEDGVyVELGKIRVGKPVvkeadgsereIYPMEARLRNLTYSAPLY-- 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   100 LRLVIYEREAPEGTVkdikeqEVYMGEIPLM-----------TDN-------------GTFVINGTERVIVSQLHRSPGV 155
Cdd:PRK09606   94 LEMSPVEGGEEEEPE------EVYIGELPVMvgskicnlyglSEEelievgedpldpgGYFIVNGSERVLMTLEDLAPNK 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   156 F---FDSDKGKTHSSGKVL-----YNARIIPYRGswldfefdpKDNL----FVRIDRRrkLPATIILRALNYTTEQildl 223
Cdd:PRK09606  168 IlveKDERYGDRIEVAKVFsqrrgYRALVTVERN---------RDGLlevsFPSVPGS--IPFVILMRALGLETDE---- 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   224 ffekvifEIrdnklqMELVperlrgetaSFDIEangkvyvekgrrITARHIRQLEKDDVKLIEVPVEYIAGKVV---AKD 300
Cdd:PRK09606  233 -------EI------VEAV---------SDDPE------------IVKFMLENLEEAEVDTQEEALEYIGKRVApgqTKE 278

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   301 YidestgelicaanmelsldllaKLsqsghKRIETLFTNdldhgpYISETLRVDPtNDRLSALVEIYRMmrpgepptrea 380
Cdd:PRK09606  279 Y----------------------RI-----KRAEYVIDR------YLLPHLGVEP-EVRRAKAHYLGRM----------- 313

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   381 AESLFEnlffsedrydlsavgrmkfnrsllreeiegsgilskddiidvmkklidIRNGKGEVDDIDHLGNRRIRSVGEMA 460
Cdd:PRK09606  314 AEACFE------------------------------------------------LALGRREEDDKDHYANKRLKLAGDLM 345

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   461 ENQFRVGLVRVERAVK---ERlslgdldtlmpQDMINAKP-ISAAVKE----------------FFGSSQLSQFMDQNNP 520
Cdd:PRK09606  346 EDLFRVAFNRLARDVKyqlER-----------ANMRNRELsIKTAVRSdvlterlehamatgnwVGGRTGVSQLLDRTDY 414

                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817   521 LSEITHKRRISAlgpgGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Cdd:PRK09606  415 MATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 151-454 8.30e-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: 56.59  E-value: 8.30e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    151 RSPGVFFDSDKGKTHSSGKvlYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQ-ILDlffekvi 229
Cdd:pfam04561    1 RSNGIYVEKELDKNGIIAT--YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDReILD------- 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    230 feirdnklqmelvperlrgetasfdieangkvyvekgrRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIdestgel 309
Cdd:pfam04561   72 --------------------------------------RLCYDFNDPQMLELLKPELEEAENIYTQEEALDYI------- 106

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131817    310 icaanmelsldllaklsqsgHKRIetlftndldhgpyisetlrvdptndrlsalveiyrMMRPGEPPTREAAESLFENLF 389
Cdd:pfam04561  107 --------------------GKGF-----------------------------------ALRRGEEPRLQRAREILYSRD 131

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16131817    390 fsedrydlsavGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIR 454
Cdd:pfam04561  132 -----------PKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 972-1029 2.44e-04

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 40.98  E-value: 2.44e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16131817  972 FSRIRAVLVAGGVEAEK---LDKLPRDRWLelGLTDEEKQ---NQLEQLAEQYDELKHEFEKKL 1029
Cdd:cd22011   12 SQEIRKNLKSQGSPEEKvpeLSKRAAEQWR--SLTLAEKQpyyDEVEVLKKQYDVEKEEYEKEL 73
 
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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