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Conserved domains on  [gi|1043653936|gb|ANS73112|]
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RPB2, partial [Pseudocercospora norchiensis]

Protein Classification

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;
1-228 1.14e-59

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: 202.11  E-value: 1.14e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043653936    1 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGFPLIDFMRQRGMDLLEEYDP 80
Cdd:PRK08565   415 LSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEARE 494

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043653936   81 VINPKATKVFLNGTWVGVHKNAGHLADTLRQLRRKGLLSFEVTI--IRDVREREIRVFTDAGRVCRPLFVVDNridsank 158
Cdd:PRK08565   495 EEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN------- 567

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1043653936  159 GSLVLDQSHLAKLaddqemlqnlegvseeeREKHIfGWKGLVDGGVVEYLDAEEEETAMI-IMISEDLEEH 228
Cdd:PRK08565   568 GKPKLTREHVEKL-----------------KKGEL-TFDDLVKMGVIEYLDAEEEENAYVaLDPEDLTPEH 620
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-228 1.14e-59

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 202.11  E-value: 1.14e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043653936    1 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGFPLIDFMRQRGMDLLEEYDP 80
Cdd:PRK08565   415 LSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEARE 494

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043653936   81 VINPKATKVFLNGTWVGVHKNAGHLADTLRQLRRKGLLSFEVTI--IRDVREREIRVFTDAGRVCRPLFVVDNridsank 158
Cdd:PRK08565   495 EEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN------- 567

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1043653936  159 GSLVLDQSHLAKLaddqemlqnlegvseeeREKHIfGWKGLVDGGVVEYLDAEEEETAMI-IMISEDLEEH 228
Cdd:PRK08565   568 GKPKLTREHVEKL-----------------KKGEL-TFDDLVKMGVIEYLDAEEEENAYVaLDPEDLTPEH 620
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 89-150 4.83e-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: 113.62  E-value: 4.83e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1043653936  89 VFLNGTWVGVHKNAGHLADTLRQLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVD 150
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-55 1.71e-26

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: 106.88  E-value: 1.71e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1043653936   1 LSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVT 55
Cdd:cd00653   326 LSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-56 6.46e-14

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: 70.14  E-value: 6.46e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1043653936    1 LSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTV 56
Cdd:COG0085    384 LTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-228 1.14e-59

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 202.11  E-value: 1.14e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043653936    1 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPGFPLIDFMRQRGMDLLEEYDP 80
Cdd:PRK08565   415 LSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEARE 494

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043653936   81 VINPKATKVFLNGTWVGVHKNAGHLADTLRQLRRKGLLSFEVTI--IRDVREREIRVFTDAGRVCRPLFVVDNridsank 158
Cdd:PRK08565   495 EEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN------- 567

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1043653936  159 GSLVLDQSHLAKLaddqemlqnlegvseeeREKHIfGWKGLVDGGVVEYLDAEEEETAMI-IMISEDLEEH 228
Cdd:PRK08565   568 GKPKLTREHVEKL-----------------KKGEL-TFDDLVKMGVIEYLDAEEEENAYVaLDPEDLTPEH 620
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 89-150 4.83e-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: 113.62  E-value: 4.83e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1043653936  89 VFLNGTWVGVHKNAGHLADTLRQLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVD 150
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-53 1.67e-27

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: 99.52  E-value: 1.67e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1043653936   1 LSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 53
Cdd:pfam04565  12 LSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 85-228 3.67e-27

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 108.51  E-value: 3.67e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1043653936  85 KATKVFLNGTWVGVHKNAGHLADTLRQLRRKGLLSFEVTIIRDVREREIRVFTDAGRVCRPLFVVDNridsankGSLVLD 164
Cdd:PRK07225    3 RKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLT 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1043653936 165 QSHLAKLADDQemlqnlegvseeerekhiFGWKGLVDGGVVEYLDAEEEETAMIIMISEDL-EEH 228
Cdd:PRK07225   76 EEHIEKLKNGE------------------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH 122
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-55 1.71e-26

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: 106.88  E-value: 1.71e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1043653936   1 LSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVT 55
Cdd:cd00653   326 LSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-59 1.22e-17

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 80.76  E-value: 1.22e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1043653936   1 LSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTP 59
Cdd:PRK09606  418 LSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGED 476
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-56 6.46e-14

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: 70.14  E-value: 6.46e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1043653936    1 LSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTV 56
Cdd:COG0085    384 LTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 196-228 6.18e-12

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: 58.71  E-value: 6.18e-12
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1043653936 196 WKGLVDGGVVEYLDAEEEETAMIIMISEDLEEH 228
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEES 33
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-61 2.36e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 48.08  E-value: 2.36e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1043653936    1 LSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLmcYVTVGTPGF 61
Cdd:PRK14844   545 ITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI--YARINKYGF 607
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-61 2.48e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 48.00  E-value: 2.48e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1043653936    1 LSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLSlmCYVTVGTPGF 61
Cdd:PRK09603   538 VTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS--TFTRVNDLGF 600
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 21-68 6.18e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 43.54  E-value: 6.18e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1043653936   21 RQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVTVGTPGFPLIDFMR 68
Cdd:CHL00207   403 RDIHPSHYGRICPIETPEGPNCGLIG--SLATNARINKFGFIETPFYK 448
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 21-49 6.53e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.55  E-value: 6.53e-05
                           10        20
                   ....*....|....*....|....*....
gi 1043653936   21 RQLHNTHWGLVCPAETPEGQACGLVKNLS 49
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 21-61 2.96e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 41.43  E-value: 2.96e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1043653936   21 RQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVTVGTPGF 61
Cdd:CHL00001   411 RDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIGHWGS 449
 
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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