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Conserved domains on  [gi|355344038|gb|AER59648|]
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RNA polymerase beta subunit, partial [Mycolicibacter kumamotonensis]

Protein Classification

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;
1-240 1.34e-152

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: 452.25  E-value: 1.34e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSR-EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH 79
Cdd:PRK00405  811 ETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRH 890

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   80 GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIdvaagvpdwadqlpeklysagp 158
Cdd:PRK00405  891 GNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKgLGIKF---------------------- 948

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  159 dtrtATPVFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:PRK00405  949 ----ATPVFDGAKEEEIKELLEEAGLPE--------DGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGP 1016


                  ..
gi 355344038  239 YS 240
Cdd:PRK00405 1017 YS 1018
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-240 1.34e-152

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 452.25  E-value: 1.34e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSR-EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH 79
Cdd:PRK00405  811 ETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRH 890

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   80 GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIdvaagvpdwadqlpeklysagp 158
Cdd:PRK00405  891 GNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKgLGIKF---------------------- 948

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  159 dtrtATPVFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:PRK00405  949 ----ATPVFDGAKEEEIKELLEEAGLPE--------DGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGP 1016


                  ..
gi 355344038  239 YS 240
Cdd:PRK00405 1017 YS 1018
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-240 6.24e-151

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: 445.32  E-value: 6.24e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:COG0085   703 ETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHG 782

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAKTGwnidvaagvpdwadqlpeklysagpDT 160
Cdd:COG0085   783 NKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALL-------------------------GR 837

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  161 RTATPVFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:COG0085   838 RVATPVFDGAPEEEIRELLEKAGLPP--------DGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYS 909
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-240 1.56e-129

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: 391.33  E-value: 1.56e-129
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038     1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:TIGR02013  769 ETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHG 848

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAKTGWnidvaagvpdwadqlpeklysaGPDT 160
Cdd:TIGR02013  849 NKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLG----------------------RKGV 906

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   161 RTATPVFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:TIGR02013  907 PIATPVFDGASEEEIKEYLEKAGLPR--------DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYS 978
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-240 1.11e-102

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: 302.14  E-value: 1.11e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTpeeRLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFsredddELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:pfam00562 160 PTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHG 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAKTGwnidvaaGVPdwadqlpeklysagpdt 160
Cdd:pfam00562 231 QKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALL-------GVF----------------- 286

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  161 rTATPVFDGAQE--AELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:pfam00562 287 -VDATPFDGASTevEDIGELLEKAGYNY--------YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGP 357


                  ..
gi 355344038  239 YS 240
Cdd:pfam00562 358 YS 359
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-240 1.99e-91

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: 286.77  E-value: 1.99e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   2 TELTPEERLLraIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREdddeLPAGVNELVRVYVAQKRKISDGDKLAGRHGN 81
Cdd:cd00653  569 TPKGETESTP--IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  82 KGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIDvaagvpdwadqlpeklysagpdt 160
Cdd:cd00653  643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAlLGKFGD----------------------- 699

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038 161 rtATPvFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:cd00653  700 --ATP-FDGAEEEDISELLGEAGLNY--------YGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYS 768
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-240 1.34e-152

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 452.25  E-value: 1.34e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSR-EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH 79
Cdd:PRK00405  811 ETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRH 890

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   80 GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIdvaagvpdwadqlpeklysagp 158
Cdd:PRK00405  891 GNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKgLGIKF---------------------- 948

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  159 dtrtATPVFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:PRK00405  949 ----ATPVFDGAKEEEIKELLEEAGLPE--------DGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGP 1016


                  ..
gi 355344038  239 YS 240
Cdd:PRK00405 1017 YS 1018
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-240 6.24e-151

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: 445.32  E-value: 6.24e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:COG0085   703 ETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHG 782

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAKTGwnidvaagvpdwadqlpeklysagpDT 160
Cdd:COG0085   783 NKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALL-------------------------GR 837

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  161 RTATPVFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:COG0085   838 RVATPVFDGAPEEEIRELLEKAGLPP--------DGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYS 909
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-240 1.56e-129

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: 391.33  E-value: 1.56e-129
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038     1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:TIGR02013  769 ETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHG 848

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAKTGWnidvaagvpdwadqlpeklysaGPDT 160
Cdd:TIGR02013  849 NKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLG----------------------RKGV 906

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   161 RTATPVFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:TIGR02013  907 PIATPVFDGASEEEIKEYLEKAGLPR--------DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYS 978
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-240 1.11e-102

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: 302.14  E-value: 1.11e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTpeeRLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFsredddELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:pfam00562 160 PTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHG 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAKTGwnidvaaGVPdwadqlpeklysagpdt 160
Cdd:pfam00562 231 QKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALL-------GVF----------------- 286

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  161 rTATPVFDGAQE--AELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:pfam00562 287 -VDATPFDGASTevEDIGELLEKAGYNY--------YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGP 357


                  ..
gi 355344038  239 YS 240
Cdd:pfam00562 358 YS 359
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-240 1.99e-91

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: 286.77  E-value: 1.99e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   2 TELTPEERLLraIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREdddeLPAGVNELVRVYVAQKRKISDGDKLAGRHGN 81
Cdd:cd00653  569 TPKGETESTP--IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  82 KGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIDvaagvpdwadqlpeklysagpdt 160
Cdd:cd00653  643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAlLGKFGD----------------------- 699

