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Conserved domains on  [gi|2603394961|gb|WON71552|]
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RNA polymerase II second largest subunit, partial [Rhizoctonia solani AG-2-2 IV]

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;
4-221 2.17e-52

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: 181.31  E-value: 2.17e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961    4 GPVIEFLEEWGLESLEEnVATGNSASATKVFVNGVWLGIHRDAPNLVKTLHRLRRMDHINSEVSI--VRDIREKELRLYT 81
Cdd:PRK08565   475 EEVEEILYELGVVPVEE-AREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNC 553

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961   82 DAGRVCRPLFIVdEQQKLTLKKKHVEWLQNGvdeegqEFKWKQLVKRGVIELLDADEEETVMISMTPEDLensrrieggg 161
Cdd:PRK08565   554 DSGRVRRPLIVV-ENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------- 616

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961  162 yvsnvndpdwdpsgTARvksvpniHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 221
Cdd:PRK08565   617 --------------TPE-------H--THLEIWPPAILGITASIIPYPEHNQSPRNTYQA 653
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 4-221 2.17e-52

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 181.31  E-value: 2.17e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961    4 GPVIEFLEEWGLESLEEnVATGNSASATKVFVNGVWLGIHRDAPNLVKTLHRLRRMDHINSEVSI--VRDIREKELRLYT 81
Cdd:PRK08565   475 EEVEEILYELGVVPVEE-AREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNC 553

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961   82 DAGRVCRPLFIVdEQQKLTLKKKHVEWLQNGvdeegqEFKWKQLVKRGVIELLDADEEETVMISMTPEDLensrrieggg 161
Cdd:PRK08565   554 DSGRVRRPLIVV-ENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------- 616

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961  162 yvsnvndpdwdpsgTARvksvpniHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 221
Cdd:PRK08565   617 --------------TPE-------H--THLEIWPPAILGITASIIPYPEHNQSPRNTYQA 653
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 33-94 2.38e-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: 111.69  E-value: 2.38e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2603394961  33 VFVNGVWLGIHRDAPNLVKTLHRLRRMDHINSEVSIVRDIREKELRLYTDAGRVCRPLFIVD 94
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 189-221 2.60e-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: 88.78  E-value: 2.60e-20
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2603394961 189 THCEIHPSMILGICASIIPFPDHNQSPRNTYQS 221
Cdd:cd00653   396 THIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 4-221 2.17e-52

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 181.31  E-value: 2.17e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961    4 GPVIEFLEEWGLESLEEnVATGNSASATKVFVNGVWLGIHRDAPNLVKTLHRLRRMDHINSEVSI--VRDIREKELRLYT 81
Cdd:PRK08565   475 EEVEEILYELGVVPVEE-AREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNC 553

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961   82 DAGRVCRPLFIVdEQQKLTLKKKHVEWLQNGvdeegqEFKWKQLVKRGVIELLDADEEETVMISMTPEDLensrrieggg 161
Cdd:PRK08565   554 DSGRVRRPLIVV-ENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------- 616

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961  162 yvsnvndpdwdpsgTARvksvpniHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQS 221
Cdd:PRK08565   617 --------------TPE-------H--THLEIWPPAILGITASIIPYPEHNQSPRNTYQA 653
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 31-221 3.80e-42

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 150.11  E-value: 3.80e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961  31 TKVFVNGVWLGIHRDAPNLVKTLHRLRRMDHINSEVSIVRDIREKELRLYTDAGRVCRPLFIVdEQQKLTLKKKHVEWLQ 110
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVV-ENGEPLLTEEHIEKLK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2603394961 111 NGvdeegqEFKWKQLVKRGVIELLDADEEETVMISMTPEDLEnsrriegggyvsnvndPDwdpsgtarvksvpniHtwTH 190
Cdd:PRK07225   84 NG------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT----------------EE---------------H--TH 124

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2603394961 191 CEIHPSMILGICASIIPFPDHNQSPRNTYQS 221
Cdd:PRK07225  125 LEIDPSLILGIGAGMIPYPEHNASPRITMGA 155
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 33-94 2.38e-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: 111.69  E-value: 2.38e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2603394961  33 VFVNGVWLGIHRDAPNLVKTLHRLRRMDHINSEVSIVRDIREKELRLYTDAGRVCRPLFIVD 94
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 122-195 1.77e-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: 86.06  E-value: 1.77e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2603394961 122 WKQLVKRGVIELLDADEEETVMISMTPEDLENSRRIEGGGyvsnvndpdwdpsgtarvksvPNIHTWTHCEIHP 195
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG---------------------PYAHTYTHCEIHP 53
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 189-221 2.60e-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: 88.78  E-value: 2.60e-20
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2603394961 189 THCEIHPSMILGICASIIPFPDHNQSPRNTYQS 221
Cdd:cd00653   396 THIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 202-221 5.52e-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: 49.07  E-value: 5.52e-07
                          10        20
                  ....*....|....*....|
gi 2603394961 202 CASIIPFPDHNQSPRNTYQS 221
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQC 20
 
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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