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Conserved domains on  [gi|2301310203|gb|UWT51932|]
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RNA polymerase II second largest subunit, partial [Alternaria cypericola]

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;
1-169 2.27e-46

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: 162.43  E-value: 2.27e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2301310203    1 LRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIIDFMTQRNMQLLEEYDQNQN 80
Cdd:PRK08565   418 LRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEY 497

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2301310203   81 PDATKVFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVENdirkpnrNHL 158
Cdd:PRK08565   498 ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKP 570

                          170
                   ....*....|.
gi 2301310203  159 IFTKEISNKLK 169
Cdd:PRK08565   571 KLTREHVEKLK 581
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-169 2.27e-46

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 162.43  E-value: 2.27e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2301310203    1 LRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIIDFMTQRNMQLLEEYDQNQN 80
Cdd:PRK08565   418 LRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEY 497

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2301310203   81 PDATKVFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVENdirkpnrNHL 158
Cdd:PRK08565   498 ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKP 570

                          170
                   ....*....|.
gi 2301310203  159 IFTKEISNKLK 169
Cdd:PRK08565   571 KLTREHVEKLK 581
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-147 2.14e-30

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: 105.53  E-value: 2.14e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2301310203  86 VFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVE 147
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-52 7.74e-24

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: 97.64  E-value: 7.74e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2301310203   1 LRRTNT-PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVS 52
Cdd:cd00653   329 KRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 18-53 5.28e-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: 69.37  E-value: 5.28e-14
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2301310203   18 RQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSV 53
Cdd:COG0085    408 RDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-169 2.27e-46

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 162.43  E-value: 2.27e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2301310203    1 LRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIIDFMTQRNMQLLEEYDQNQN 80
Cdd:PRK08565   418 LRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEY 497

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2301310203   81 PDATKVFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVENdirkpnrNHL 158
Cdd:PRK08565   498 ISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKP 570

                          170
                   ....*....|.
gi 2301310203  159 IFTKEISNKLK 169
Cdd:PRK08565   571 KLTREHVEKLK 581
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 86-147 2.14e-30

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: 105.53  E-value: 2.14e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2301310203  86 VFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVE 147
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-50 1.10e-24

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: 91.05  E-value: 1.10e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2301310203   1 LRRTNTPVG---RDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCY 50
Cdd:pfam04565  15 LRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-52 7.74e-24

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: 97.64  E-value: 7.74e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2301310203   1 LRRTNT-PVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVS 52
Cdd:cd00653   329 KRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-64 4.60e-17

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 78.07  E-value: 4.60e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2301310203   1 LRRTNTPVGRDGKLAKPRQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSDASPIIDFM 64
Cdd:PRK09606  421 LRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL 484
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 84-148 3.60e-15

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 72.69  E-value: 3.60e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2301310203  84 TKVFVNGVWVGVHSNAQQLVTVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVEN 148
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN 69
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 18-53 5.28e-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: 69.37  E-value: 5.28e-14
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2301310203   18 RQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVSV 53
Cdd:COG0085    408 RDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
18-46 1.05e-05

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 45.30  E-value: 1.05e-05
                           10        20
                   ....*....|....*....|....*....
gi 2301310203   18 RQLHNSHWGLVCPAETPEGQACGLVKNLS 46
Cdd:PRK09603   562 RDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 18-46 1.34e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 44.70  E-value: 1.34e-05
                           10        20
                   ....*....|....*....|....*....
gi 2301310203   18 RQLHNSHWGLVCPAETPEGQACGLVKNLS 46
Cdd:CHL00207   403 RDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 18-46 2.65e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 2.65e-05
                           10        20
                   ....*....|....*....|....*....
gi 2301310203   18 RQLHNSHWGLVCPAETPEGQACGLVKNLS 46
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
18-52 3.39e-05

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 43.84  E-value: 3.39e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2301310203   18 RQLHNSHWGLVCPAETPEGQACGLVKNLSLMCYVS 52
Cdd:PRK14844   569 RDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
rpoB CHL00001
RNA polymerase beta subunit
 18-58 8.64e-05

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.20  E-value: 8.64e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2301310203   18 RQLHNSHWGLVCPAETPEGQACGLVKnlSLMCYVSVGSDAS 58
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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