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Conserved domains on  [gi|1377052617|gb|AVY53760|]
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DNA-dependent RNA polymerase, partial [Leptolyngbyaceae cyanobacterium WOS-LAB13]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
rpoC1 super family cl29785
DNA-directed RNA polymerase subunit gamma; Provisional
3-301 0e+00

DNA-directed RNA polymerase subunit gamma; Provisional


The actual alignment was detected with superfamily member PRK02625:

Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 659.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:PRK02625   46 NYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYV 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 AILLDMPLRDVEQIVYFNAYVVLNPGNADNLSYKQLLTEDQWIEIEDQLYSEDSQLSGVE-VGIGAEALQRLLQDIKLEE 161
Cdd:PRK02625  126 AILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSELEGEEvVGIGAEALKRLLEDLNLEE 205
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 162 EAERLREDIATSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:PRK02625  206 EAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 285
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:PRK02625  286 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 345
 
Name Accession Description Interval E-value
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
3-301 0e+00

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 659.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:PRK02625   46 NYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYV 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 AILLDMPLRDVEQIVYFNAYVVLNPGNADNLSYKQLLTEDQWIEIEDQLYSEDSQLSGVE-VGIGAEALQRLLQDIKLEE 161
Cdd:PRK02625  126 AILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSELEGEEvVGIGAEALKRLLEDLNLEE 205
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 162 EAERLREDIATSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:PRK02625  206 EAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 285
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:PRK02625  286 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 345
rpoC1_cyan TIGR02387
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ...
3-301 0e+00

DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.


Pssm-ID: 131440 [Multi-domain]  Cd Length: 619  Bit Score: 614.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:TIGR02387  39 NYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYV 118
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 AILLDMPLRDVEQIVYFNAYVVLNPGNADNLSYKQLLTEDQWIEIEDQLYSEDSQLSGVE-VGIGAEALQRLLQDIKLEE 161
Cdd:TIGR02387 119 SILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSELENEEvVGIGAEALKQLLADLNLEE 198
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 162 EAERLREDIATSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:TIGR02387 199 VAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 278
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:TIGR02387 279 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 338
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
3-301 7.62e-176

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 517.02  E-value: 7.62e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617    3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:COG0086     35 NYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRI 114
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   83 AILLDMPLRDVEQIVYFNAYVVLNPGNADnLSYKQLLTEDQWIEIEDQLYSEdsqlsgVEVGIGAEALQRLLQDIKLEEE 162
Cdd:COG0086    115 GLLLDMSLRDLERVLYFESYVVIDPGDTP-LEKGQLLTEDEYREILEEYGDE------FVAKMGAEAIKDLLGRIDLEKE 187
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  163 AERLREDIATSKG-QKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:COG0086    188 SEELREELKETTSeQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNN 267
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:COG0086    268 RLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGR 327
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
3-301 3.91e-154

Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.


Pssm-ID: 259845 [Multi-domain]  Cd Length: 659  Bit Score: 445.81  E-value: 3.91e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:cd01609    31 NYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRI 110
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 AILLDMPLRDVEQIVYFnayvvlnpgnadnlsykqlltedqwieiedqlysedsqlsgvevgigaealqrllqdikleee 162
Cdd:cd01609   111 GLLLDLSPKDLERVIYF--------------------------------------------------------------- 127
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 163 aerlrediatskgqkraklikrlrVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNR 242
Cdd:cd01609   128 ------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNR 183
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1377052617 243 LARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:cd01609   184 LKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGR 242
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
3-301 2.15e-77

