NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|106734121|gb|ABF82547|]
View 

DNA-directed RNA polymerase III, partial [Exiguobacterium oxidotolerans]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-337 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: 729.21  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIvqgELDRYKIQKFIRSNQGTCYN 80
Cdd:PRK00405  609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGED---GVDIYNLIKFQRSNQNTCIN 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:PRK00405  686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:PRK00405  766 PEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEG 845

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  241 IILDVKIFDR-DNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPS 319
Cdd:PRK00405  846 TVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPS 925

                         330
                  ....*....|....*...
gi 106734121  320 RMNIGQLLELHLGMAARH 337
Cdd:PRK00405  926 RMNIGQILETHLGWAAKG 943
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-337 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 729.21  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIvqgELDRYKIQKFIRSNQGTCYN 80
Cdd:PRK00405  609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGED---GVDIYNLIKFQRSNQNTCIN 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:PRK00405  686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:PRK00405  766 PEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEG 845

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  241 IILDVKIFDR-DNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPS 319
Cdd:PRK00405  846 TVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPS 925

                         330
                  ....*....|....*...
gi 106734121  320 RMNIGQLLELHLGMAARH 337
Cdd:PRK00405  926 RMNIGQILETHLGWAAKG 943
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-336 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: 638.63  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121     1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNivQGELDRYKIQKFIRSNQGTCYN 80
Cdd:TIGR02013  566 QAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEP--DGGIDIYRLLKYQRSNQDTCIN 643

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:TIGR02013  644 QRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG 723

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:TIGR02013  724 PEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEG 803

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   241 IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSR 320
Cdd:TIGR02013  804 TVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883

                          330
                   ....*....|....*.
gi 106734121   321 MNIGQLLELHLGMAAR 336
Cdd:TIGR02013  884 MNIGQILETHLGWAGK 899
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 62-339 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: 600.94  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   62 LDRYKIQKFIRSNQGTCYNQKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDV 141
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  142 YTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFG 221
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  222 EKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPY 301
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 106734121  302 MPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAARHSN 339
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLG 836
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 30-336 1.05e-137

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: 395.36  E-value: 1.05e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   30 VAKHSGIAERVTAREILVRRTTEvdgnivQGELDRYKIQKFIRSNQGT---CYNQKPIIKAGDpVDKGeiladgpsmDGG 106
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMG------KQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAG---------GFG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  107 ELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECesRDTKLGP-EEITRDIPNVGDDALKNLDDRGII 185
Cdd:pfam00562  65 ELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEA--RKTKLGPiEEITRDIPNVSEEALKKLDEDGIV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  186 RVGAEVKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDrdngdeLSPGVNQLIR 265
Cdd:pfam00562 143 RVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVK 210

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 106734121  266 AYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAAR 336
Cdd:pfam00562 211 VYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAA 281
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 78-339 8.18e-115

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: 352.26  E-value: 8.18e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  78 CYNQKPIIKAGDPvdkgEILAdgpsmdGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDT 157
Cdd:cd00653  454 LYPQKPLVGTGIE----EYIA------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKT 523

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121 158 KLGPEEITR-DIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPH 236
Cdd:cd00653  524 KNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPG 596

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121 237 GGDGIILDVKIFDRdngdELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLG 316
Cdd:cd00653  597 GEKGIVDDVKIFSR----ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHG 672

                        250       260
                 ....*....|....*....|...
gi 106734121 317 VPSRMNIGQLLELHLGMAARHSN 339
Cdd:cd00653  673 FPSRMTIGQLLESLLGKAGALLG 695
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-337 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 729.21  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIvqgELDRYKIQKFIRSNQGTCYN 80
Cdd:PRK00405  609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGED---GVDIYNLIKFQRSNQNTCIN 685

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:PRK00405  686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLG 765

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:PRK00405  766 PEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEG 845

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  241 IILDVKIFDR-DNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPS 319
Cdd:PRK00405  846 TVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPS 925

                         330
                  ....*....|....*...
gi 106734121  320 RMNIGQLLELHLGMAARH 337
Cdd:PRK00405  926 RMNIGQILETHLGWAAKG 943
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-336 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: 638.63  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121     1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNivQGELDRYKIQKFIRSNQGTCYN 80
Cdd:TIGR02013  566 QAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEP--DGGIDIYRLLKYQRSNQDTCIN 643

