NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1221815261|dbj|BBA13768|]
View 

RNA polymerase II second largest subunit, partial [Xenostigmina zilleri]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 1000145)

DNA-directed RNA polymerase subunit B family protein similar to fungal DNA-directed RNA polymerase II subunit RPB2

CATH:  3.90.1110.10|3.90.1070.20
EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0000428|GO:0008270|GO:0003677|GO:0006351
PubMed:  11839495
SCOP:  4003708

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-338 9.64e-79

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK08565:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1103  Bit Score: 260.27  E-value: 9.64e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261    1 LTKDVYKYLQKCVENNQDFNVQMAVKASVITNGLKYSLATGNWGdqkkaaSAKAGVSQVLNRYTYASTLSHLRRTNTPVG 80
Cdd:PRK08565   353 LVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLS 426

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   81 RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMSQRNMELLEEYDSVVNPNATKVFVN 160
Cdd:PRK08565   427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261  161 GVWVGVHSSPAQLVNVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVETsyqknnrGCLVLDKSHIQK 238
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261  239 LNddkdidtfgmndedtaNAKFGWRGLIHSGVVEYLDAEEEETAMIVMTPDDLAEwrdvcagrpapeandkdrhrrfkpk 318
Cdd:PRK08565   580 LK----------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTP------------------------- 618

                          330       340
                   ....*....|....*....|
gi 1221815261  319 pnpaiaNYTHCEIHPSMILG 338
Cdd:PRK08565   619 ------EHTHLEIWPPAILG 632
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-338 9.64e-79

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 260.27  E-value: 9.64e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261    1 LTKDVYKYLQKCVENNQDFNVQMAVKASVITNGLKYSLATGNWGdqkkaaSAKAGVSQVLNRYTYASTLSHLRRTNTPVG 80
Cdd:PRK08565   353 LVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLS 426

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   81 RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMSQRNMELLEEYDSVVNPNATKVFVN 160
Cdd:PRK08565   427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261  161 GVWVGVHSSPAQLVNVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVETsyqknnrGCLVLDKSHIQK 238
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261  239 LNddkdidtfgmndedtaNAKFGWRGLIHSGVVEYLDAEEEETAMIVMTPDDLAEwrdvcagrpapeandkdrhrrfkpk 318
Cdd:PRK08565   580 LK----------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTP------------------------- 618

                          330       340
                   ....*....|....*....|
gi 1221815261  319 pnpaiaNYTHCEIHPSMILG 338
Cdd:PRK08565   619 ------EHTHLEIWPPAILG 632
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-123 3.82e-49

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: 175.83  E-value: 3.82e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   1 LTKDVYKYLQKCVENNQDFNVQMAVKASVITNGLKYSLATGNWGDQKKAASaKAGVSQVLNRYTYASTLSHLRRTNT-PV 79
Cdd:cd00653   259 LEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGL 337

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1221815261  80 GRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 123
Cdd:cd00653   338 FRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 58-121 5.03e-32

RNA polymerase Rpb2, domain 3; 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 114.16  E-value: 5.03e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1221815261  58 QVLNRYTYASTLSHLRRTNTPVG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 121
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 20-124 3.48e-18

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: 85.55  E-value: 3.48e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   20 NVQMAVKASVITNGLKYSLATGnwgdqkkaasakaGVSQVLNRYTYASTLSHLRRTNT----PVGRDgklaKP----RQL 91
Cdd:COG0085    348 TPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDV 410

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1221815261   92 HNTHWGLVCPAETPEGQACGLVKNLSLMCYVSV 124
Cdd:COG0085    411 HPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-338 9.64e-79

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 260.27  E-value: 9.64e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261    1 LTKDVYKYLQKCVENNQDFNVQMAVKASVITNGLKYSLATGNWGdqkkaaSAKAGVSQVLNRYTYASTLSHLRRTNTPVG 80
Cdd:PRK08565   353 LVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLS 426

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   81 RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMSQRNMELLEEYDSVVNPNATKVFVN 160
Cdd:PRK08565   427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261  161 GVWVGVHSSPAQLVNVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVETsyqknnrGCLVLDKSHIQK 238
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261  239 LNddkdidtfgmndedtaNAKFGWRGLIHSGVVEYLDAEEEETAMIVMTPDDLAEwrdvcagrpapeandkdrhrrfkpk 318
Cdd:PRK08565   580 LK----------------KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTP------------------------- 618

