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Conserved domains on  [gi|1168042295|gb|ARB12767|]
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RNA polymerase II second largest subunit, partial [Sporidesmioides thailandica]

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;
1-275 7.80e-63

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: 213.28  E-value: 7.80e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295    1 TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMsqRNMDL--LEE 78
Cdd:PRK08565   414 TLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEIL--YELGVvpVEE 491

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295   79 YDPVVNPTATKVFVNGVWVGVHSQPSQLVSVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVETdyrk 156
Cdd:PRK08565   492 AREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN---- 567

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295  157 pnrGSLVLNKGHVQKLledkeidTSGyndedaaamKFGWRGLIHNGVVEYLDAEEEETSMIIMTPEDLdehrdlmqgipa 236
Cdd:PRK08565   568 ---GKPKLTREHVEKL-------KKG---------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------ 616

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 1168042295  237 pegvaadrhkrikpkpnptVKTYTHCEIHPSMILGICAS 275
Cdd:PRK08565   617 -------------------TPEHTHLEIWPPAILGITAS 636
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-275 7.80e-63

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 213.28  E-value: 7.80e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295    1 TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMsqRNMDL--LEE 78
Cdd:PRK08565   414 TLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEIL--YELGVvpVEE 491

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295   79 YDPVVNPTATKVFVNGVWVGVHSQPSQLVSVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVETdyrk 156
Cdd:PRK08565   492 AREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN---- 567

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295  157 pnrGSLVLNKGHVQKLledkeidTSGyndedaaamKFGWRGLIHNGVVEYLDAEEEETSMIIMTPEDLdehrdlmqgipa 236
Cdd:PRK08565   568 ---GKPKLTREHVEKL-------KKG---------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------ 616

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 1168042295  237 pegvaadrhkrikpkpnptVKTYTHCEIHPSMILGICAS 275
Cdd:PRK08565   617 -------------------TPEHTHLEIWPPAILGITAS 636
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 90-151 5.29e-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: 107.45  E-value: 5.29e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1168042295  90 VFVNGVWVGVHSQPSQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVE 151
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-56 6.56e-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: 6.56e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1168042295   1 TLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 56
Cdd:cd00653   325 ELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-275 2.26e-15

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: 75.92  E-value: 2.26e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295    1 TLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgsestpitdfmsqrn 72
Cdd:COG0085    383 ELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------- 442

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295   73 mdlleEYdpvvnptatkvfvngvwvgvhsqpsqlvsvvqelrrngtlsyemslirdirdrefkiftdaGRVMRPLFVVEt 152
Cdd:COG0085    443 -----EY-------------------------------------------------------------GFIETPYRKVE- 455

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295  153 dyrkpnrgslvlnKGHVqklledkeidtsgyNDEdaaamkfgwrglihngvVEYLDAEEEETSMIIMTPEDLDEHrdlmq 232
Cdd:COG0085    456 -------------NGKV--------------TDE-----------------IEYLTADEEENYYIAQANAPLDED----- 486

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 1168042295  233 GIPAPEGVAADRHKRIKPKPNPTVktyTHCEIHPSMILGICAS 275
Cdd:COG0085    487 GNFLEERVLVRYRGEEVLVPPEEV---DYMDVSPKQIVSVATS 526
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-275 7.80e-63

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 213.28  E-value: 7.80e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295    1 TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMsqRNMDL--LEE 78
Cdd:PRK08565   414 TLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEIL--YELGVvpVEE 491

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295   79 YDPVVNPTATKVFVNGVWVGVHSQPSQLVSVVQELRRNGTLSYEMSL--IRDIRDREFKIFTDAGRVMRPLFVVETdyrk 156
Cdd:PRK08565   492 AREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN---- 567

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295  157 pnrGSLVLNKGHVQKLledkeidTSGyndedaaamKFGWRGLIHNGVVEYLDAEEEETSMIIMTPEDLdehrdlmqgipa 236
Cdd:PRK08565   568 ---GKPKLTREHVEKL-------KKG---------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------ 616

