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Conserved domains on  [gi|374251333|gb|AEZ00238|]
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DNA-directed RNA polymerase beta subunit, partial [Streptococcus porcinus]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 1000195)

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

CATH:  3.90.1110.10
EC:  2.7.7.6
Gene Ontology:  GO:0000428|GO:0003899|GO:0006351
PubMed:  6266829
SCOP:  4003708

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-384 0e+00

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 846.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    1 QHDGKVVFSDAEKVEVRRE-----DGSLDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNP 75
Cdd:PRK00405  640 KRDGVVEYVDASRIVVRVEeldpgEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNV 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   76 VVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEG 155
Cdd:PRK00405  720 LVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPG 799

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  156 DILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTR-ANGDELQSGVNMLVRVYIAQKRK 234
Cdd:PRK00405  800 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRK 879

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  235 IKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAE 314
Cdd:PRK00405  880 IQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEE 959

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  315 DLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:PRK00405  960 EIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-384 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 846.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    1 QHDGKVVFSDAEKVEVRRE-----DGSLDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNP 75
Cdd:PRK00405  640 KRDGVVEYVDASRIVVRVEeldpgEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNV 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   76 VVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEG 155
Cdd:PRK00405  720 LVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPG 799

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  156 DILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTR-ANGDELQSGVNMLVRVYIAQKRK 234
Cdd:PRK00405  800 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRK 879

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  235 IKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAE 314
Cdd:PRK00405  880 IQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEE 959

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  315 DLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:PRK00405  960 EIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 23-384 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: 762.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   23 LDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDV 102
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  103 YTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFG 182
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  183 DKSREVRDTSLRVPHGGDGIVRDVKIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPY 262
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  263 LPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAEDLWETVAEAGMDSDAKTVLYDGRTGEPF 342
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPF 878

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 374251333  343 DNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:COG0085   879 DNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKA 920
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-384 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: 721.06  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333     1 QHDGKVVFSDAEKVEVRR------EDGSLDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQN 74
Cdd:TIGR02013  597 KRGGVVEYVDAKRIVIRYdedeeePDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRN 676

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    75 PVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKE 154
Cdd:TIGR02013  677 VLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKA 756

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   155 GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRANGDELQSGVNMLVRVYIAQKRK 234
Cdd:TIGR02013  757 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRK 836

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   235 IKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLG---IHIATPVFDGA 311
Cdd:TIGR02013  837 IQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGA 916

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374251333   312 SAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:TIGR02013  917 SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKA 989
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-384 0e+00

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 530.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    2 HDGKVVFSDAEKVEVRREDG--SLDVYHVTKFRRSNSGT---AYNQRTLVKVGdIIEKGDFiadgpsmenGEMALGQNPV 76
Cdd:pfam00562   4 LIPFVDHNQSPRNTYQCAMGkqAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGGF---------GELPLGQNAI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   77 VAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFEseTRDTKLGP-EEITREVPNVGEEALKDLDEMGIIRIGAEVKEG 155
Cdd:pfam00562  74 VAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPG 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  156 DILVGKVTPkgekdlSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTrangdeLQSGVNMLVRVYIAQKRKI 235
Cdd:pfam00562 152 DILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQKRKP 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  236 KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGAS--A 313
Cdd:pfam00562 220 EVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteV 299

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 374251333  314 EDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:pfam00562 300 EDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRA 370
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 40-384 4.40e-164

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: 481.68  E-value: 4.40e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  40 YNQRTLVKVGdIIEKGDFiadgpsmenGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTK 119
Cdd:cd00653  455 YPQKPLVGTG-IEEYIAF---------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK 524

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 120 LGPEEITR-EVPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAeerllhaIFGDKSREVRDTSLRVPHG 198
Cdd:cd00653  525 NGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGG 597

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 199 GDGIVRDVKIFTRangdELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGV 278
Cdd:cd00653  598 EKGIVDDVKIFSR----ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 279 PSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHH 358
Cdd:cd00653  674 PSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKH 753

                        330       340
                 ....*....|....*....|....*.
gi 374251333 359 MVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:cd00653  754 MVDDKIHARSTGPYSLLTRQPLKGRS 779
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-384 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 846.69  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    1 QHDGKVVFSDAEKVEVRRE-----DGSLDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNP 75
Cdd:PRK00405  640 KRDGVVEYVDASRIVVRVEeldpgEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNV 719

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   76 VVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEG 155
Cdd:PRK00405  720 LVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPG 799

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  156 DILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTR-ANGDELQSGVNMLVRVYIAQKRK 234
Cdd:PRK00405  800 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRK 879

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  235 IKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAE 314
Cdd:PRK00405  880 IQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEE 959

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  315 DLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:PRK00405  960 EIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 23-384 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: 762.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   23 LDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDV 102
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  103 YTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAEERLLHAIFG 182
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  183 DKSREVRDTSLRVPHGGDGIVRDVKIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPY 262
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  263 LPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAEDLWETVAEAGMDSDAKTVLYDGRTGEPF 342
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPF 878