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038 161 rtATPvFDGAQEAELQGLLSSTLPNRdgevmvngDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:cd00653  700 --ATP-FDGAEEEDISELLGEAGLNY--------YGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYS 768
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-240 1.23e-80

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 261.18  E-value: 1.23e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:CHL00207  742 ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHG 821

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGwiaKTGWNIDVaagvpdwadqlpeklysagpdt 160
Cdd:CHL00207  822 NKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLG---LAGDNLNK---------------------- 876

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  161 RTATPVFDGAQEAELQGLLS-------STLPNRDGEVMVNGDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHA 233
Cdd:CHL00207  877 RFKILPFDEMYGSEYSRILInnklnqaSIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHA 956


                  ....*..
gi 355344038  234 RSTGPYS 240
Cdd:CHL00207  957 RTTGPYS 963
rpoB CHL00001
RNA polymerase beta subunit
 1-240 2.85e-80

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 259.83  E-value: 2.85e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDElpaGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:CHL00001  749 ESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSS---YNPETIHVYILQKREIQVGDKVAGRHG 825

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGwiaktgwnidvaagvpdWADQLPEKLYSAGPdt 160
Cdd:CHL00001  826 NKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLG-----------------LAGDLLNRHYRIAP-- 886

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  161 rtatpvFDGAQEAEL-QGLLSSTLpNRDGEVMVN-------GDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIH 232
Cdd:CHL00001  887 ------FDERYEQEAsRKLVFSEL-YEASKQTANpwvfepeYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIH 959


                  ....*...
gi 355344038  233 ARSTGPYS 240
Cdd:CHL00001  960 ARSSGPYA 967
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
46-240 3.32e-59

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 201.69  E-value: 3.32e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   46 EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETH 125
Cdd:PRK09603 1065 EKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMH 1144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  126 LGWIAKT-GWNID--VAAGVPDWADQL--------------------------PEKLYSAGPD----TRTATPVFDGAQE 172
Cdd:PRK09603 1145 LGLVGKEfGKQIAsmLEDKTKDFAKELrakmleianainekdpltihalencsDEELLEYAKDwskgVKMAIPVFEGISQ 1224

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 355344038  173 AELQGLLSStlpnrdgeVMVNGDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:PRK09603 1225 EKFYKLFEL--------AKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYS 1284
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
50-240 1.28e-48

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 171.34  E-value: 1.28e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   50 ELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWI 129
Cdd:PRK14844 1062 DLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWA 1141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  130 AK-------------TGWNIDVAAGVPDWAD-----------------------------QLPEK--------------- 152
Cdd:PRK14844 1142 CKklgekvgnildeiNKIKSAFCKGIRSLNDdnftkfaaayldnkkienidddeitasvlNTPNKnalndelnelvenyl 1221

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  153 ----------------LYSAGPDTR-------------------------TATPVFDGAQEAELQGLLssTLPNRDGEvm 191
Cdd:PRK14844 1222 nscksaysnlrnflieVYSCGSNVSicnnirdisdnnliefarklrdgipVAAPVFEGPKDEQIAKLF--ELAGLDNS-- 1297

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 355344038  192 vngdGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYS 240
Cdd:PRK14844 1298 ----GQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYS 1342
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 12-238 8.03e-44

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: 155.57  E-value: 8.03e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   12 RAIFGEKAREVRDTSLKVPHGESGKVIgiRVFSREDDDElpagvNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPV 91
Cdd:TIGR03670 302 LREFGLVTERRRDTSVTVRHGEKGIVD--KVIITETEEG-----NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQ 374

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   92 EDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIDvaagvpdwadqlpeklysagpdtrtATPvFDGA 170
Cdd:TIGR03670 375 EDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAAlEGRRVD-------------------------GTP-FEGE 428

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 355344038  171 QEAELQGLLSstlpnrdgEVMVNGDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:TIGR03670 429 PEEELRKELL--------KLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGP 488
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 6-238 2.91e-42

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 152.80  E-value: 2.91e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038    6 PEERLLRAIFGEKarevRDTSLKVPHGESGKVIgiRVFSREDDDElpagvNELVRVYVAQKRKISDGDKLAGRHGNKGVI 85
Cdd:PRK08565  804 EELEELSLGLQER----RDTSVTVRHGEKGIVD--TVLITESPEG-----NKLVKVRVRDLRIPELGDKFASRHGQKGVI 872

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038   86 GKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIDvaagvpdwadqlpeklysagpdtrtAT 164
Cdd:PRK08565  873 GMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAAlEGRFVD-------------------------AT 927

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 355344038  165 PvFDGAQEAELQGLLsstlpnrdgevMVNG---DGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:PRK08565  928 P-FYGEPEEELRKEL-----------LKLGykpDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGP 992
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 14-238 2.10e-38

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 140.48  E-value: 2.10e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  14 IFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDdelpagvNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVED 93
Cdd:PRK07225 310 DFGISPEKRRETSVTMRSGEEGIVDTVILTETEEG-------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQED 382

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 355344038  94 MPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWIAK-TGWNIDvaagvpdwadqlpeklysagpdtrtATPvFDGAQE 172
Cdd:PRK07225 383 MPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSlEGRRVD-------------------------GTA-FSGEDE 436

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 355344038 173 AELQGLLSstlpnrdgEVMVNGDGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGP 238
Cdd:PRK07225 437 EDLREALE--------KLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGP 494
 
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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