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:TIGR02013  644 QRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLG 723

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:TIGR02013  724 PEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEG 803

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   241 IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSR 320
Cdd:TIGR02013  804 TVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883

                          330
                   ....*....|....*.
gi 106734121   321 MNIGQLLELHLGMAAR 336
Cdd:TIGR02013  884 MNIGQILETHLGWAGK 899
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 62-339 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: 600.94  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   62 LDRYKIQKFIRSNQGTCYNQKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDV 141
Cdd:COG0085   559 LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  142 YTSIHIEEYECESRDTKLGPEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFG 221
Cdd:COG0085   639 LTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  222 EKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPY 301
Cdd:COG0085   719 EKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF 798

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 106734121  302 MPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAARHSN 339
Cdd:COG0085   799 LEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLG 836
rpoB CHL00001
RNA polymerase beta subunit
 1-335 7.15e-153

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 456.29  E-value: 7.15e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRrttevdgniVQGELDRYKIQKFIRSNQGTCYN 80
Cdd:CHL00001  551 QAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILS---------GNGDTLSIPLVMYQRSNKNTCMH 621

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:CHL00001  622 QKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQG 701

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTEL--TAEERLLHAIFGEKAREVRDTSLRVPHGG 238
Cdd:CHL00001  702 PERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESsyAPEGRLLRAIFGIQVSTSKETCLKLPIGG 781

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  239 DGIILDVKIFDRDNGDELSPGVnqlIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVP 318
Cdd:CHL00001  782 RGRVIDVRWIQKKGGSSYNPET---IHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVP 858

                         330
                  ....*....|....*..
gi 106734121  319 SRMNIGQLLELHLGMAA 335
Cdd:CHL00001  859 SRMNVGQIFECLLGLAG 875
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-339 3.38e-149

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 447.23  E-value: 3.38e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRrttEVDGNIVQgeldrYKIQKFIRSNQGTCYN 80
Cdd:CHL00207  545 QAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ---DDNNRYIH-----YYLQKYQRSNQNTCIN 616

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:CHL00207  617 YRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLG 696

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:CHL00207  697 SEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYG 776

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  241 IILDVKIFDRDNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSR 320
Cdd:CHL00207  777 RVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSR 856

                         330
                  ....*....|....*....
gi 106734121  321 MNIGQLLELHLGMAARHSN 339
Cdd:CHL00207  857 MNVGQLFECLLGLAGDNLN 875
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 30-336 1.05e-137

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: 395.36  E-value: 1.05e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   30 VAKHSGIAERVTAREILVRRTTEvdgnivQGELDRYKIQKFIRSNQGT---CYNQKPIIKAGDpVDKGeiladgpsmDGG 106
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMG------KQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAG---------GFG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  107 ELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECesRDTKLGP-EEITRDIPNVGDDALKNLDDRGII 185
Cdd:pfam00562  65 ELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEA--RKTKLGPiEEITRDIPNVSEEALKKLDEDGIV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  186 RVGAEVKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDrdngdeLSPGVNQLIR 265
Cdd:pfam00562 143 RVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVK 210

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 106734121  266 AYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAAR 336
Cdd:pfam00562 211 VYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAA 281
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-336 2.22e-116

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 370.41  E-value: 2.22e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEVDGNIvqgelDRYKIQKFIRSNQGTCYN 80
Cdd:PRK09603  702 QAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEAYI-----DAYSLQKNLRTNQNTSFN 776

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:PRK09603  777 QVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHG 856

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:PRK09603  857 VEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEG 936

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  241 IILDVKIF---------------------------DR------------------------------------------- 250
Cdd:PRK09603  937 TVIDVKVFtkkgyekdarvlsayeeekakldmehfDRltmlnreellrvssllsqaileepfshngkdykegdqipkeei 1016

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  251 ------------------------------------------------DNGDELSPGVNQLIRAYIVQKRKIHEGDKMAG 282
Cdd:PRK09603 1017 asinrftlaslvkkyskevqnhyeitknnfleqkkvlgeeheeklsilEKDDILPNGVIKKVKLYIATKRKLKVGDKMAG 1096

