NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|208609831|dbj|BAG72377|]
View 

RNA polymerase II second largest subunit, partial [Litsea maingayi]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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. ...
 1-167 3.67e-85

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: 267.13  E-value: 3.67e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   1 GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQ-DETQQGQTSRYTRRDHSTSLRHSESGMVDQVLLTT---NADG 76
Cdd:cd00653  537 NVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGEtESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGG 616

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831  77 LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGK 156
Cdd:cd00653  617 NKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGK 696

                        170
                 ....*....|.
gi 208609831 157 EGDATPFTDVT 167
Cdd:cd00653  697 FGDATPFDGAE 707
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-167 3.67e-85

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: 267.13  E-value: 3.67e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   1 GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQ-DETQQGQTSRYTRRDHSTSLRHSESGMVDQVLLTT---NADG 76
Cdd:cd00653  537 NVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGEtESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGG 616

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831  77 LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGK 156
Cdd:cd00653  617 NKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGK 696

                        170
                 ....*....|.
gi 208609831 157 EGDATPFTDVT 167
Cdd:cd00653  697 FGDATPFDGAE 707
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 5-164 1.07e-74

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: 227.80  E-value: 1.07e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    5 GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDETQQ---GQTSRyTRRDHSTSLRHSESGMVDQVLL-TTNADGLRFV 80
Cdd:pfam00562 131 EALKKLDEDGIVRVGAEVKPGDILVGKVGPTELTKLLRaifGEKAR-DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMV 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   81 KVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDA 160
Cdd:pfam00562 210 KVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDA 289


                  ....
gi 208609831  161 TPFT 164
Cdd:pfam00562 290 TPFD 293
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 7-163 6.62e-74

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 239.47  E-value: 6.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    7 YDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDETQQ-GQTSRYTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMR 85
Cdd:PRK08565  772 YRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEeLSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVR 851

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 208609831   86 SVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPF 163
Cdd:PRK08565  852 DLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 7-164 6.27e-73

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: 229.53  E-value: 6.27e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    7 YDKLDDDGLAPPGTRVSGEDVIIGKTTPIG-QDETQQGQTSRYTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMR 85
Cdd:TIGR03670 268 YKHLDEDGIVYPEVEVKGGDVLIGKTSPPRfLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVR 347

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 208609831   86 SVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164
Cdd:TIGR03670 348 DLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFE 426
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 6-163 3.89e-59

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: 197.64  E-value: 3.89e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    6 SYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGqdETQQ-----------GQTSRYtRRDHSTSLRHSESGMVDQVLLTTNA 74
Cdd:COG0085   672 ALRNLDEDGIIRIGAEVKGGDILVGKVTPKG--ETELtpeerllraifGEKARE-VRDTSLRVPHGEKGKVIDVKVFSRE 748

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   75 DG-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIM 147
Cdd:COG0085   749 EGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHL 828

                         170
                  ....*....|....*.
gi 208609831  148 GKVAAHMGKEGDATPF 163
Cdd:COG0085   829 GWAAALLGRRVATPVF 844
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-167 3.67e-85

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: 267.13  E-value: 3.67e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   1 GMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQ-DETQQGQTSRYTRRDHSTSLRHSESGMVDQVLLTT---NADG 76
Cdd:cd00653  537 NVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGEtESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGG 616

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831  77 LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGK 156
Cdd:cd00653  617 NKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGK 696

                        170
                 ....*....|.
gi 208609831 157 EGDATPFTDVT 167
Cdd:cd00653  697 FGDATPFDGAE 707
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 5-164 1.07e-74

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: 227.80  E-value: 1.07e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    5 GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDETQQ---GQTSRyTRRDHSTSLRHSESGMVDQVLL-TTNADGLRFV 80
Cdd:pfam00562 131 EALKKLDEDGIVRVGAEVKPGDILVGKVGPTELTKLLRaifGEKAR-DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMV 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   81 KVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDA 160
Cdd:pfam00562 210 KVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDA 289


                  ....
gi 208609831  161 TPFT 164
Cdd:pfam00562 290 TPFD 293
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 7-163 6.62e-74

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 239.47  E-value: 6.62e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    7 YDKLDDDGLAPPGTRVSGEDVIIGKTTPIGQDETQQ-GQTSRYTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMR 85
Cdd:PRK08565  772 YRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEeLSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVR 851

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 208609831   86 SVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPF 163
Cdd:PRK08565  852 DLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 7-164 6.27e-73

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: 229.53  E-value: 6.27e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    7 YDKLDDDGLAPPGTRVSGEDVIIGKTTPIG-QDETQQGQTSRYTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVKVRMR 85
Cdd:TIGR03670 268 YKHLDEDGIVYPEVEVKGGDVLIGKTSPPRfLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVR 347

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 208609831   86 SVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFT 164
Cdd:TIGR03670 348 DLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFE 426
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 6-164 9.52e-68

