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Conserved domains on  [gi|1474741479|gb|AXX69828|]
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RNA polymerase II second largest subunit, partial [Gyroporus subalbellus]

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

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
5-280 1.19e-83

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: 271.83  E-value: 1.19e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479    5 HKEFNLSLAVKHQTITNGLKYSLATGNWGdqkksmAAKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTH 84
Cdd:PRK08565   368 GRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQ 441

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   85 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVK 163
Cdd:PRK08565   442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAE 521

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479  164 TIKKLRRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLVLQKKHIKWLSQGyrddd*eEFKWEHLVKGG 241
Cdd:PRK08565   522 KIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMG 594

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1474741479  242 IIELLDAEEEETVMISMTPEDL--ENSRLQ---------AAGINPYENEN 280
Cdd:PRK08565   595 VIEYLDAEEEENAYVALDPEDLtpEHTHLEiwppailgiTASIIPYPEHN 644
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 5-280 1.19e-83

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 271.83  E-value: 1.19e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479    5 HKEFNLSLAVKHQTITNGLKYSLATGNWGdqkksmAAKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTH 84
Cdd:PRK08565   368 GRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQ 441

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   85 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVK 163
Cdd:PRK08565   442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAE 521

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479  164 TIKKLRRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLVLQKKHIKWLSQGyrddd*eEFKWEHLVKGG 241
Cdd:PRK08565   522 KIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMG 594

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1474741479  242 IIELLDAEEEETVMISMTPEDL--ENSRLQ---------AAGINPYENEN 280
Cdd:PRK08565   595 VIEYLDAEEEENAYVALDPEDLtpEHTHLEiwppailgiTASIIPYPEHN 644
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 6-121 2.24e-46

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: 166.59  E-value: 2.24e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   6 KEFNLSLAVKHQTITNGLKYSLATGNWGDQKKSMAaKAGVSQVLNRYTYASTLSHLRRCNT-PLGREGKIAKPRQLHNTH 84
Cdd:cd00653   275 KDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSH 353

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1474741479  85 WGMVCPAETPEGQACGLVKNLALMACISvGSYSAPVI 121
Cdd:cd00653   354 WGRICPIETPEGENCGLVKNLALMARIS-GRIERPYR 389
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 145-206 1.43e-36

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: 124.79  E-value: 1.43e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1474741479 145 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 206
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 41-113 1.43e-19

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: 88.63  E-value: 1.43e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   41 AKAGVSQVLNRYTYASTLSHLRRCNT----PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLALMACIS 112
Cdd:COG0085    367 GSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN 442


                   .
gi 1474741479  113 V 113
Cdd:COG0085    443 E 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 5-280 1.19e-83

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 271.83  E-value: 1.19e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479    5 HKEFNLSLAVKHQTITNGLKYSLATGNWGdqkksmAAKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTH 84
Cdd:PRK08565   368 GRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQ 441

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   85 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVK 163
Cdd:PRK08565   442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAE 521

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479  164 TIKKLRRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLVLQKKHIKWLSQGyrddd*eEFKWEHLVKGG 241
Cdd:PRK08565   522 KIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMG 594

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1474741479  242 IIELLDAEEEETVMISMTPEDL--ENSRLQ---------AAGINPYENEN 280
Cdd:PRK08565   595 VIEYLDAEEEENAYVALDPEDLtpEHTHLEiwppailgiTASIIPYPEHN 644
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 6-121 2.24e-46

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: 166.59  E-value: 2.24e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   6 KEFNLSLAVKHQTITNGLKYSLATGNWGDQKKSMAaKAGVSQVLNRYTYASTLSHLRRCNT-PLGREGKIAKPRQLHNTH 84
Cdd:cd00653   275 KDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSH 353

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1474741479  85 WGMVCPAETPEGQACGLVKNLALMACISvGSYSAPVI 121
Cdd:cd00653   354 WGRICPIETPEGENCGLVKNLALMARIS-GRIERPYR 389
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 5-130 1.04e-36

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 136.62  E-value: 1.04e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   5 HKEFNLSLAVKHQTITNGLKYSLATGNWgdqkksMAAKAGVSQVLNRYTYASTLSHLRRCNTPLGREGKIAKPRQLHNTH 84
Cdd:PRK09606  371 NRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1474741479  85 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLE 130
Cdd:PRK09606  445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 145-206 1.43e-36

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: 124.79  E-value: 1.43e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1474741479 145 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 206
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 143-280 1.41e-33

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 128.93  E-value: 1.41e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479 143 TKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLVLQKKHIKWLSQ 222
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1474741479 223 Gyrddd*eEFKWEHLVKGGIIELLDAEEEETVMISMTPEDL--ENSRLQ---------AAGINPYENEN 280
Cdd:PRK07225   85 G-------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLteEHTHLEidpslilgiGAGMIPYPEHN 146
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 47-109 9.86e-33

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: 114.93  E-value: 9.86e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1474741479  47 QVLNRYTYASTLSHLRRCNTP---LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMA 109
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPrggLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 41-113 1.43e-19

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: 88.63  E-value: 1.43e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   41 AKAGVSQVLNRYTYASTLSHLRRCNT----PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLALMACIS 112
Cdd:COG0085    367 GSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN 442


                   .
gi 1474741479  113 V 113
Cdd:COG0085    443 E 443
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 234-274 1.81e-14

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: 66.41  E-value: 1.81e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1474741479 234 WEHLVKGGIIELLDAEEEETVMISMTPEDLENS-RLQAAGIN 274
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREGPY 42
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
45-112 4.59e-08

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 54.24  E-value: 4.59e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1474741479   45 VSQVLNRYTYASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACIS 112
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
45-106 3.82e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.46  E-value: 3.82e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1474741479   45 VSQVLNRYTYASTLSHLRRCNTpLGrEGKIAK------PRQLHNTHWGMVCPAETPEGQACGLVKNLA 106
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 45-106 4.26e-06

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 48.16  E-value: 4.26e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1474741479   45 VSQVLNRYTYASTLSHLRRCNTpLGREG----KIAKP-RQLHNTHWGMVCPAETPEGQACGLVKNLA 106
Cdd:CHL00207   366 LSQYMDQTNPLSELTHKRRISI-LGPGGldkdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 78-111 3.20e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 45.48  E-value: 3.20e-05
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1474741479   78 RQLHNTHWGMVCPAETPEGQACGLVKNLALMACI 111
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLATYARV 502
rpoB CHL00001
RNA polymerase beta subunit
 46-111 5.02e-05

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 44.89  E-value: 5.02e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474741479   46 SQVLNRYTYASTLSHLRRCNT--PLGREGKIA--KPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACI 111
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARI 444
 
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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