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 106734121  283 RHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAAR 336
Cdd:PRK09603 1097 RHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGK 1150
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 78-339 8.18e-115

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: 352.26  E-value: 8.18e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  78 CYNQKPIIKAGDPvdkgEILAdgpsmdGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDT 157
Cdd:cd00653  454 LYPQKPLVGTGIE----EYIA------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKT 523

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121 158 KLGPEEITR-DIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPH 236
Cdd:cd00653  524 KNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPG 596

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121 237 GGDGIILDVKIFDRdngdELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLG 316
Cdd:cd00653  597 GEKGIVDDVKIFSR----ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHG 672

                        250       260
                 ....*....|....*....|...
gi 106734121 317 VPSRMNIGQLLELHLGMAARHSN 339
Cdd:cd00653  673 FPSRMTIGQLLESLLGKAGALLG 695
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-336 1.50e-106

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 342.37  E-value: 1.50e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121    1 QAVPLLDPESPIVGTGMEYVSAKDSGAAVVAKHSGIAERVTAREILVRRTTEvdGNIVQGELDRYKIQKFIRSNQGTCYN 80
Cdd:PRK14844  709 QAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDK--ERVNYLDVDIYHLRKFQRSNHNTCIN 786

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121   81 QKPIIKAGDPVDKGEILADGPSMDGGELALGRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLG 160
Cdd:PRK14844  787 QKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLG 866

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  161 PEEITRDIPNVGDDALKNLDDRGIIRVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGDG 240
Cdd:PRK14844  867 SEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEG 946

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  241 IILDVKIFDR---------------------------------------------------------------------- 250
Cdd:PRK14844  947 TVIDVQVFTRrgveenerallikqkeindfekerdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknq 1026

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  251 -------------------------------DNGDELSPGVNQLIRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDM 299
Cdd:PRK14844 1027 siseqvkslkkdfdekvshaiaqfkrkveklHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDM 1106

                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 106734121  300 PYMPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAAR 336
Cdd:PRK14844 1107 PYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACK 1143
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 111-335 1.32e-41

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: 152.87  E-value: 1.32e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  111 GRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPE-EITRDIPNV----GDDALKNLDDRGII 185
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIV 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  186 RVGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGdelspgvNQL 263
Cdd:TIGR03670 278 YPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEG-------NKL 341

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 106734121  264 IRAYIVQKRKIHEGDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAA 335
Cdd:TIGR03670 342 VKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVA 413
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 111-335 3.30e-40

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 150.49  E-value: 3.30e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  111 GRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPE-EITRDIPNV----GDDALKNLDDRGII 185
Cdd:PRK08565  702 GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIV 781

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121  186 RVGAEVKDGDILVGKVTPKGVTELTAEERLlhaifGEKARevRDTSLRVPHGGDGIILDVKIFDrdngdelSPGVNQLIR 265
Cdd:PRK08565  782 SPEVEVKGGDVLIGKTSPPRFLEELEELSL-----GLQER--RDTSVTVRHGEKGIVDTVLITE-------SPEGNKLVK 847

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 106734121  266 AYiVQKRKIHE-GDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSRMNIGQLLELHLGMAA 335
Cdd:PRK08565  848 VR-VRDLRIPElGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVA 917
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 111-329 4.15e-38

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 143.18  E-value: 4.15e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121 111 GRNVLVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYECESRDTKLGPE-EITRDIPNV----GDDALKNLDDRGII 185
Cdd:PRK07225 204 GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEdRFEIPDKDVrgyrGEEAYRHLDEDGLV 283

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 106734121 186 RVGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKAREVRDTSLRVPHGGDGIILDVKIFDRDNGDELSPgvnql 263
Cdd:PRK07225 284 NPETEVKEGDVLIGKTSPP---------RFLeePDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVK----- 349

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 106734121 264 IRayiVQKRKIHE-GDKMAGRHGNKGVISRILPEEDMPYMPDGTPIDIMLNPLGVPSRMNIGQLLEL 329
Cdd:PRK07225 350 VR---VRDLRIPElGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM 413
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH