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Conserved domains on  [gi|501288776|emb|CCO02518|]
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RNA dependent RNA polymerase II second largest subunit, partial [Kwoniella sp. K30]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_B_RPB2 super family cl46395
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-224 3.95e-99

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.


The actual alignment was detected with superfamily member cd00653:

Pssm-ID: 480735 [Multi-domain]  Cd Length: 866  Bit Score: 306.42  E-value: 3.95e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGmikaetiEKPDRNETLRMKHGSSDRYAKLDVDGLVSPATNINGDD 80
Cdd:cd00653  490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK-------NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGD 562

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776  81 ILIGKTAPLPEESEELGQRTQMHQKRDISTPLKSTEQGVVDQVMLTT---NGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:cd00653  563 ILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501288776 158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:cd00653  643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEE 709
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-224 3.95e-99

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: 306.42  E-value: 3.95e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGmikaetiEKPDRNETLRMKHGSSDRYAKLDVDGLVSPATNINGDD 80
Cdd:cd00653  490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK-------NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGD 562

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776  81 ILIGKTAPLPEESEELGQRTQMHQKRDISTPLKSTEQGVVDQVMLTT---NGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:cd00653  563 ILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501288776 158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:cd00653  643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEE 709
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-218 1.88e-89

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 284.54  E-value: 1.88e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGMIKAETIEKPDRNetLRMKHGSsDRYAKLDVDGLVSPATNINGDD 80
Cdd:PRK08565  715 YNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPN--VRGYRGE-EYYRKLDEDGIVSPEVEVKGGD 791

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   81 ILIGKTAPlP---EESEELGQRTQmhQKRDISTPLKSTEQGVVDQVMLTTNGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:PRK08565  792 VLIGKTSP-PrflEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQ 868

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501288776  158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPF 218
Cdd:PRK08565  869 KGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 1-224 8.98e-89

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: 273.06  E-value: 8.98e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGMIKAETIEKPDRNetLRmKHGSSDRYAKLDVDGLVSPATNINGDD 80
Cdd:TIGR03670 211 YNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPD--VR-GYRGEEAYKHLDEDGIVYPEVEVKGGD 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   81 ILIGKTAPlP---EESEELGQRTQmhQKRDISTPLKSTEQGVVDQVMLTTNGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:TIGR03670 288 VLIGKTSP-PrflEELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQ 364

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501288776  158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:TIGR03670 365 KGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEE 431
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-224 7.80e-88

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: 263.62  E-value: 7.80e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSYtDTEKMKGMIKAETIEKPDRNetlrmkhgSSDRYAKLDVDGLVSPATNINGDD 80
Cdd:pfam00562  82 YNQEDAIIINKSSVDRGFFTSIHIKEI-EARKTKLGPIEEITRDIPNV--------SEEALKKLDEDGIVRVGAEVKPGD 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   81 ILIGKTAPlPEESEEL----GQRTQmhQKRDISTPLKSTEQGVVDQVML-TTNGEGHKFVKIRVRSTRVPQIGDKFASRH 155
Cdd:pfam00562 153 ILVGKVGP-TELTKLLraifGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRH 229

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501288776  156 GQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:pfam00562 230 GQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE 298
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-224 8.70e-63

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: 210.35  E-value: 8.70e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSY-TDTEKMKGMIKAETIEKPDRNEtlrmkhgssDRYAKLDVDGLVSPATNINGD 79
Cdd:COG0085   621 YNYEDAIIISERLVKDDVLTSIHIEEYeIEARDTKLGPEEITRDIPNVSE---------EALRNLDEDGIIRIGAEVKGG 691

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   80 DILIGKTAP---LPEESEELGQRTQMHQK----RDISTPLKSTEQGVVDQVMLTTNGEGH-------KFVKIRVRSTRVP 145
Cdd:COG0085   692 DILVGKVTPkgeTELTPEERLLRAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGDelppgvnKLVRVYVAQKRKI 771

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501288776  146 QIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:COG0085   772 EVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEE 850
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-224 3.95e-99