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 374251333  343 DNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:COG0085   879 DNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKA 920
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-384 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: 721.06  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333     1 QHDGKVVFSDAEKVEVRR------EDGSLDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQN 74
Cdd:TIGR02013  597 KRGGVVEYVDAKRIVIRYdedeeePDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRN 676

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    75 PVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKE 154
Cdd:TIGR02013  677 VLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKA 756

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   155 GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRANGDELQSGVNMLVRVYIAQKRK 234
Cdd:TIGR02013  757 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRK 836

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   235 IKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLG---IHIATPVFDGA 311
Cdd:TIGR02013  837 IQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGA 916

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374251333   312 SAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:TIGR02013  917 SEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKA 989
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-384 0e+00

RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 530.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    2 HDGKVVFSDAEKVEVRREDG--SLDVYHVTKFRRSNSGT---AYNQRTLVKVGdIIEKGDFiadgpsmenGEMALGQNPV 76
Cdd:pfam00562   4 LIPFVDHNQSPRNTYQCAMGkqAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGGF---------GELPLGQNAI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   77 VAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFEseTRDTKLGP-EEITREVPNVGEEALKDLDEMGIIRIGAEVKEG 155
Cdd:pfam00562  74 VAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPG 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  156 DILVGKVTPkgekdlSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTrangdeLQSGVNMLVRVYIAQKRKI 235
Cdd:pfam00562 152 DILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQKRKP 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  236 KVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFDGAS--A 313
Cdd:pfam00562 220 EVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteV 299

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 374251333  314 EDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:pfam00562 300 EDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRA 370
rpoB CHL00001
RNA polymerase beta subunit
 1-384 3.51e-168

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 497.89  E-value: 3.51e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    1 QHDGKVVFSDAEKVEVRREDGSLDvYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNPVVAYM 80
Cdd:CHL00001  582 EHEGKIIYTDTDKIILSGNGDTLS-IPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYM 660

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   81 TWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEGDILVG 160
Cdd:CHL00001  661 PWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVG 740

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  161 KVTPKGEKDLS--AEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRangDELQSGVNMLVRVYIAQKRKIKVG 238
Cdd:CHL00001  741 KLTPQEAEESSyaPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQK---KGGSSYNPETIHVYILQKREIQVG 817

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  239 DKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFD---GASA-- 313
Cdd:CHL00001  818 DKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDeryEQEAsr 897

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  314 ----EDLWETVAEAG------MDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGK 383
Cdd:CHL00001  898 klvfSELYEASKQTAnpwvfePEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGR 977


                  .
gi 374251333  384 A 384
Cdd:CHL00001  978 S 978
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-384 2.00e-165

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 491.14  E-value: 2.00e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    1 QHDGKVVFSDAEKVEVRREDGSLDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNPVVAYM 80
Cdd:CHL00207  576 LTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYM 655

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   81 TWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEGDILVG 160
Cdd:CHL00207  656 PWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVG 735

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  161 KVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRANGDELQSGVNMLVRVYIAQKRKIKVGDK 240
Cdd:CHL00207  736 KITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDK 815

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  241 MAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHIATPVFD-----GASAED 315
Cdd:CHL00207  816 LAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDemygsEYSRIL 895

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 374251333  316 LWETVAEAGMDSD----------AKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:CHL00207  896 INNKLNQASIKNNeywlfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKA 974
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 40-384 4.40e-164

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: 481.68  E-value: 4.40e-164
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  40 YNQRTLVKVGdIIEKGDFiadgpsmenGEMALGQNPVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTK 119
Cdd:cd00653  455 YPQKPLVGTG-IEEYIAF---------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK 524

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 120 LGPEEITR-EVPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKGEKDLSAeerllhaIFGDKSREVRDTSLRVPHG 198
Cdd:cd00653  525 NGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGG 597

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 199 GDGIVRDVKIFTRangdELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGV 278
Cdd:cd00653  598 EKGIVDDVKIFSR----ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 279 PSRMNIGQVMELHLGMAARNLGIHIATPVFDGASAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHH 358
Cdd:cd00653  674 PSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKH 753

                        330       340
                 ....*....|....*....|....*.
gi 374251333 359 MVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:cd00653  754 MVDDKIHARSTGPYSLLTRQPLKGRS 779
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
10-384 4.60e-131

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 414.71  E-value: 4.60e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   10 DAEKVEVRREDGS---LDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQNPVVAYMTWEGYN 86
Cdd:PRK09603  742 DSKNIYILGEGKEeayIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYN 821

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   87 FEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKEGDILVGKVTPKG 166
Cdd:PRK09603  822 FEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKG 901

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  167 EKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA---------------------------------- 212
Cdd:PRK09603  902 EIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKgyekdarvlsayeeekakldmehfdrltmlnree 981

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  213 -------------------NG----------------------------------------------------------- 214
Cdd:PRK09603  982 llrvssllsqaileepfshNGkdykegdqipkeeiasinrftlaslvkkyskevqnhyeitknnfleqkkvlgeeheekl 1061

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  215 ------DELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVM 288
Cdd:PRK09603 1062 silekdDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQIL 1141

