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Conserved domains on  [gi|530748596|gb|AGT46408|]
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RNA polymerase II subunit, partial [Septoria lycopicola]

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;
1-105 1.22e-30

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: 113.90  E-value: 1.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530748596    1 FGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQkkasssKAGVS 80
Cdd:PRK08565  330 YANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------RTGVS 403

                          90       100
                  ....*....|....*....|....*
gi 530748596   81 QVLNRYTYASTLSHLRRTNTPIGRD 105
Cdd:PRK08565  404 QLLDRTNYLSTLSHLRRVVSPLSRG 428
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-105 1.22e-30

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 113.90  E-value: 1.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530748596    1 FGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQkkasssKAGVS 80
Cdd:PRK08565  330 YANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------RTGVS 403

                          90       100
                  ....*....|....*....|....*
gi 530748596   81 QVLNRYTYASTLSHLRRTNTPIGRD 105
Cdd:PRK08565  404 QLLDRTNYLSTLSHLRRVVSPLSRG 428
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-55 6.87e-15

RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 68.95  E-value: 6.87e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 530748596    1 FGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVETGREFNITLAVKTNIITS 55
Cdd:pfam04563 342 LGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-105 1.22e-30

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 113.90  E-value: 1.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530748596    1 FGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWGDQkkasssKAGVS 80
Cdd:PRK08565  330 YANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG------RTGVS 403

                          90       100
                  ....*....|....*....|....*
gi 530748596   81 QVLNRYTYASTLSHLRRTNTPIGRD 105
Cdd:PRK08565  404 QLLDRTNYLSTLSHLRRVVSPLSRG 428
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 4-104 7.80e-28

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 105.42  E-value: 7.80e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530748596   4 KRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVETGREFNITLAVKTNIITSGLRYCLATGNWgdqkkaSSSKAGVSQVL 83
Cdd:PRK09606 336 KRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLL 409

                         90       100
                 ....*....|....*....|.
gi 530748596  84 NRYTYASTLSHLRRTNTPIGR 104
Cdd:PRK09606 410 DRTDYMATLSHLRRVVSPLSR 430
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-55 6.87e-15

RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 68.95  E-value: 6.87e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 530748596    1 FGKKRLDLAGPLMAQVFRLKFQQLVKEMKQYLHRCVETGREFNITLAVKTNIITS 55
Cdd:pfam04563 342 LGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 81-114 5.40e-09

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: 48.68  E-value: 5.40e-09
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 530748596   81 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQL 114
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDL 37
 
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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