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: 306.42  E-value: 3.95e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGmikaetiEKPDRNETLRMKHGSSDRYAKLDVDGLVSPATNINGDD 80
Cdd:cd00653  490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTK-------NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGD 562

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776  81 ILIGKTAPLPEESEELGQRTQMHQKRDISTPLKSTEQGVVDQVMLTT---NGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:cd00653  563 ILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501288776 158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:cd00653  643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEE 709
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-218 1.88e-89

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 284.54  E-value: 1.88e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGMIKAETIEKPDRNetLRMKHGSsDRYAKLDVDGLVSPATNINGDD 80
Cdd:PRK08565  715 YNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPN--VRGYRGE-EYYRKLDEDGIVSPEVEVKGGD 791

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   81 ILIGKTAPlP---EESEELGQRTQmhQKRDISTPLKSTEQGVVDQVMLTTNGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:PRK08565  792 VLIGKTSP-PrflEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQ 868

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501288776  158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPF 218
Cdd:PRK08565  869 KGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 1-224 8.98e-89

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: 273.06  E-value: 8.98e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGMIKAETIEKPDRNetLRmKHGSSDRYAKLDVDGLVSPATNINGDD 80
Cdd:TIGR03670 211 YNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPD--VR-GYRGEEAYKHLDEDGIVYPEVEVKGGD 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   81 ILIGKTAPlP---EESEELGQRTQmhQKRDISTPLKSTEQGVVDQVMLTTNGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:TIGR03670 288 VLIGKTSP-PrflEELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQ 364

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501288776  158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:TIGR03670 365 KGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEE 431
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-224 7.80e-88

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: 263.62  E-value: 7.80e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSYtDTEKMKGMIKAETIEKPDRNetlrmkhgSSDRYAKLDVDGLVSPATNINGDD 80
Cdd:pfam00562  82 YNQEDAIIINKSSVDRGFFTSIHIKEI-EARKTKLGPIEEITRDIPNV--------SEEALKKLDEDGIVRVGAEVKPGD 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   81 ILIGKTAPlPEESEEL----GQRTQmhQKRDISTPLKSTEQGVVDQVML-TTNGEGHKFVKIRVRSTRVPQIGDKFASRH 155
Cdd:pfam00562 153 ILVGKVGP-TELTKLLraifGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRH 229

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501288776  156 GQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:pfam00562 230 GQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE 298
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 1-220 1.15e-84

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 262.59  E-value: 1.15e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   1 YNQEDSVIMNQSSIDRGLFRSLYYRSYTDTEKMKGMIKAETIEKPDRNetLRMKHGSsDRYAKLDVDGLVSPATNINGDD 80
Cdd:PRK07225 217 YNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKD--VRGYRGE-EAYRHLDEDGLVNPETEVKEGD 293

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776  81 ILIGKTAPlP---EESEELGQRTQmhQKRDISTPLKSTEQGVVDQVMLTTNGEGHKFVKIRVRSTRVPQIGDKFASRHGQ 157
Cdd:PRK07225 294 VLIGKTSP-PrflEEPDDFGISPE--KRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQ 370

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501288776 158 KGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTE 220
Cdd:PRK07225 371 KGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSG 433
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-224 8.70e-63

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: 210.35  E-value: 8.70e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSY-TDTEKMKGMIKAETIEKPDRNEtlrmkhgssDRYAKLDVDGLVSPATNINGD 79
Cdd:COG0085   621 YNYEDAIIISERLVKDDVLTSIHIEEYeIEARDTKLGPEEITRDIPNVSE---------EALRNLDEDGIIRIGAEVKGG 691

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   80 DILIGKTAP---LPEESEELGQRTQMHQK----RDISTPLKSTEQGVVDQVMLTTNGEGH-------KFVKIRVRSTRVP 145
Cdd:COG0085   692 DILVGKVTPkgeTELTPEERLLRAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGDelppgvnKLVRVYVAQKRKI 771

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501288776  146 QIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTELTVE 224
Cdd:COG0085   772 EVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEE 850
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-202 1.02e-25