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 215.98  E-value: 9.52e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   6 SYDKLDDDGLAPPGTRVSGEDVIIGKTTPI----GQDETQQgqtSRYTRRDHSTSLRHSESGMVDQVLLTTNADGLRFVK 81
Cdd:PRK07225 273 AYRHLDEDGLVNPETEVKEGDVLIGKTSPPrfleEPDDFGI---SPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVK 349

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831  82 VRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDAT 161
Cdd:PRK07225 350 VRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGT 429


                 ...
gi 208609831 162 PFT 164
Cdd:PRK07225 430 AFS 432
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 6-163 3.89e-59

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: 197.64  E-value: 3.89e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    6 SYDKLDDDGLAPPGTRVSGEDVIIGKTTPIGqdETQQ-----------GQTSRYtRRDHSTSLRHSESGMVDQVLLTTNA 74
Cdd:COG0085   672 ALRNLDEDGIIRIGAEVKGGDILVGKVTPKG--ETELtpeerllraifGEKARE-VRDTSLRVPHGEKGKVIDVKVFSRE 748

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   75 DG-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIM 147
Cdd:COG0085   749 EGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHL 828

                         170
                  ....*....|....*.
gi 208609831  148 GKVAAHMGKEGDATPF 163
Cdd:COG0085   829 GWAAALLGRRVATPVF 844
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 8-165 1.16e-30

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: 116.30  E-value: 1.16e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831     8 DKLDDDGLAPPGTRVSGEDVIIGKTTPIGqdETQQGQTSRYTR----------RDHSTSLRHSESGMVDQVLLTTNADG- 76
Cdd:TIGR02013  740 RNLDENGIVRIGAEVKAGDILVGKVTPKG--ETELTPEEKLLRaifgekardvRDTSLRVPPGVEGTVIDVKVFSREQGd 817

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    77 ------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKV 150
Cdd:TIGR02013  818 elppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWA 897

                          170
                   ....*....|....*..
gi 208609831   151 AAHMGKEGD--ATPFTD 165
Cdd:TIGR02013  898 GKRLGRKGVpiATPVFD 914
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 9-162 2.51e-25

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 101.33  E-value: 2.51e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    9 KLDDDGLAPPGTRVSGEDVIIGKTTPIGqdETQQ-----------GQTSRyTRRDhsTSLR--HSESGMV-DQVLLTTNA 74
Cdd:PRK00405  783 NLDESGIVRIGAEVKPGDILVGKVTPKG--ETELtpeekllraifGEKAR-DVKD--TSLRvpHGEEGTViDVKVFTRIE 857

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   75 DG-------LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWtLEGITP-DIIVNPHAIPSRMTIGQLIECI 146
Cdd:PRK00405  858 QGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPY-LEDGTPvDIVLNPLGVPSRMNIGQILETH 936

                         170
                  ....*....|....*.
gi 208609831  147 MGKVAAHMGKEGdATP 162
Cdd:PRK00405  937 LGWAAKGLGIKF-ATP 951
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 9-166 1.26e-23

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 96.31  E-value: 1.26e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    9 KLDDDGLAPPGTRVSGEDVIIGKTTPIGQDETQQ---------GQTSRYTRrDHSTSLRHSESGMVDQVLLTTNADGLRF 79
Cdd:CHL00207  714 NLDENGIISIGSKVLAGDILVGKITPKGESDQLPegkllraifGEKAKDVK-DTSLRMPNGGYGRVIKVEIFSRSKGDEL 792

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   80 -------VKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 152
Cdd:CHL00207  793 kfgyylkIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGD 872

                         170
                  ....*....|....
gi 208609831  153 HMGKEGDATPFTDV 166
Cdd:CHL00207  873 NLNKRFKILPFDEM 886
rpoB CHL00001
RNA polymerase beta subunit
 2-163 1.94e-16

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 75.71  E-value: 1.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831    2 MRHgsydkLDDDGLAPPGTRVSGEDVIIGKTTPigqdetQQGQTSRYT--------------RRDHSTSLRhsesgmvdq 67
Cdd:CHL00001  717 LRN-----LDKNGIVMLGSWVETGDILVGKLTP------QEAEESSYApegrllraifgiqvSTSKETCLK--------- 776

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   68 vlLTTNADGlRFVKVRM-----------RSVRI-------PQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVN 129
Cdd:CHL00001  777 --LPIGGRG-RVIDVRWiqkkggssynpETIHVyilqkreIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLN 853

                         170       180       190
                  ....*....|....*....|....*....|....
gi 208609831  130 PHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPF 163
Cdd:CHL00001  854 PLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPF 887
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
77-157 4.06e-16

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 74.96  E-value: 4.06e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 208609831   77 LRFVKVRMRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGK 156
Cdd:PRK09603 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGK 1154


                  .
gi 208609831  157 E 157
Cdd:PRK09603 1155 Q 1155
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
91-157 2.87e-13

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 66.57  E-value: 2.87e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 208609831   91 QIGDKFSSRHGQKGTVGMTYTQEDMPWTLEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKE 157
Cdd:PRK14844 1082 QPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEK 1148
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH