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Conserved domains on  [gi|315435604|gb|ADU18192|]
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RNA polymerase beta-subunit, partial [Mycobacterium sp. FI-09045]

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;
1-237 8.11e-155

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: 458.03  E-value: 8.11e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSR-EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH 79
Cdd:PRK00405  811 ETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRH 890

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   80 GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKingspdwasalpkellesepgsi 158
Cdd:PRK00405  891 GNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGlGIK----------------------- 947

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 315435604  159 VSTPVFDGAREAELQGLLgstlpnrdGETLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:PRK00405  948 FATPVFDGAKEEEIKELL--------EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYS 1018
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-237 8.11e-155

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 458.03  E-value: 8.11e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSR-EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH 79
Cdd:PRK00405  811 ETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRH 890

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   80 GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKingspdwasalpkellesepgsi 158
Cdd:PRK00405  891 GNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGlGIK----------------------- 947

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 315435604  159 VSTPVFDGAREAELQGLLgstlpnrdGETLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:PRK00405  948 FATPVFDGAKEEEIKELL--------EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYS 1018
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-237 3.51e-152

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: 448.40  E-value: 3.51e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:COG0085   703 ETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHG 782

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKSGwkingspdwasalpkellesepGSIVS 160
Cdd:COG0085   783 NKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALL----------------------GRRVA 840

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604  161 TPVFDGAREAELQGLLgstlpnrdGETLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:COG0085   841 TPVFDGAPEEEIRELL--------EKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYS 909
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-237 1.30e-130

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: 394.03  E-value: 1.30e-130
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604     1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:TIGR02013  769 ETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHG 848

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKSGWKingspdwasalpkellesePGSIVS 160
Cdd:TIGR02013  849 NKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGR-------------------KGVPIA 909

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604   161 TPVFDGAREAELQGLLGSTLPNRdgetlvdeDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:TIGR02013  910 TPVFDGASEEEIKEYLEKAGLPR--------DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYS 978
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-237 1.98e-104

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: 306.38  E-value: 1.98e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTpeeRLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFsredddELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:pfam00562 160 PTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHG 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKSGwkingspdwasalpkellesepGSIVS 160
Cdd:pfam00562 231 QKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALL----------------------GVFVD 288

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604  161 TPVFDGAREAELQglLGSTLpNRDGetlVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:pfam00562 289 ATPFDGASTEVED--IGELL-EKAG---YNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYS 359
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-237 2.76e-92

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: 289.08  E-value: 2.76e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   2 TELTPEERLLraIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREdddeLPAGVNELVRVYVAQKRKISDGDKLAGRHGN 81
Cdd:cd00653  569 TPKGETESTP--IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  82 KGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAK-SGWKINGSPdwasalpkellesepgsivs 160
Cdd:cd00653  643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAlLGKFGDATP-------------------- 702

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604 161 tpvFDGAREAELQGLLGSTLPNRdgetlvdeDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:cd00653  703 ---FDGAEEEDISELLGEAGLNY--------YGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYS 768
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-237 8.11e-155

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 458.03  E-value: 8.11e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSR-EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRH 79
Cdd:PRK00405  811 ETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRH 890

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   80 GNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKS-GWKingspdwasalpkellesepgsi 158
Cdd:PRK00405  891 GNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGlGIK----------------------- 947

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 315435604  159 VSTPVFDGAREAELQGLLgstlpnrdGETLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:PRK00405  948 FATPVFDGAKEEEIKELL--------EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYS 1018
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-237 3.51e-152

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: 448.40  E-value: 3.51e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:COG0085   703 ETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHG 782

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKSGwkingspdwasalpkellesepGSIVS 160
Cdd:COG0085   783 NKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALL----------------------GRRVA 840

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604  161 TPVFDGAREAELQGLLgstlpnrdGETLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:COG0085   841 TPVFDGAPEEEIRELL--------EKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYS 909
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-237 1.30e-130

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: 394.03  E-value: 1.30e-130
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604     1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:TIGR02013  769 ETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHG 848

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKSGWKingspdwasalpkellesePGSIVS 160
Cdd:TIGR02013  849 NKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGR-------------------KGVPIA 909

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604   161 TPVFDGAREAELQGLLGSTLPNRdgetlvdeDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:TIGR02013  910 TPVFDGASEEEIKEYLEKAGLPR--------DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYS 978
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-237 1.98e-104

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: 306.38  E-value: 1.98e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTpeeRLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFsredddELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:pfam00562 160 PTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHG 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAKSGwkingspdwasalpkellesepGSIVS 160
Cdd:pfam00562 231 QKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALL----------------------GVFVD 288

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604  161 TPVFDGAREAELQglLGSTLpNRDGetlVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:pfam00562 289 ATPFDGASTEVED--IGELL-EKAG---YNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYS 359
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-237 2.76e-92

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: 289.08  E-value: 2.76e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   2 TELTPEERLLraIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREdddeLPAGVNELVRVYVAQKRKISDGDKLAGRHGN 81
Cdd:cd00653  569 TPKGETESTP--IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  82 KGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAK-SGWKINGSPdwasalpkellesepgsivs 160
Cdd:cd00653  643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAlLGKFGDATP-------------------- 702

