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Conserved domains on  [gi|1697170521|gb|QDH75197|]
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RNA polymerase II second largest subunit, partial [Penicillium cyaneum]

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

Graphical summary

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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;
3-290 2.22e-76

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: 253.34  E-value: 2.22e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521    3 RDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGeqkkaaSAKAGVSQVLSRYTYASTLSHLRRTNTPIGRD 82
Cdd:PRK08565   355 KDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRG 428
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   83 GKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDfmIQRNMEV--LEEFEPQVTPNATKVFVN 160
Cdd:PRK08565   429 QPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLN 506
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521  161 GVWVGIHRDPSHLVNTMSSLRRRNMISHEVSL--IRDIREREFKIFTDAGRVCRPLFVVDNdpksenaGSLVLNKEHIRK 238
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1697170521  239 LeqdkdlpmnldpeerRERYFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDL 290
Cdd:PRK08565   580 L---------------KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL 616
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
3-290 2.22e-76

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 253.34  E-value: 2.22e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521    3 RDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGeqkkaaSAKAGVSQVLSRYTYASTLSHLRRTNTPIGRD 82
Cdd:PRK08565   355 KDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRG 428
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   83 GKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDfmIQRNMEV--LEEFEPQVTPNATKVFVN 160
Cdd:PRK08565   429 QPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLN 506
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521  161 GVWVGIHRDPSHLVNTMSSLRRRNMISHEVSL--IRDIREREFKIFTDAGRVCRPLFVVDNdpksenaGSLVLNKEHIRK 238
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1697170521  239 LeqdkdlpmnldpeerRERYFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDL 290
Cdd:PRK08565   580 L---------------KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL 616
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
3-123 2.04e-45

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: 165.05  E-value: 2.04e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   3 RDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGeQKKAASAKAGVSQVLSRYTYASTLSHLRRTNT-PIGR 81
Cdd:cd00653   261 REVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFR 339
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1697170521  82 DGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT 123
Cdd:cd00653   340 ERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
157-218 1.71e-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: 115.16  E-value: 1.71e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1697170521 157 VFVNGVWVGIHRDPSHLVNTMSSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVD 218
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
48-124 1.84e-17

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: 83.24  E-value: 1.84e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   48 KAASAKAGVSQVLSRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALM 119
Cdd:COG0085    363 KEFFGSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALY 438

                   ....*
gi 1697170521  120 CYITV 124
Cdd:COG0085    439 ARVNE 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
3-290 2.22e-76

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 253.34  E-value: 2.22e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521    3 RDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGeqkkaaSAKAGVSQVLSRYTYASTLSHLRRTNTPIGRD 82
Cdd:PRK08565   355 KDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRG 428
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   83 GKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDfmIQRNMEV--LEEFEPQVTPNATKVFVN 160
Cdd:PRK08565   429 QPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLN 506
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521  161 GVWVGIHRDPSHLVNTMSSLRRRNMISHEVSL--IRDIREREFKIFTDAGRVCRPLFVVDNdpksenaGSLVLNKEHIRK 238
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1697170521  239 LeqdkdlpmnldpeerRERYFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDL 290
Cdd:PRK08565   580 L---------------KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL 616
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
3-123 2.04e-45

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: 165.05  E-value: 2.04e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   3 RDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGeQKKAASAKAGVSQVLSRYTYASTLSHLRRTNT-PIGR 81
Cdd:cd00653   261 REVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFR 339
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1697170521  82 DGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT 123
Cdd:cd00653   340 ERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
2-135 2.05e-35

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 133.92  E-value: 2.05e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   2 TRDLQRYVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWgeqkkaASAKAGVSQVLSRYTYASTLSHLRRTNTPIGR 81
Cdd:PRK09606  357 ARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSR 430
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1697170521  82 DGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPIIDFM 135
Cdd:PRK09606  431 SQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL 484
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
157-218 1.71e-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: 115.16  E-value: 1.71e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1697170521 157 VFVNGVWVGIHRDPSHLVNTMSSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVD 218
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
58-121 3.69e-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: 3.69e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1697170521  58 QVLSRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 121
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
155-299 7.66e-28

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 113.52  E-value: 7.66e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521 155 TKVFVNGVWVGIHRDPSHLVNTMSSLRRRNMISHEVSLIRDIREREFKIFTDAGRVCRPLFVVDNdpksenaGSLVLNKE 234
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1697170521 235 HIRKLEQDKdlpmnldpeerreryFGWDGLVRSGAVEYVDAEEEETIMIVMTPED-------LEISKQLQAG 299
Cdd:PRK07225   78 HIEKLKNGE---------------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDlteehthLEIDPSLILG 134
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
48-124 1.84e-17

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: 83.24  E-value: 1.84e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   48 KAASAKAGVSQVLSRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALM 119
Cdd:COG0085    363 KEFFGSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALY 438

                   ....*
gi 1697170521  120 CYITV 124
Cdd:COG0085    439 ARVNE 443
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
261-297 5.21e-16

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: 71.03  E-value: 5.21e-16
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1697170521 261 WDGLVRSGAVEYVDAEEEETIMIVMTPEDLEISKQLQ 297
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE 37
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
56-143 1.63e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 53.09  E-value: 1.63e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697170521   56 VSQVLSRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT----VGTP 127
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygfIESP 611
                           90
                   ....*....|....*.
gi 1697170521  128 SEPIIDFMIQRNMEVL 143
Cdd:PRK14844   612 YRKVVNRVVTDQIEYL 627
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
56-117 4.74e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 48.38  E-value: 4.74e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1697170521   56 VSQVLSRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 117
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
55-117 1.73e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 46.62  E-value: 1.73e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1697170521   55 GVSQvLSRYTYA----STLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLA 117
Cdd:CHL00207   362 GSSQ-LSQYMDQtnplSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
89-117 9.47e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.32  E-value: 9.47e-05
                           10        20
                   ....*....|....*....|....*....
gi 1697170521   89 RQLHNTHWGLVCPAETPEGQACGLVKNLA 117
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
57-117 4.46e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.20  E-value: 4.46e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1697170521   57 SQVLSRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 117
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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