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Conserved domains on  [gi|199580787|gb|ACH89095|]
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RNA polymerase subunit beta, partial [Staphylococcus succinus subsp. succinus]

Protein Classification

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

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-231 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: 530.44  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:PRK00405  769 ITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVI 848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:PRK00405  849 DVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMN 928

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:PRK00405  929 IGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYML 999
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-231 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 530.44  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:PRK00405  769 ITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVI 848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:PRK00405  849 DVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMN 928

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:PRK00405  929 IGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYML 999
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-231 2.87e-169

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: 491.93  E-value: 2.87e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:COG0085   661 ITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVI 740

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:COG0085   741 DVKVFSREEGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMN 819

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:COG0085   820 VGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYL 890
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-231 2.56e-153

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: 452.58  E-value: 2.56e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787     1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:TIGR02013  727 ITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVI 806

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    81 DVKVFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:TIGR02013  807 DVKVFSREQGDE-LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMN 885

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 199580787   161 IGQVLELHLGMAAKNLG---IHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:TIGR02013  886 IGQILETHLGWAGKRLGrkgVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYML 959
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-231 5.27e-121

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: 348.37  E-value: 5.27e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:pfam00562 121 ITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVD 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFnreegddTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:pfam00562 195 DVIVF-------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMT 267

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFDGASD--EDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:pfam00562 268 IGQLLETHLGKAAALLGVFVDATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQ 340
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-231 3.86e-105

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: 322.60  E-value: 3.86e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:cd00653  531 TRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVD 603

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  81 DVKVFNREegddtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:cd00653  604 DVKIFSRE-----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMT 678

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199580787 161 IGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:cd00653  679 IGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQ 749
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-231 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 530.44  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:PRK00405  769 ITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVI 848

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFNREEGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:PRK00405  849 DVKVFTRIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMN 928

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:PRK00405  929 IGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYML 999
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-231 2.87e-169

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: 491.93  E-value: 2.87e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:COG0085   661 ITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVI 740

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:COG0085   741 DVKVFSREEGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMN 819

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:COG0085   820 VGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYL 890
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-231 2.56e-153

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: 452.58  E-value: 2.56e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787     1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:TIGR02013  727 ITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVI 806

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    81 DVKVFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:TIGR02013  807 DVKVFSREQGDE-LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMN 885

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 199580787   161 IGQVLELHLGMAAKNLG---IHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:TIGR02013  886 IGQILETHLGWAGKRLGrkgVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYML 959
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-231 5.27e-121

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: 348.37  E-value: 5.27e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:pfam00562 121 ITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVD 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFnreegddTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:pfam00562 195 DVIVF-------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMT 267

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFDGASD--EDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:pfam00562 268 IGQLLETHLGKAAALLGVFVDATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQ 340
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-231 3.86e-105

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: 322.60  E-value: 3.86e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:cd00653  531 TRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVD 603

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  81 DVKVFNREegddtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:cd00653  604 DVKIFSRE-----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMT 678

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 199580787 161 IGQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:cd00653  679 IGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQ 749
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-231 5.56e-94

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 297.00  E-value: 5.56e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:CHL00207  700 ITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVI 779

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFNREEGDdTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMN 160
Cdd:CHL00207  780 KVEIFSRSKGD-ELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMN 858

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  161 IGQVLELHLGMAAKNLGIHVASPVFD-----GASDEDVWSTIEEAGMARD----------GKTVLYDGRTGEPFDNRISV 225
Cdd:CHL00207  859 VGQLFECLLGLAGDNLNKRFKILPFDemygsEYSRILINNKLNQASIKNNeywlfnsyhpGKMVLRDGRTGYKFKNPVTV 938


                  ....*.
gi 199580787  226 GVMYML 231
Cdd:CHL00207  939 GIAYML 944
rpoB CHL00001
RNA polymerase beta subunit
 1-231 1.72e-88

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 281.79  E-value: 1.72e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTEL--TAEERLLHAIFGEKAREVRDTSLRVPHGAGGI 78
Cdd:CHL00001  705 ITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESsyAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGR 784

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   79 VLDVKVFNREEGDDtlspGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSR 158
Cdd:CHL00001  785 VIDVRWIQKKGGSS----YNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSR 860

