NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|89274936|gb|ABD65909|]
View 

RNA polymerase II second largest subunit, partial [Insolibasidium deformans]

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;
2-349 2.68e-100

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: 319.21  E-value: 2.68e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936     2 KRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVETQKPFNLNAAVKSNTITHGLKYSLATGNWGdqkkaaSARAGVSQVL 81
Cdd:PRK08565  333 KRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLL 406

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    82 NRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYISVGSPSAPVVEFFEEWGM 161
Cdd:PRK08565  407 DRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGV 486

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   162 ESLEE-FSADMSKGTKVFVNGVWQGVHRAPAELLRTIIHLRRCGDIEPEVSI--VRDVRERELRVFTDAGRVCRPLFIVN 238
Cdd:PRK08565  487 VPVEEaREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE 566

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   239 DQQLVLKKEDVMALSQGQtddgapFGWTQLVEKGIVEYLDAEEEETVMICMTPEDLeqsreyqqtgyvpqeafdpaarvk 318
Cdd:PRK08565  567 NGKPKLTREHVEKLKKGE------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------------------ 616

                         330       340       350
                  ....*....|....*....|....*....|.
gi 89274936   319 gnTSMYshtwTHCEIHPAMILGICASIIPFP 349
Cdd:PRK08565  617 --TPEH----THLEIWPPAILGITASIIPYP 641
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-349 2.68e-100

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 319.21  E-value: 2.68e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936     2 KRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVETQKPFNLNAAVKSNTITHGLKYSLATGNWGdqkkaaSARAGVSQVL 81
Cdd:PRK08565  333 KRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLL 406

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    82 NRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYISVGSPSAPVVEFFEEWGM 161
Cdd:PRK08565  407 DRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGV 486

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   162 ESLEE-FSADMSKGTKVFVNGVWQGVHRAPAELLRTIIHLRRCGDIEPEVSI--VRDVRERELRVFTDAGRVCRPLFIVN 238
Cdd:PRK08565  487 VPVEEaREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE 566

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   239 DQQLVLKKEDVMALSQGQtddgapFGWTQLVEKGIVEYLDAEEEETVMICMTPEDLeqsreyqqtgyvpqeafdpaarvk 318
Cdd:PRK08565  567 NGKPKLTREHVEKLKKGE------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------------------ 616

                         330       340       350
                  ....*....|....*....|....*....|.
gi 89274936   319 gnTSMYshtwTHCEIHPAMILGICASIIPFP 349
Cdd:PRK08565  617 --TPEH----THLEIWPPAILGITASIIPYP 641
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-144 1.80e-59

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: 205.11  E-value: 1.80e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   2 KRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVETQKPFNLNAAVKSNTITHGLKYSLATGNWGDQKKAASaRAGVSQVL 81
Cdd:cd00653 239 KRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVL 317

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 89274936  82 NRYTFASTLSHLRRCNT-PIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYIS 144
Cdd:cd00653 318 DRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 79-142 6.38e-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: 6.38e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 89274936    79 QVLNRYTFASTLSHLRRCNTPIG---RDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSY 142
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-349 8.06e-26

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: 108.66  E-value: 8.06e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    2 KRLDLAGPLLAGLFRMLFRKLTKDV-YRhlqkcVETQKP--FNLNAAVKSNTITHGLKYSLATGnwgdqkkaasaraGVS 78
Cdd:COG0085  311 RRVRLVGELLQNQFRVGLSRMERVVrER-----MTTQDVeaITPQSLINIRPVVAAIKEFFGSS-------------QLS 372

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   79 QVLNRYTFASTLSHLRRCNT----PIGRDgkiaKP----RQLHNSHWGMVCPAETPEGQACGLVKNLALMSYISvgspsa 150
Cdd:COG0085  373 QFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------ 442

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936  151 pvvEFfeewgmesleefsadmskgtkvfvngvwqgvhrapaellrtiihlrrcgdiepevsivrdvrerelrvftdaGRV 230
Cdd:COG0085  443 ---EY------------------------------------------------------------------------GFI 447

