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Conserved domains on  [gi|1876240005|gb|QLJ84198|]
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RNA polymerase II second largest subunit, partial [Talaromyces resedanus]

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;
17-277 1.62e-73

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: 244.87  E-value: 1.62e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   17 LTGGLKYALATGNWGeqkkamSSKAGVSQVLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 96
Cdd:PRK08565   382 ITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPN 455

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   97 CGLVKNLALMCSITVGSPSEPIVDfmIQRNMEV--LEEFEPLVTPNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRNMIS 174
Cdd:PRK08565   456 CGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKIS 533

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005  175 HEVSlVRDIRDREFK---IFTDAGRVCRPLFVIDNdprsencGSLVLNKDHIRKLeadrelppdldpeerREQYYGWEGL 251
Cdd:PRK08565   534 DEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKL---------------KKGELTFDDL 590

                          250       260
                   ....*....|....*....|....*.
gi 1876240005  252 VKSGVIEYVDAEEEETIMIAMTPEDL 277
Cdd:PRK08565   591 VKMGVIEYLDAEEEENAYVALDPEDL 616
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 17-277 1.62e-73

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 244.87  E-value: 1.62e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   17 LTGGLKYALATGNWGeqkkamSSKAGVSQVLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 96
Cdd:PRK08565   382 ITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPN 455

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   97 CGLVKNLALMCSITVGSPSEPIVDfmIQRNMEV--LEEFEPLVTPNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRNMIS 174
Cdd:PRK08565   456 CGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKIS 533

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005  175 HEVSlVRDIRDREFK---IFTDAGRVCRPLFVIDNdprsencGSLVLNKDHIRKLeadrelppdldpeerREQYYGWEGL 251
Cdd:PRK08565   534 DEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKL---------------KKGELTFDDL 590

                          250       260
                   ....*....|....*....|....*.
gi 1876240005  252 VKSGVIEYVDAEEEETIMIAMTPEDL 277
Cdd:PRK08565   591 VKMGVIEYLDAEEEENAYVALDPEDL 616
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 12-110 2.36e-41

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: 152.72  E-value: 2.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005  12 LKAATLTGGLKYALATGNWGeQKKAMSSKAGVSQVLSRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAE 90
Cdd:cd00653   283 INSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIE 361

                          90       100
                  ....*....|....*....|
gi 1876240005  91 TPEGQACGLVKNLALMCSIT 110
Cdd:cd00653   362 TPEGENCGLVKNLALMARIS 381
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 144-205 7.82e-33

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: 115.54  E-value: 7.82e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1876240005 144 VFVNGVWVGVHRDPAHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVID 205
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 34-111 1.11e-16

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: 80.54  E-value: 1.11e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   34 KKAMSSkAGVSQVLSRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLAL 105
Cdd:COG0085    363 KEFFGS-SQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLAL 437


                   ....*.
gi 1876240005  106 MCSITV 111
Cdd:COG0085    438 YARVNE 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 17-277 1.62e-73

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 244.87  E-value: 1.62e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   17 LTGGLKYALATGNWGeqkkamSSKAGVSQVLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQA 96
Cdd:PRK08565   382 ITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPN 455

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   97 CGLVKNLALMCSITVGSPSEPIVDfmIQRNMEV--LEEFEPLVTPNATKVFVNGVWVGVHRDPAHLVSTVQSLRRRNMIS 174
Cdd:PRK08565   456 CGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKIS 533

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005  175 HEVSlVRDIRDREFK---IFTDAGRVCRPLFVIDNdprsencGSLVLNKDHIRKLeadrelppdldpeerREQYYGWEGL 251
Cdd:PRK08565   534 DEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKL---------------KKGELTFDDL 590

                          250       260
                   ....*....|....*....|....*.
gi 1876240005  252 VKSGVIEYVDAEEEETIMIAMTPEDL 277
Cdd:PRK08565   591 VKMGVIEYLDAEEEENAYVALDPEDL 616
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 12-110 2.36e-41

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: 152.72  E-value: 2.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005  12 LKAATLTGGLKYALATGNWGeQKKAMSSKAGVSQVLSRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAE 90
Cdd:cd00653   283 INSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIE 361

                          90       100
                  ....*....|....*....|
gi 1876240005  91 TPEGQACGLVKNLALMCSIT 110
Cdd:cd00653   362 TPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 3-122 1.70e-33

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 128.14  E-value: 1.70e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   3 NREVVLNVGLKAATLTGGLKYALATGNWgeqkkaMSSKAGVSQVLSRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTH 82
Cdd:PRK09606  371 NRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1876240005  83 WGLVCPAETPEGQACGLVKNLALMCSITVGSPSEPIVDFM 122
Cdd:PRK09606  445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL 484
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 144-205 7.82e-33

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: 115.54  E-value: 7.82e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1876240005 144 VFVNGVWVGVHRDPAHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVID 205
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 45-108 5.50e-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: 113.39  E-value: 5.50e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1876240005  45 QVLSRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCS 108
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 142-296 1.27e-29

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 118.14  E-value: 1.27e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005 142 TKVFVNGVWVGVHRDPAHLVSTVQSLRRRNMISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNdprsencGSLVLNKD 221
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005 222 HIRKLEaDRELppdldpeerreqyyGWEGLVKSGVIEYVDAEEEETIMIAMTPED-------LEISKQLQAGYAL----- 289
Cdd:PRK07225   78 HIEKLK-NGEL--------------TFDDLVKQGVIEYLDAEEEENAYIAVYEEDlteehthLEIDPSLILGIGAgmipy 142


                  ....*..
gi 1876240005 290 PEDNADP 296
Cdd:PRK07225  143 PEHNASP 149
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 248-284 5.91e-18

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: 76.04  E-value: 5.91e-18
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1876240005 248 WEGLVKSGVIEYVDAEEEETIMIAMTPEDLEISKQLQ 284
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE 37
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 34-111 1.11e-16

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: 80.54  E-value: 1.11e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   34 KKAMSSkAGVSQVLSRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLAL 105
Cdd:COG0085    363 KEFFGS-SQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLAL 437


                   ....*.
gi 1876240005  106 MCSITV 111
Cdd:COG0085    438 YARVNE 443
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
43-130 3.40e-08

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 55.01  E-value: 3.40e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   43 VSQVLSRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCSIT----VGSP 114
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygfIESP 611

                           90
                   ....*....|....*.
gi 1876240005  115 SEPIVDFMIQRNMEVL 130
Cdd:PRK14844   612 YRKVVNRVVTDQIEYL 627
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
43-148 1.24e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 49.92  E-value: 1.24e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1876240005   43 VSQVLSRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCSIT----VGS 113
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNdlgfIEA 603

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1876240005  114 PSEPIVDFMIQRNMEVL---EEFEPLVTPNATKVFVNG 148
Cdd:PRK09603   604 PYKKVVDGKVVGETIYLtaiQEDSHIIAPASTPIDEEG 641
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 42-104 1.59e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 46.62  E-value: 1.59e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1876240005   42 GVSQvLSRYTYA----STLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLA 104
Cdd:CHL00207   362 GSSQ-LSQYMDQtnplSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 76-104 8.07e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.32  E-value: 8.07e-05
                           10        20
                   ....*....|....*....|....*....
gi 1876240005   76 RQLHNTHWGLVCPAETPEGQACGLVKNLA 104
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 44-104 3.23e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.20  E-value: 3.23e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1876240005   44 SQVLSRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 104
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
 
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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