RNA polymerase Rpb1, domain 1; 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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 238.34  E-value: 2.15e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECH-CGKYKRvrhrgivceRCGVevtesrvrrhRMGYIKLAAPVAHVWYLKGIpsy 81
Cdd:pfam04997  32 NYGSLKPEEGGLLDERMGTIDKDYECEtCGKKKK---------DCPG----------HFGHIELAKPVFHIGFFKKT--- 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  82 mailldmpLRDVEQIVYFNAYVVLNPGNadnlsyKQLLTEDQWIEIEDQLysedsqlsgvevGIGAEALQRLLQDIKLEE 161
Cdd:pfam04997  90 --------LKILECVCKYCSKLLLDPGK------PKLFNKDKKRLGLENL------------KMGAKAILELCKKKDLCE 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 162 EAERLREDIATSK---------------------------GQKRAKLIKRLRVID----NFIATGSSPDWMVLTVVPVIP 210
Cdd:pfam04997 144 HCGGKNGVCGSQQpvsrkeglklkaaikkskeeeekeilnPEKVLKIFKRISDEDveilGFNPSGSRPEWMILTVLPVPP 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 211 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRG-RTVVGANNRPLK 289
Cdd:pfam04997 224 PCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGlPPALQKSKRPLK 303
                         330
                  ....*....|..
gi 1377052617 290 SLSDIIEGKQGR 301
Cdd:pfam04997 304 SISQRLKGKEGR 315
 
Name Accession Description Interval E-value
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
3-301 0e+00

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 659.52  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:PRK02625   46 NYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYV 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 AILLDMPLRDVEQIVYFNAYVVLNPGNADNLSYKQLLTEDQWIEIEDQLYSEDSQLSGVE-VGIGAEALQRLLQDIKLEE 161
Cdd:PRK02625  126 AILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSELEGEEvVGIGAEALKRLLEDLNLEE 205
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 162 EAERLREDIATSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:PRK02625  206 EAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 285
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:PRK02625  286 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 345
rpoC1_cyan TIGR02387
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ...
3-301 0e+00

DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.


Pssm-ID: 131440 [Multi-domain]  Cd Length: 619  Bit Score: 614.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:TIGR02387  39 NYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYV 118
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 AILLDMPLRDVEQIVYFNAYVVLNPGNADNLSYKQLLTEDQWIEIEDQLYSEDSQLSGVE-VGIGAEALQRLLQDIKLEE 161
Cdd:TIGR02387 119 SILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSELENEEvVGIGAEALKQLLADLNLEE 198
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 162 EAERLREDIATSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:TIGR02387 199 VAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 278
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:TIGR02387 279 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 338
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
3-301 0e+00

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 586.26  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617    3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:PRK00566    35 NYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRI 114
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   83 AILLDMPLRDVEQIVYFNAYVVLNPGNADnLSYKQLLTEDQWIEIEDQlYSEDsqlsgVEVGIGAEALQRLLQDIKLEEE 162
Cdd:PRK00566   115 GLLLDMSLKDLERVLYFESYVVIDPGDTP-LEKKQLLTEEEYREALEE-YGDE-----FVAKMGAEAIKELLKNIDLEAE 187
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  163 AERLREDIA-TSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:PRK00566   188 AEELREELKeTGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNN 267
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:PRK00566   268 RLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQGR 327
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
3-301 7.62e-176

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 517.02  E-value: 7.62e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617    3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:COG0086     35 NYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRI 114
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   83 AILLDMPLRDVEQIVYFNAYVVLNPGNADnLSYKQLLTEDQWIEIEDQLYSEdsqlsgVEVGIGAEALQRLLQDIKLEEE 162
Cdd:COG0086    115 GLLLDMSLRDLERVLYFESYVVIDPGDTP-LEKGQLLTEDEYREILEEYGDE------FVAKMGAEAIKDLLGRIDLEKE 187
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  163 AERLREDIATSKG-QKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:COG0086    188 SEELREELKETTSeQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNN 267
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:COG0086    268 RLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGR 327
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
3-301 2.42e-169

DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274103 [Multi-domain]  Cd Length: 1140  Bit Score: 499.19  E-value: 2.42e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617    3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:TIGR02386   27 NYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRI 106
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   83 AILLDMPLRDVEQIVYFNAYVVLNPGNADnLSYKQLLTEDQWIEIEDQlYSedsqlSGVEVGIGAEALQRLLQDIKLEEE 162
Cdd:TIGR02386  107 GLLLDITAKELESVLYFENYVVLDPGDTK-LDKKEVLDETEYREVLKR-YG-----DGFRAGMGAEAIKELLEKIDLDKE 179
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  163 AERLREDIATSKG-QKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:TIGR02386  180 IEELKIQLRESKSdQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNN 259
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:TIGR02386  260 RLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGR 319
rpoC1 CHL00018
RNA polymerase beta' subunit
3-301 3.33e-162