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936  231 CRPLFIVNDQQLvlkkedvmalsqgqTDDgapfgwtqlvekgiVEYLDAEEEETVMICMTPEDLEQSREYQQTgYVPqea 310
Cdd:COG0085  448 ETPYRKVENGKV--------------TDE--------------IEYLTADEEENYYIAQANAPLDEDGNFLEE-RVL--- 495

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|..
gi 89274936  311 fdpaARVKGNTSMYS---HtwTHCEIHPAMILGICASIIPFP 349
Cdd:COG0085  496 ----VRYRGEEVLVPpeeV--DYMDVSPKQIVSVATSLIPFL 531
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-349 2.68e-100

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 319.21  E-value: 2.68e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936     2 KRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVETQKPFNLNAAVKSNTITHGLKYSLATGNWGdqkkaaSARAGVSQVL 81
Cdd:PRK08565  333 KRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLL 406

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    82 NRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYISVGSPSAPVVEFFEEWGM 161
Cdd:PRK08565  407 DRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGV 486

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   162 ESLEE-FSADMSKGTKVFVNGVWQGVHRAPAELLRTIIHLRRCGDIEPEVSI--VRDVRERELRVFTDAGRVCRPLFIVN 238
Cdd:PRK08565  487 VPVEEaREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVE 566

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   239 DQQLVLKKEDVMALSQGQtddgapFGWTQLVEKGIVEYLDAEEEETVMICMTPEDLeqsreyqqtgyvpqeafdpaarvk 318
Cdd:PRK08565  567 NGKPKLTREHVEKLKKGE------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------------------ 616

                         330       340       350
                  ....*....|....*....|....*....|.
gi 89274936   319 gnTSMYshtwTHCEIHPAMILGICASIIPFP 349
Cdd:PRK08565  617 --TPEH----THLEIWPPAILGITASIIPYP 641
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-144 1.80e-59

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: 205.11  E-value: 1.80e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   2 KRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVETQKPFNLNAAVKSNTITHGLKYSLATGNWGDQKKAASaRAGVSQVL 81
Cdd:cd00653 239 KRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVL 317

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 89274936  82 NRYTFASTLSHLRRCNT-PIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYIS 144
Cdd:cd00653 318 DRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 2-162 3.95e-44

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 158.19  E-value: 3.95e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    2 KRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVETQKPFNLNAAVKSNTITHGLKYSLATGNWgdqkkaASARAGVSQVL 81
Cdd:PRK09606 336 KRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLL 409

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   82 NRYTFASTLSHLRRCNTPIGRDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYISVGSPSAPVVEFFEEWGM 161
Cdd:PRK09606 410 DRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGV 489


                 .
gi 89274936  162 E 162
Cdd:PRK09606 490 E 490
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 171-349 2.88e-35

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 135.47  E-value: 2.88e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936  171 MSKGTKVFVNGVWQGVHRAPAELLRTIIHLRRCGDIEPEVSIVRDVRERELRVFTDAGRVCRPLFIVNDQQLVLKKEDVM 250
Cdd:PRK07225   1 MMRKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936  251 ALSQGQTDdgapfgWTQLVEKGIVEYLDAEEEETVMICMTPEDLEQsreyqqtgyvpqeafdpaarvkgntsmySHtwTH 330
Cdd:PRK07225  81 KLKNGELT------FDDLVKQGVIEYLDAEEEENAYIAVYEEDLTE----------------------------EH--TH 124

                        170
                 ....*....|....*....
gi 89274936  331 CEIHPAMILGICASIIPFP 349
Cdd:PRK07225 125 LEIDPSLILGIGAGMIPYP 143
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 79-142 6.38e-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: 6.38e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 89274936    79 QVLNRYTFASTLSHLRRCNTPIG---RDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSY 142
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 177-238 9.11e-32

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: 113.62  E-value: 9.11e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 89274936   177 VFVNGVWQGVHRAPAELLRTIIHLRRCGDIEPEVSIVRDVRERELRVFTDAGRVCRPLFIVN 238
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 265-335 5.80e-26

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: 98.00  E-value: 5.80e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 89274936   265 WTQLVEKGIVEYLDAEEEETVMICMTPEDLEQSREYQQTGyvpqeafdpaarvkgntsMYSHTWTHCEIHP 335
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG------------------PYAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-349 8.06e-26