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 1168042295  237 pegvaadrhkrikpkpnptVKTYTHCEIHPSMILGICAS 275
Cdd:PRK08565   617 -------------------TPEHTHLEIWPPAILGITAS 636
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 88-275 1.21e-30

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 120.07  E-value: 1.21e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295  88 TKVFVNGVWVGVHSQPSQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVETdyrkpnrGSLVLNKG 167
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295 168 HVQKlLEDKEIDtsgyndedaaamkfgWRGLIHNGVVEYLDAEEEETSMIIMTPEDL-DEHrdlmqgipapegvaadrhk 246
Cdd:PRK07225   78 HIEK-LKNGELT---------------FDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH------------------- 122

                         170       180
                  ....*....|....*....|....*....
gi 1168042295 247 rikpkpnptvktyTHCEIHPSMILGICAS 275
Cdd:PRK07225  123 -------------THLEIDPSLILGIGAG 138
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 90-151 5.29e-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: 107.45  E-value: 5.29e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1168042295  90 VFVNGVWVGVHSQPSQLVSVVQELRRNGTLSYEMSLIRDIRDREFKIFTDAGRVMRPLFVVE 151
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-54 2.42e-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: 100.68  E-value: 2.42e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1168042295   1 TLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 54
Cdd:pfam04565  11 TLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-56 6.56e-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: 6.56e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1168042295   1 TLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 56
Cdd:cd00653   325 ELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 195-266 4.06e-23

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: 89.14  E-value: 4.06e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1168042295 195 WRGLIHNGVVEYLDAEEEETSMIIMTPEDLDEHRDLMQGIpapegvaadrhkrikpkpnPTVKTYTHCEIHP 266
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG-------------------PYAHTYTHCEIHP 53
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-80 2.34e-19

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 87.31  E-value: 2.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295   1 TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSESTPITDFMSqrNMDLLEEYD 80
Cdd:PRK09606  417 TLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILK--ELGVEPERG 494
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-275 2.26e-15

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: 75.92  E-value: 2.26e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295    1 TLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgsestpitdfmsqrn 72
Cdd:COG0085    383 ELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------- 442

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295   73 mdlleEYdpvvnptatkvfvngvwvgvhsqpsqlvsvvqelrrngtlsyemslirdirdrefkiftdaGRVMRPLFVVEt 152
Cdd:COG0085    443 -----EY-------------------------------------------------------------GFIETPYRKVE- 455

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1168042295  153 dyrkpnrgslvlnKGHVqklledkeidtsgyNDEdaaamkfgwrglihngvVEYLDAEEEETSMIIMTPEDLDEHrdlmq 232
Cdd:COG0085    456 -------------NGKV--------------TDE-----------------IEYLTADEEENYYIAQANAPLDED----- 486

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 1168042295  233 GIPAPEGVAADRHKRIKPKPNPTVktyTHCEIHPSMILGICAS 275
Cdd:COG0085    487 GNFLEERVLVRYRGEEVLVPPEEV---DYMDVSPKQIVSVATS 526
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
2-50 8.85e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 46.84  E-value: 8.85e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1168042295    2 LSHLRRTNTpIGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLS 50
Cdd:PRK09603   538 VTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS 590
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
2-56 1.64e-05

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 46.15  E-value: 1.64e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1168042295    2 LSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS 56
Cdd:PRK14844   545 ITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 22-50 8.42e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 8.42e-05
                           10        20
                   ....*....|....*....|....*....
gi 1168042295   22 RQLHNTHWGLVCPAETPEGQACGLVKNLS 50
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 2-50 1.62e-04

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 42.77  E-value: 1.62e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1168042295    2 LSHLRRTNT--PIGRDgKLAKP---RQLHNTHWGLVCPAETPEGQACGLVKNLS 50
Cdd:CHL00207   379 LTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB CHL00001
RNA polymerase beta subunit
 22-59 3.72e-03

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 38.73  E-value: 3.72e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1168042295   22 RQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVSVGS 59
Cdd:CHL00001   411 RDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIGH 446
 
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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