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Conserved domains on  [gi|68131886|gb|AAY85221|]
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RNA polymerase II second largest subunit, partial [Meconopsis betonicifolia]

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;
1-219 2.96e-62

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: 209.04  E-value: 2.96e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886     1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEFGMENFEEISPAVIPQSTKIFVNGCWVGIHRNPEPLVKTLRRLRR 80
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886    81 RVDVNTEVGV--IREVRLKELRLYTDYGRCSRPLFIVEKQRLLIKKRDIRALQQRESPeedgWHDLVAKGYIEYVDTEEE 158
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELT----FDDLVKMGVIEYLDAEEE 604

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 68131886   159 ETTMISMtindlvsarhNPEEAYSEtYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 219
Cdd:PRK08565  605 ENAYVAL----------DPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAA 654
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-219 2.96e-62

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 209.04  E-value: 2.96e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886     1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEFGMENFEEISPAVIPQSTKIFVNGCWVGIHRNPEPLVKTLRRLRR 80
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886    81 RVDVNTEVGV--IREVRLKELRLYTDYGRCSRPLFIVEKQRLLIKKRDIRALQQRESPeedgWHDLVAKGYIEYVDTEEE 158
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELT----FDDLVKMGVIEYLDAEEE 604

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 68131886   159 ETTMISMtindlvsarhNPEEAYSEtYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 219
Cdd:PRK08565  605 ENAYVAL----------DPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAA 654
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 141-192 8.14e-22

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: 84.51  E-value: 8.14e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 68131886   141 WHDLVAKGYIEYVDTEEEETTMISMTINDLVSA-RHNPEEAYSETYTHCEIHP 192
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREGPYAHTYTHCEIHP 53
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 183-219 1.03e-20

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: 89.94  E-value: 1.03e-20
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 68131886 183 ETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 219
Cdd:cd00653 393 KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSN 429
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-219 1.52e-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: 77.84  E-value: 1.52e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886    1 ETPEGQACGLVKNLALMVYITVgsaanpilefleefgmenfeeispavipqstkifvngcwvgihrnpeplvktlrrlrr 80
Cdd:COG0085  422 ETPEGPNIGLIGSLALYARVNE---------------------------------------------------------- 443

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886   81 rvdvntevgvirevrlkelrlytdYGRCSRPLFIVEKQRLLikkrdiralqqrespEEdgwhdlvakgyIEYVDTEEEET 160
Cdd:COG0085  444 ------------------------YGFIETPYRKVENGKVT---------------DE-----------IEYLTADEEEN 473

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 68131886  161 TMIS----------MTINDLVSARHNPEEAYSET--YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 219
Cdd:COG0085  474 YYIAqanapldedgNFLEERVLVRYRGEEVLVPPeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-219 2.96e-62

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 209.04  E-value: 2.96e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886     1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEFGMENFEEISPAVIPQSTKIFVNGCWVGIHRNPEPLVKTLRRLRR 80
Cdd:PRK08565  449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886    81 RVDVNTEVGV--IREVRLKELRLYTDYGRCSRPLFIVEKQRLLIKKRDIRALQQRESPeedgWHDLVAKGYIEYVDTEEE 158
Cdd:PRK08565  529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELT----FDDLVKMGVIEYLDAEEE 604

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 68131886   159 ETTMISMtindlvsarhNPEEAYSEtYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 219
Cdd:PRK08565  605 ENAYVAL----------DPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAA 654
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 53-219 2.65e-41

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 147.80  E-value: 2.65e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886   53 TKIFVNGCWVGIHRNPEPLVKTLRRLRRRVDVNTEVGVIREVRLKELRLYTDYGRCSRPLFIVEKQRLLIKKRDIRALQQ 132
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886  133 RESpeedGWHDLVAKGYIEYVDTEEEETTMISMTINDLvsarhNPEeaysetYTHCEIHPSLILGVCASIIPFPDHNQSP 212
Cdd:PRK07225  85 GEL----TFDDLVKQGVIEYLDAEEEENAYIAVYEEDL-----TEE------HTHLEIDPSLILGIGAGMIPYPEHNASP 149


                 ....*..
gi 68131886  213 RNTYQSA 219
Cdd:PRK07225 150 RITMGAG 156
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 141-192 8.14e-22

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: 84.51  E-value: 8.14e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 68131886   141 WHDLVAKGYIEYVDTEEEETTMISMTINDLVSA-RHNPEEAYSETYTHCEIHP 192
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREGPYAHTYTHCEIHP 53
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 183-219 1.03e-20

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: 89.94  E-value: 1.03e-20
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 68131886 183 ETYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 219
Cdd:cd00653 393 KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSN 429
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 55-116 3.47e-19

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: 77.79  E-value: 3.47e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 68131886    55 IFVNGCWVGIHRNPEPLVKTLRRLRRRVDVNTEVGVIREVRLKELRLYTDYGRCSRPLFIVE 116
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-219 1.52e-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: 77.84  E-value: 1.52e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886    1 ETPEGQACGLVKNLALMVYITVgsaanpilefleefgmenfeeispavipqstkifvngcwvgihrnpeplvktlrrlrr 80
Cdd:COG0085  422 ETPEGPNIGLIGSLALYARVNE---------------------------------------------------------- 443

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68131886   81 rvdvntevgvirevrlkelrlytdYGRCSRPLFIVEKQRLLikkrdiralqqrespEEdgwhdlvakgyIEYVDTEEEET 160
Cdd:COG0085  444 ------------------------YGFIETPYRKVENGKVT---------------DE-----------IEYLTADEEEN 473

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 68131886  161 TMIS----------MTINDLVSARHNPEEAYSET--YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSA 219
Cdd:COG0085  474 YYIAqanapldedgNFLEERVLVRYRGEEVLVPPeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-43 4.06e-09

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 55.73  E-value: 4.06e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 68131886    1 ETPEGQACGLVKNLALMVYITVGSAANPILEFLEEFGMENFEE 43
Cdd:PRK09606 452 ETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPERG 494
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 199-219 2.67e-07

RNA polymerase Rpb2, domain 6; 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). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 50.22  E-value: 2.67e-07
                          10        20
                  ....*....|....*....|.
gi 68131886   199 CASIIPFPDHNQSPRNTYQSA 219
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCA 21
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-17 1.25e-05

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: 41.74  E-value: 1.25e-05
                          10
                  ....*....|....*..
gi 68131886     1 ETPEGQACGLVKNLALM 17
Cdd:pfam04565  49 ETPEGPNCGLVKHLALY 65
 
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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