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  289 ELHLGMAARNLGIHI----------------------------------------------------------ATPVFDG 310
Cdd:PRK09603 1142 EMHLGLVGKEFGKQIasmledktkdfakelrakmleianainekdpltihalencsdeelleyakdwskgvkmAIPVFEG 1221

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 374251333  311 ASAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:PRK09603 1222 ISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKA 1295
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-384 1.08e-121

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 387.83  E-value: 1.08e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333    1 QHDGKVVFSDAEKVEVRREDGS------LDVYHVTKFRRSNSGTAYNQRTLVKVGDIIEKGDFIADGPSMENGEMALGQN 74
Cdd:PRK14844  740 KRDGIVDSSDSNSIVIRAFDKErvnyldVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQN 819

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   75 PVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEITREVPNVGEEALKDLDEMGIIRIGAEVKE 154
Cdd:PRK14844  820 LLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGP 899

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  155 GDILVGKVTPKGEKDLSAEERLLHAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRA---------------------- 212
Cdd:PRK14844  900 GYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRgveenerallikqkeindfeke 979

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  213 -------------------------------------------------------------------------------N 213
Cdd:PRK14844  980 rdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhE 1059

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  214 GDELQSGVNMLVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLG 293
Cdd:PRK14844 1060 GYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVG 1139

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  294 MAARNL-------------------------------------------------------------------------- 299
Cdd:PRK14844 1140 WACKKLgekvgnildeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelven 1219

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  300 -------------------------------------------------GIHIATPVFDGASAEDLWETVAEAGMDSDAK 330
Cdd:PRK14844 1220 ylnscksaysnlrnflievyscgsnvsicnnirdisdnnliefarklrdGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQ 1299

                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....
gi 374251333  331 TVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:PRK14844 1300 AVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKS 1353
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 72-384 7.86e-79

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: 253.80  E-value: 7.86e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   72 GQNPVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPE-EITREVPNV----GEEALKDLDEMGII 146
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIV 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  147 RIGAEVKEGDILVGKVTPKgekdlsaeeRLL--HAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRANGdelqsgvNML 224
Cdd:TIGR03670 278 YPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEG-------NKL 341

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  225 VRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI- 303
Cdd:TIGR03670 342 VKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVd 421

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  304 ATPvFDGASAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGK 383
Cdd:TIGR03670 422 GTP-FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGR 500


                  .
gi 374251333  384 A 384
Cdd:TIGR03670 501 A 501
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 72-384 6.51e-74

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 241.02  E-value: 6.51e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  72 GQNPVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPEEiTREVPNV------GEEALKDLDEMGI 145
Cdd:PRK07225 204 GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQED-RFEIPDKdvrgyrGEEAYRHLDEDGL 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 146 IRIGAEVKEGDILVGKVTPKgekdlsaeeRLL--HAIFGDKSREVRDTSLRVPHGGDGIVRDVKIFTRANGdelqsgvNM 223
Cdd:PRK07225 283 VNPETEVKEGDVLIGKTSPP---------RFLeePDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEG-------SR 346

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 224 LVRVYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI 303
Cdd:PRK07225 347 LVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRV 426

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333 304 ATPVFDGASAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGK 383
Cdd:PRK07225 427 DGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGR 506


                 .
gi 374251333 384 A 384
Cdd:PRK07225 507 A 507
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 72-384 4.03e-72

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 243.71  E-value: 4.03e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333   72 GQNPVVAYMTWEGYNFEDAVIMSERLVKEDVYTSVHLEEFESETRDTKLGPE-EITREVPNV----GEEALKDLDEMGII 146
Cdd:PRK08565  702 GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIV 781

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  147 RIGAEVKEGDILVGKVTPKgeKDLSAEERLLHAIFgdksrEVRDTSLRVPHGGDGIVRDVKIFTRANGdelqsgvNMLVR 226
Cdd:PRK08565  782 SPEVEVKGGDVLIGKTSPP--RFLEELEELSLGLQ-----ERRDTSVTVRHGEKGIVDTVLITESPEG-------NKLVK 847

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374251333  227 VYIAQKRKIKVGDKMAGRHGNKGVVSRIVPVEDMPYLPDGTPVDIMLNPLGVPSRMNIGQVMELHLGMAARNLGIHI-AT 305
Cdd:PRK08565  848 VRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVdAT 927

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 374251333  306 PvFDGASAEDLWETVAEAGMDSDAKTVLYDGRTGEPFDNRVSVGVMYMIKLHHMVDDKLHARSVGPYSLVTQQPLGGKA 384
Cdd:PRK08565  928 P-FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRA 1005
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 3-62 7.84e-03

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 38.51  E-value: 7.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 374251333    3 DGKVVFSDAEK----VEVRREDGSLDVYHVTKfrrsnsgtayNQRTLVKVGDIIEKGDFIADGP 62
Cdd:PRK00566  935 DGTVSFGKETKgkrrIVITPDDGEEREYLIPK----------GKHLLVQEGDHVEAGDKLTDGS 988
 
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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