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: 104.36  E-value: 1.02e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776     1 YNQEDSVIMNQSSIDRGLFRSLYYRSY-TDTEKMKGMIKAETIEKPDRNEtlrmkhgssDRYAKLDVDGLVSPATNINGD 79
Cdd:TIGR02013  687 YNYEDAILISERLVKDDVFTSIHIEEYeVEARDTKLGPEEITRDIPNVSE---------EALRNLDENGIVRIGAEVKAG 757

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    80 DILIGKTAPLPEES---EELGQRTQMHQK----RDISTPLKSTEQGVVDQVMLTTNGEG-------HKFVKIRVRSTRVP 145
Cdd:TIGR02013  758 DILVGKVTPKGETEltpEEKLLRAIFGEKardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKI 837

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 501288776   146 QIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALL 202
Cdd:TIGR02013  838 QVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHL 894
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-202 7.79e-24

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 99.01  E-value: 7.79e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSY-TDTEKMKGMIKAETIEKPDRNEtlrmkhgsSDRYaKLDVDGLVSPATNINGD 79
Cdd:CHL00207  660 YNFEDAILINKRLVYEDLFTSIHIEKYeIELRQTKLGSEEITRNIPNVSE--------YSLK-NLDENGIISIGSKVLAG 730

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   80 DILIGKTAPLPEeSEELGQ----RTQMHQK----RDISTPLKSTEQG-VVDQVMLTTN-GEGHKF---VKIRV--RSTRV 144
Cdd:CHL00207  731 DILVGKITPKGE-SDQLPEgkllRAIFGEKakdvKDTSLRMPNGGYGrVIKVEIFSRSkGDELKFgyyLKIRVfiAQIRK 809

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 501288776  145 PQIGDKFASRHGQKGTIG-ITYRQeDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALL 202
Cdd:CHL00207  810 IQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLL 867
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 62-202 8.52e-18

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 81.69  E-value: 8.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   62 AKLDVDGLVSPATNINGDDILIGKTAPLPEE---SEE------LGQRTQMHqkRDISTPLKSTEQG-VVDQVMLTTNGEG 131
Cdd:PRK00405  782 RNLDESGIVRIGAEVKPGDILVGKVTPKGETeltPEEkllraiFGEKARDV--KDTSLRVPHGEEGtVIDVKVFTRIEQG 859

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501288776  132 -------HKFVKIRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALL 202
Cdd:PRK00405  860 delppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHL 937
rpoB CHL00001
RNA polymerase beta subunit
 1-220 1.56e-16

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 78.02  E-value: 1.56e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776    1 YNQEDSVIMNQSSIDRGLFRSLYYRSYtDTEKMKGMIKAETIEKP-DRNETLRMKHgssdryakLDVDGLVSPATNINGD 79
Cdd:CHL00001  665 YNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERITKEiPHLEAHLLRN--------LDKNGIVMLGSWVETG 735

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776   80 DILIGKTAPlpEESEELGQRTQMHQKRDIS---------TPLKSTEQG---VVDQVMLT---TNGEGHKFVKIRVRSTRV 144
Cdd:CHL00001  736 DILVGKLTP--QEAEESSYAPEGRLLRAIFgiqvstskeTCLKLPIGGrgrVIDVRWIQkkgGSSYNPETIHVYILQKRE 813

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501288776  145 PQIGDKFASRHGQKGTIG-ITYRQeDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSEGDATPFTE 220
Cdd:CHL00001  814 IQVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDE 889
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
133-212 7.99e-15

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 73.03  E-value: 7.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501288776  133 KFVKIRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVEALLSKVSTLTGSE 212
Cdd:PRK09603 1076 KKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQ 1155
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
135-199 2.49e-11

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 62.72  E-value: 2.49e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501288776  135 VKIRVRSTRVPQIGDKFASRHGQKGTIGITYRQEDMPFSAEGLVPDIIINPHAIPSRMTIGHLVE 199
Cdd:PRK14844 1071 VKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILE 1135
 
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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