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 466.69  E-value: 3.33e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHR---GIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIP 79
Cdd:CHL00018   44 HYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEkedPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLP 123
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  80 SYMAILLDMPLRDVEQIVYFN-AYVVLNPGNADNLSYKQLLTED--QWIEIEDQLYS--EDSQLSGVEVGIGAEALQRLL 154
Cdd:CHL00018  124 SYIANLLDKPLKELEGLVYCDfSFARPIAKKPTFLRLRGLFEYEiqSWKYSIPLFFStqGFDTFRNREISTGAGAIREQL 203
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 155 QDIKLEEEAERLREDIAT--------------SKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLD 220
Cdd:CHL00018  204 ADLDLRIIIDNSLVEWKElgeegstgnewedrKIGRRKDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLD 283
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 221 GGRFATSDLNDLYRRVINRNNRLARLQEI--LAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGK 298
Cdd:CHL00018  284 GGKLMSSDLNELYRRVIYRNNTLTDLLTTsrSTPGELVMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGK 363

                  ...
gi 1377052617 299 QGR 301
Cdd:CHL00018  364 EGR 366
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
3-301 3.91e-154

Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.


Pssm-ID: 259845 [Multi-domain]  Cd Length: 659  Bit Score: 445.81  E-value: 3.91e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:cd01609    31 NYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRI 110
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 AILLDMPLRDVEQIVYFnayvvlnpgnadnlsykqlltedqwieiedqlysedsqlsgvevgigaealqrllqdikleee 162
Cdd:cd01609   111 GLLLDLSPKDLERVIYF--------------------------------------------------------------- 127
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 163 aerlrediatskgqkraklikrlrVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNR 242
Cdd:cd01609   128 ------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNR 183
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1377052617 243 LARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:cd01609   184 LKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGR 242
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
3-301 1.74e-127

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 395.78  E-value: 1.74e-127
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617    3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:PRK14906    37 NYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGSPSRL 116
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   83 AILLDMPLRDVEQIVYFNAYVVLN------PGNADNL------SYKQLLTE-DQWIEIEDQL--------------YSED 135
Cdd:PRK14906   117 GYLLDIKPKDLEKVLYFASYIITSvdkearEEDADDLrdelaaDLEELDAErDRLIEATRRLsvdyvpeddefvddIGDD 196
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  136 SQLSGVEV-----------------------------------------------------GIGAEALQRLLQDIKLEEE 162
Cdd:PRK14906   197 ERLTAEEVraevadiyeeynerkalrreafdafmqiepkqlisdealyremrlnysiyfkgGMGAEAVRDLLDAIDLEKE 276
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  163 AERLREDIATSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNR 242
Cdd:PRK14906   277 AEELRAIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNR 356
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1377052617  243 LARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:PRK14906   357 LKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLADMLKGKQGR 415
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
3-301 9.48e-125

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 392.75  E-value: 9.48e-125
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617    3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGI-VCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSY 81
Cdd:PRK09603  1424 NYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSR 1503
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   82 MAILLDMPLRDVEQIVYFNAYVVLNPGNA--DNLSYKQLLTEDQWIEIEDQLYSEDSQLSGVEVGIGAEALQRLLQDIKL 159
Cdd:PRK09603  1504 IGTLLGVKMKDLERVLYYEAYIVKEPGEAayDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEIDL 1583
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  160 EEEAERLREDI-ATSKGQKRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVIN 238
Cdd:PRK09603  1584 ITLLQSLKEEVkDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVIN 1663
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1377052617  239 RNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:PRK09603  1664 RNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGR 1726
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
3-301 1.35e-99