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 315435604 161 tpvFDGAREAELQGLLGSTLPNRdgetlvdeDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:cd00653  703 ---FDGAEEEDISELLGEAGLNY--------YGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYS 768
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-237 1.11e-80

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 261.18  E-value: 1.11e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:CHL00207  742 ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHG 821

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGwvaKSGWKINGSpdwASALP-KELLESEPGSIV 159
Cdd:CHL00207  822 NKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLG---LAGDNLNKR---FKILPfDEMYGSEYSRIL 895

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 315435604  160 STPVFDGAREAELQG-LLGSTLPnrdgetlvdedGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:CHL00207  896 INNKLNQASIKNNEYwLFNSYHP-----------GKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYS 963
rpoB CHL00001
RNA polymerase beta subunit
 1-237 3.70e-78

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 254.06  E-value: 3.70e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    1 ETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDDElpaGVNELVRVYVAQKRKISDGDKLAGRHG 80
Cdd:CHL00001  749 ESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSS---YNPETIHVYILQKREIQVGDKVAGRHG 825

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   81 NKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGwvaksgwkingspdwasaLPKELLESE----Pg 156
Cdd:CHL00001  826 NKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLG------------------LAGDLLNRHyriaP- 886

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  157 sivstpvFDGAREAEL-QGLLGSTLPNRDGET----LVDED--GKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIH 229
Cdd:CHL00001  887 -------FDERYEQEAsRKLVFSELYEASKQTanpwVFEPEypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIH 959


                  ....*...
gi 315435604  230 ARSTGPYS 237
Cdd:CHL00001  960 ARSSGPYA 967
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
46-237 2.94e-60

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 204.77  E-value: 2.94e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   46 EDDDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETH 125
Cdd:PRK09603 1065 EKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMH 1144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  126 LGWVAKS-GWKI-----NGSPDWASALPKELLE-----SEPGSIV-------------------------STPVFDGARE 169
Cdd:PRK09603 1145 LGLVGKEfGKQIasmleDKTKDFAKELRAKMLEianaiNEKDPLTihalencsdeelleyakdwskgvkmAIPVFEGISQ 1224

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 315435604  170 AELQGLLGStlpnrdgeTLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:PRK09603 1225 EKFYKLFEL--------AKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYS 1284
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
50-237 1.13e-48

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 171.34  E-value: 1.13e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   50 ELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWV 129
Cdd:PRK14844 1062 DLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWA 1141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  130 AKS-GWKI------------------------------------------------------------------------ 136
Cdd:PRK14844 1142 CKKlGEKVgnildeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenyl 1221

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  137 NGSPDWASALPKELLES----------------------------EPGSIVSTPVFDGAREAELQGLLgsTLPNrdgetl 188
Cdd:PRK14844 1222 NSCKSAYSNLRNFLIEVyscgsnvsicnnirdisdnnliefarklRDGIPVAAPVFEGPKDEQIAKLF--ELAG------ 1293

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 315435604  189 VDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGPYS 237
Cdd:PRK14844 1294 LDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYS 1342
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 12-235 1.73e-45

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: 159.81  E-value: 1.73e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   12 RAIFGEKAREVRDTSLKVPHGESGKVIgiRVFSREDDDElpagvNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPV 91
Cdd:TIGR03670 302 LREFGLVTERRRDTSVTVRHGEKGIVD--KVIITETEEG-----NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQ 374

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   92 EDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAK-SGWKINGSPdwasalpkellesepgsivstpvFDGAREA 170
Cdd:TIGR03670 375 EDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAAlEGRRVDGTP-----------------------FEGEPEE 431

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 315435604  171 ELQGLLgstlpnrdGETLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGP 235
Cdd:TIGR03670 432 ELRKEL--------LKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGP 488
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 6-235 1.13e-41

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 150.88  E-value: 1.13e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604    6 PEERLLRAIFGEKarevRDTSLKVPHGESGKVIgiRVFSREDDDElpagvNELVRVYVAQKRKISDGDKLAGRHGNKGVI 85
Cdd:PRK08565  804 EELEELSLGLQER----RDTSVTVRHGEKGIVD--TVLITESPEG-----NKLVKVRVRDLRIPELGDKFASRHGQKGVI 872

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604   86 GKILPVEDMPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAK-SGWKINGSPdwasalpkellesepgsivstpvF 164
Cdd:PRK08565  873 GMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAAlEGRFVDATP-----------------------F 929

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 315435604  165 DGAREAELQGLLgstlpnrdGETLVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGP 235
Cdd:PRK08565  930 YGEPEEELRKEL--------LKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGP 992
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 14-235 2.57e-41

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 148.57  E-value: 2.57e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  14 IFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDDdelpagvNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVED 93
Cdd:PRK07225 310 DFGISPEKRRETSVTMRSGEEGIVDTVILTETEEG-------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQED 382

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 315435604  94 MPFLPDGTPVDIILNTHGVPRRMNIGQILETHLGWVAK-SGWKINGSPdwasalpkellesepgsivstpvFDGAREAEL 172
Cdd:PRK07225 383 MPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSlEGRRVDGTA-----------------------FSGEDEEDL 439

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 315435604 173 QGLLgstlpNRDGetlVDEDGKAMLFDGRSGEPFPYPVTVGYMYILKLHHLVDDKIHARSTGP 235
Cdd:PRK07225 440 REAL-----EKLG---FEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGP 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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