                          330       340
                   ....*....|....*....|
gi 1221815261  319 pnpaiaNYTHCEIHPSMILG 338
Cdd:PRK08565   619 ------EHTHLEIWPPAILG 632
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-123 3.82e-49

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: 175.83  E-value: 3.82e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   1 LTKDVYKYLQKCVENNQDFNVQMAVKASVITNGLKYSLATGNWGDQKKAASaKAGVSQVLNRYTYASTLSHLRRTNT-PV 79
Cdd:cd00653   259 LEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGL 337

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1221815261  80 GRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 123
Cdd:cd00653   338 FRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-145 2.50e-37

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 139.70  E-value: 2.50e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   1 LTKDVyKY-LQKCVENNQDFNVQMAVKASVITNGLKYSLATGNWgdqkkaASAKAGVSQVLNRYTYASTLSHLRRTNTPV 79
Cdd:PRK09606  356 LARDV-KYqLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPL 428

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1221815261  80 GRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMSQRNMELLEE 145
Cdd:PRK09606  429 SRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPERG 494
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 58-121 5.03e-32

RNA polymerase Rpb2, domain 3; 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 114.16  E-value: 5.03e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1221815261  58 QVLNRYTYASTLSHLRRTNTPVG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 121
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 157-218 1.71e-30

RNA polymerase Rpb2, domain 4; 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). Domain 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 110.15  E-value: 1.71e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1221815261 157 VFVNGVWVGVHSSPAQLVNVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVE 218
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 155-338 1.50e-29

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 118.91  E-value: 1.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261 155 TKVFVNGVWVGVHSSPAQLVNVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVETsyqknnrGCLVLDKS 234
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261 235 HIQKLnddkdidtfgmndedtANAKFGWRGLIHSGVVEYLDAEEEETAMIVMTPDDLAEwrdvcagrpapeandkdrhrr 314
Cdd:PRK07225   78 HIEKL----------------KNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTE--------------------- 120

                         170       180
                  ....*....|....*....|....
gi 1221815261 315 fkpkpnpaiaNYTHCEIHPSMILG 338
Cdd:PRK07225  121 ----------EHTHLEIDPSLILG 134
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 262-333 7.67e-22

RNA polymerase Rpb2, domain 5; 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). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 86.83  E-value: 7.67e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1221815261 262 WRGLIHSGVVEYLDAEEEETAMIVMTPDDLAEWRDVCagrpapeandkdrhrrfkpKPNPAIANYTHCEIHP 333
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE-------------------REGPYAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 20-124 3.48e-18

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: 85.55  E-value: 3.48e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   20 NVQMAVKASVITNGLKYSLATGnwgdqkkaasakaGVSQVLNRYTYASTLSHLRRTNT----PVGRDgklaKP----RQL 91
Cdd:COG0085    348 TPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDV 410

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1221815261   92 HNTHWGLVCPAETPEGQACGLVKNLSLMCYVSV 124
Cdd:COG0085    411 HPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
56-161 8.12e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.08  E-value: 8.12e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221815261   56 VSQVLNRYTYASTLSHLRRTNTpVGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS-VGSES 128
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNdLGFIE 602

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1221815261  129 TP----ITDFMSQRNMEL--LEEYDSVVNPNATKVFVNG 161
Cdd:PRK09603   603 APykkvVDGKVVGETIYLtaIQEDSHIIAPASTPIDEEG 641
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
56-123 8.81e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 50.78  E-value: 8.81e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1221815261   56 VSQVLNRYTYASTLSHLRRTNT--PVG--RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 123
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 56-117 1.78e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 46.62  E-value: 1.78e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1221815261   56 VSQVLNRYTYASTLSHLRRTNT--PVGRDgKLAKP---RQLHNTHWGLVCPAETPEGQACGLVKNLS 117
Cdd:CHL00207   366 LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 89-117 1.04e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.32  E-value: 1.04e-04
                           10        20
                   ....*....|....*....|....*....
gi 1221815261   89 RQLHNTHWGLVCPAETPEGQACGLVKNLS 117
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-32 5.87e-04

RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 41.21  E-value: 5.87e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1221815261   1 LTKDVYKYLQKCVENNQDFNVQMAVKASVITN 32
Cdd:pfam04563 365 LVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
rpoB CHL00001
RNA polymerase beta subunit
 57-126 8.07e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 41.43  E-value: 8.07e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1221815261   57 SQVLNRYTYASTLSHLRRTNT--PVGRDGKLA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVSVGS 126
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIGH 446
 
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