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  159 MNIGQVLELHLGMAAKNLGIHVASPVFD-----GASDEDVWSTIEEAGMARD----------GKTVLYDGRTGEPFDNRI 223
Cdd:CHL00001  861 MNVGQIFECLLGLAGDLLNRHYRIAPFDeryeqEASRKLVFSELYEASKQTAnpwvfepeypGKSRLFDGRTGDPFEQPV 940


                  ....*...
gi 199580787  224 SVGVMYML 231
Cdd:CHL00001  941 TIGKAYIL 948
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-231 2.72e-67

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 224.42  E-value: 2.72e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:PRK09603  860 FTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVI 939

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVF---------------------------------NREE-------------------------------------- 89
Cdd:PRK09603  940 DVKVFtkkgyekdarvlsayeeekakldmehfdrltmlNREEllrvssllsqaileepfshngkdykegdqipkeeiasi 1019

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   90 ----------------------------------------------GDDTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHG 123
Cdd:PRK09603 1020 nrftlaslvkkyskevqnhyeitknnfleqkkvlgeeheeklsileKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHG 1099

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  124 NKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNL--------------------------- 176
Cdd:PRK09603 1100 NKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFgkqiasmledktkdfakelrakmleia 1179

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  177 -------------------------------GIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISV 225
Cdd:PRK09603 1180 nainekdpltihalencsdeelleyakdwskGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNV 1259


                  ....*.
gi 199580787  226 GVMYML 231
Cdd:PRK09603 1260 GYMYMI 1265
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 9-229 2.65e-51

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: 175.22  E-value: 2.65e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    9 SDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKgvteltaeeRLL--HAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFN 86
Cdd:TIGR03670 264 GEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTERRRDTSVTVRHGEKGIVDKVIITE 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   87 REEGddtlspgvNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLE 166
Cdd:TIGR03670 335 TEEG--------NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 406

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199580787  167 LHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMY 229
Cdd:TIGR03670 407 MIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIY 469
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-231 4.55e-51

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 177.89  E-value: 4.55e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    1 ITRDIPNVSDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVL 80
Cdd:PRK14844  870 ITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVI 949

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   81 DVKVFNR------------------------------------------------------------------------- 87
Cdd:PRK14844  950 DVQVFTRrgveenerallikqkeindfekerdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsis 1029

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   88 ----------------------------EEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPY 139
Cdd:PRK14844 1030 eqvkslkkdfdekvshaiaqfkrkveklHEGYD-LPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPY 1108

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  140 LPDGTPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNL------------------------------------------- 176
Cdd:PRK14844 1109 LEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLgekvgnildeinkiksafckgirslnddnftkfaaayldnkki 1188

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787      --------------------------------------------------------------------------------
Cdd:PRK14844 1189 enidddeitasvlntpnknalndelnelvenylnscksaysnlrnflievyscgsnvsicnnirdisdnnliefarklrd 1268

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 199580787  177 GIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYML 231
Cdd:PRK14844 1269 GIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 9-229 1.75e-48

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 167.83  E-value: 1.75e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   9 SDSALKNLDDRGIIYVGAEVNDGDILVGKVTPKgvteltaeeRLL--HAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFN 86
Cdd:PRK07225 270 GEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPP---------RFLeePDDFGISPEKRRETSVTMRSGEEGIVDTVILTE 340

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787  87 REEGddtlspgvNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMNIGQVLE 166
Cdd:PRK07225 341 TEEG--------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLE 412

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 199580787 167 LHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMY 229
Cdd:PRK07225 413 MIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIY 475
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 6-229 2.00e-47

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 167.44  E-value: 2.00e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787    6 PNVSDS----ALKNLDDRGIIYVGAEVNDGDILVGKVTPKGVTELTAEERLlhaifGEKARevRDTSLRVPHGAGGIVLD 81
Cdd:PRK08565  761 PNVRGYrgeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSL-----GLQER--RDTSVTVRHGEKGIVDT 833

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 199580787   82 VKVfnreegddTLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGTPIDIMLNPLGVPSRMNI 161
Cdd:PRK08565  834 VLI--------TESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTV 905

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 199580787  162 GQVLELHLGMAAKNLGIHVASPVFDGASDEDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMY 229
Cdd:PRK08565  906 GQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVY 973
 
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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