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Conserved domains on  [gi|269853939|gb|ACZ51225|]
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RNA polymerase II second largest subunit, partial [Clitopilus geminus]

Protein Classification

DNA-directed RNA polymerase III subunit RPC2( domain architecture ID 10518874)

DNA-directed RNA polymerase III subunit RPC2 is the second largest core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs

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;
1-160 9.00e-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: 161.28  E-value: 9.00e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269853939    1 KNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTLRKLRRKDDISPEVSV- 78
Cdd:PRK08565  460 KNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269853939   79 -VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHVKWLNEGinedaeEYKWEHLVKGGIVELLDAEEEETVMISMTP 157
Cdd:PRK08565  540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDP 613


                  ...
gi 269853939  158 EDL 160
Cdd:PRK08565  614 EDL 616
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 131-201 3.03e-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: 84.90  E-value: 3.03e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 269853939  131 WEHLVKGGIVELLDAEEEETVMISMTPEDLETSRLQQsgistsptegdfdpa*rlKAGINSHTWTHCEIHP 201
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCEIHP 53
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-160 9.00e-46

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 161.28  E-value: 9.00e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269853939    1 KNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTLRKLRRKDDISPEVSV- 78
Cdd:PRK08565  460 KNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269853939   79 -VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHVKWLNEGinedaeEYKWEHLVKGGIVELLDAEEEETVMISMTP 157
Cdd:PRK08565  540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDP 613


                  ...
gi 269853939  158 EDL 160
Cdd:PRK08565  614 EDL 616
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 43-104 8.87e-38

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: 125.17  E-value: 8.87e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 269853939   43 VFVNGVWMGVHRDPANLVKTLRKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 104
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 131-201 3.03e-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: 84.90  E-value: 3.03e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 269853939  131 WEHLVKGGIVELLDAEEEETVMISMTPEDLETSRLQQsgistsptegdfdpa*rlKAGINSHTWTHCEIHP 201
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCEIHP 53
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-160 9.00e-46

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 161.28  E-value: 9.00e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269853939    1 KNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTLRKLRRKDDISPEVSV- 78
Cdd:PRK08565  460 KNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269853939   79 -VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHVKWLNEGinedaeEYKWEHLVKGGIVELLDAEEEETVMISMTP 157
Cdd:PRK08565  540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDP 613


                  ...
gi 269853939  158 EDL 160
Cdd:PRK08565  614 EDL 616
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 43-104 8.87e-38

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: 125.17  E-value: 8.87e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 269853939   43 VFVNGVWMGVHRDPANLVKTLRKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 104
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 41-160 1.49e-32

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 122.76  E-value: 1.49e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269853939  41 TKVFVNGVWMGVHRDPANLVKTLRKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHVKWLNE 120
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 269853939 121 GinedaeEYKWEHLVKGGIVELLDAEEEETVMISMTPEDL 160
Cdd:PRK07225  85 G------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL 118
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 131-201 3.03e-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: 84.90  E-value: 3.03e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 269853939  131 WEHLVKGGIVELLDAEEEETVMISMTPEDLETSRLQQsgistsptegdfdpa*rlKAGINSHTWTHCEIHP 201
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCEIHP 53
 
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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