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: 108.66  E-value: 8.06e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    2 KRLDLAGPLLAGLFRMLFRKLTKDV-YRhlqkcVETQKP--FNLNAAVKSNTITHGLKYSLATGnwgdqkkaasaraGVS 78
Cdd:COG0085  311 RRVRLVGELLQNQFRVGLSRMERVVrER-----MTTQDVeaITPQSLINIRPVVAAIKEFFGSS-------------QLS 372

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936   79 QVLNRYTFASTLSHLRRCNT----PIGRDgkiaKP----RQLHNSHWGMVCPAETPEGQACGLVKNLALMSYISvgspsa 150
Cdd:COG0085  373 QFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------ 442

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936  151 pvvEFfeewgmesleefsadmskgtkvfvngvwqgvhrapaellrtiihlrrcgdiepevsivrdvrerelrvftdaGRV 230
Cdd:COG0085  443 ---EY------------------------------------------------------------------------GFI 447

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936  231 CRPLFIVNDQQLvlkkedvmalsqgqTDDgapfgwtqlvekgiVEYLDAEEEETVMICMTPEDLEQSREYQQTgYVPqea 310
Cdd:COG0085  448 ETPYRKVENGKV--------------TDE--------------IEYLTADEEENYYIAQANAPLDEDGNFLEE-RVL--- 495

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|..
gi 89274936  311 fdpaARVKGNTSMYS---HtwTHCEIHPAMILGICASIIPFP 349
Cdd:COG0085  496 ----VRYRGEEVLVPpeeV--DYMDVSPKQIVSVATSLIPFL 531
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-52 4.55e-15

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: 75.49  E-value: 4.55e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 89274936     1 KKRLDLAGPLLAGLFRMLFRKLTKDVYRHLQKCVETQKPFNLNAAVKSNTIT 52
Cdd:pfam04563 344 NKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPIT 395
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
6-151 1.64e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 53.39  E-value: 1.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936     6 LAGPLLAGLFRMlfRKLTKDVYRHLQKCVETQKPFNLnaaVKSNTITHGLKYSLATGNwgdqkkaasaragVSQVLNRYT 85
Cdd:PRK09603  472 LANELHSGLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITSTIMEFFMGGQ-------------LSQFMDQTN 533

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 89274936    86 FASTLSHLRRCNTpIGRDGKIA-----KPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYIS-VGSPSAP 151
Cdd:PRK09603  534 PLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNdLGFIEAP 604
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
77-153 3.96e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 51.93  E-value: 3.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    77 VSQVLNRYTFASTLSHLRRCNT--PIG--RDGKIAKPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYIS----VGSP 148
Cdd:PRK14844  532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygfIESP 611


                  ....*
gi 89274936   149 SAPVV 153
Cdd:PRK14844  612 YRKVV 616
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-138 1.46e-06

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 50.09  E-value: 1.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936     1 KKRLDLAGPLLAGLFRM----LFRKLTKDVYrhlqKCVETQKpfnlnaaVKSNTITHGLKYSLATGNWGDQKkaasarag 76
Cdd:CHL00207  305 NRRVRSVGELLQNQFRIglkrLERILRNRMT----ICDIDSL-------SKFNLINPKPLIALIREFFGSSQ-------- 365

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 89274936    77 VSQVLNRYTFASTLSHLRRCNT--PIGRDG-KIAKP-RQLHNSHWGMVCPAETPEGQACGLVKNLA 138
Cdd:CHL00207  366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB CHL00001
RNA polymerase beta subunit
 78-164 7.59e-06

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 47.97  E-value: 7.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274936    78 SQVLNRYTFASTLSHLRRCNT--PIGRDGKIA--KPRQLHNSHWGMVCPAETPEGQACGLVKNLALMSYI----SVGSPS 149
Cdd:CHL00001  375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIghwgSLESPF 454

                          90
                  ....*....|....*
gi 89274936   150 APVVEFFEEWGMESL 164
Cdd:CHL00001  455 YEISERSKEERMVYL 469
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 110-138 7.28e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.71  E-value: 7.28e-05
                          10        20
                  ....*....|....*....|....*....
gi 89274936   110 RQLHNSHWGMVCPAETPEGQACGLVKNLA 138
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
 
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