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 320.42  E-value: 1.35e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617    3 NYRTLKPEMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSYM 82
Cdd:PRK14844  1476 NYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRI 1555
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   83 AILLDMPLRDVEQIVYFNAYVVLNPgNADNLSYKQLLTEDQWIEIEDQlYSEDSQLSGVevgiGAEALQRLLQDIKLEEE 162
Cdd:PRK14844  1556 GALLDMSLRDIENILYSDNYIVIDP-LVSPFEKGEIISEKAYNEAKDS-YGIDSFVAMQ----GVEAIRELLTRLDLHEI 1629
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  163 AERLREDIATSKGQ-KRAKLIKRLRVIDNFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNN 241
Cdd:PRK14844  1630 RKDLRLELESVASEiRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNN 1709
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1377052617  242 RLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTV--VGANNRPlKSLSDIIEGKQGR 301
Cdd:PRK14844  1710 RLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVnkAGAVGYK-KSISDMLKGKQGR 1770
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
3-301 2.15e-77

RNA polymerase Rpb1, domain 1; 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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 238.34  E-value: 2.15e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGLFCERIFGPAKDWECH-CGKYKRvrhrgivceRCGVevtesrvrrhRMGYIKLAAPVAHVWYLKGIpsy 81
Cdd:pfam04997  32 NYGSLKPEEGGLLDERMGTIDKDYECEtCGKKKK---------DCPG----------HFGHIELAKPVFHIGFFKKT--- 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  82 mailldmpLRDVEQIVYFNAYVVLNPGNadnlsyKQLLTEDQWIEIEDQLysedsqlsgvevGIGAEALQRLLQDIKLEE 161
Cdd:pfam04997  90 --------LKILECVCKYCSKLLLDPGK------PKLFNKDKKRLGLENL------------KMGAKAILELCKKKDLCE 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 162 EAERLREDIATSK---------------------------GQKRAKLIKRLRVID----NFIATGSSPDWMVLTVVPVIP 210
Cdd:pfam04997 144 HCGGKNGVCGSQQpvsrkeglklkaaikkskeeeekeilnPEKVLKIFKRISDEDveilGFNPSGSRPEWMILTVLPVPP 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 211 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRG-RTVVGANNRPLK 289
Cdd:pfam04997 224 PCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGlPPALQKSKRPLK 303
                         330
                  ....*....|..
gi 1377052617 290 SLSDIIEGKQGR 301
Cdd:pfam04997 304 SISQRLKGKEGR 315
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
3-301 6.01e-28

Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.


Pssm-ID: 259843 [Multi-domain]  Cd Length: 528  Bit Score: 112.91  E-value: 6.01e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617   3 NYRTLKPEMDGlfcerifgpakdwechcgKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVAHVWYLKGIPSym 82
Cdd:cd00399    21 DNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPS-- 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  83 ailldmplrdveqivyfnayvvlnpgnadnlsykqlltedqwieiedqlysedsqlsgvevgigaealqrLLQdikleee 162
Cdd:cd00399    81 ----------------------------------------------------------------------FLG------- 83
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 163 aerlrediatskgqkraklikrlrvidnfiatgssPDWMVLTVVPVIPPDLRPMVqldggrfatsdlndlyrrvinrnnr 242
Cdd:cd00399    84 -----------------------------------PEWMILTCLPVPPPCLRPSV------------------------- 103
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1377052617 243 larlqeilapeiIVRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGR 301
Cdd:cd00399   104 ------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGR 150
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
190-301 1.06e-13

A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.


Pssm-ID: 259846 [Multi-domain]  Cd Length: 861  Bit Score: 71.51  E-value: 1.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617 190 NFIATGSSPDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDA 269
Cdd:cd02582   194 GIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTT 273
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1377052617 270 LIDNG------RRGRTvvganNRPLKSLSDIIEGKQGR 301
Cdd:cd02582   274 YFDNEipgippARHRS-----GRPLKTLAQRLKGKEGR 306
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
198-301 1.33e-11

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 65.05  E-value: 1.33e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1377052617  198 PDWMVLTVVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRG 277
Cdd:PRK14977   215 PEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAG 294
                           90       100
                   ....*....|....*....|....*.
gi 1377052617  278 RTVV--GANNRPLKSLSDIIEGKQGR 301
Cdd:PRK14977   295 IPQAhhKGSGRPLKSLFQRLKGKEGR 320
 
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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