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Conserved domains on  [gi|1063742909|ref|NP_001332450|]
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RNA polymerase II, Rpb4, core protein [Arabidopsis thaliana]

Protein Classification

Rpb4 family DNA-directed RNA polymerase subunit( domain architecture ID 1266)

Rpb4 family DNA-directed RNA polymerase subunit similar to Arabidopsis thaliana DNA-directed RNA polymerases IV and V subunit 4 that catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

CATH:  1.20.1250.40
EC:  2.7.7.6
Gene Ontology:  GO:0000166|GO:0006352|GO:0030880

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPOL4c super family cl00638
DNA-directed RNA-polymerase II subunit;
4-93 2.95e-26

DNA-directed RNA-polymerase II subunit;


The actual alignment was detected with superfamily member smart00657:

Pssm-ID: 469853  Cd Length: 118  Bit Score: 94.34  E-value: 2.95e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063742909    4 VKANAGALTNFEVLDFLNSRGASKDTTRVIAPIARSEYKVYDYLVETAaSTQTRESINKFADKCKDFKLAKAEILNIINL 83
Cdd:smart00657   2 EFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFA-RFKNREIVRAVRTLLKSKKLHKFEIAQLGNL 80

                           90
                   ....*....|
gi 1063742909   84 RPSSIVELLP 93
Cdd:smart00657  81 RPETAEEAQL 90
 
Name Accession Description Interval E-value
RPOL4c smart00657
DNA-directed RNA-polymerase II subunit;
4-93 2.95e-26

DNA-directed RNA-polymerase II subunit;


Pssm-ID: 128904  Cd Length: 118  Bit Score: 94.34  E-value: 2.95e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063742909    4 VKANAGALTNFEVLDFLNSRGASKDTTRVIAPIARSEYKVYDYLVETAaSTQTRESINKFADKCKDFKLAKAEILNIINL 83
Cdd:smart00657   2 EFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFA-RFKNREIVRAVRTLLKSKKLHKFEIAQLGNL 80

                           90
                   ....*....|
gi 1063742909   84 RPSSIVELLP 93
Cdd:smart00657  81 RPETAEEAQL 90
RNA_pol_Rpb4 pfam03874
RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka ...
 10-91 1.67e-10

RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II.


Pssm-ID: 461080  Cd Length: 115  Bit Score: 53.73  E-value: 1.67e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063742909  10 ALTNFEVLDFLN-----SRGASKDTTRVIAPIARSE--YKVYDYLvETAASTQTRESINKFADKCKDFKLAKAEILNIIN 82
Cdd:pfam03874   1 FLSNSEVLLLLKkeleeRRNWDFKEEKEDVPPNLNTilRKTLDYL-NRFSRLKNEEAFKELVELLNEFELTKAEKLQIVN 79


                  ....*....
gi 1063742909  83 LRPSSIVEL 91
Cdd:pfam03874  80 LLPEDAVEL 88
 
Name Accession Description Interval E-value
RPOL4c smart00657
DNA-directed RNA-polymerase II subunit;
4-93 2.95e-26

DNA-directed RNA-polymerase II subunit;


Pssm-ID: 128904  Cd Length: 118  Bit Score: 94.34  E-value: 2.95e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063742909    4 VKANAGALTNFEVLDFLNSRGASKDTTRVIAPIARSEYKVYDYLVETAaSTQTRESINKFADKCKDFKLAKAEILNIINL 83
Cdd:smart00657   2 EFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFA-RFKNREIVRAVRTLLKSKKLHKFEIAQLGNL 80

                           90
                   ....*....|
gi 1063742909   84 RPSSIVELLP 93
Cdd:smart00657  81 RPETAEEAQL 90
RNA_pol_Rpb4 pfam03874
RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka ...
 10-91 1.67e-10

RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II.


Pssm-ID: 461080  Cd Length: 115  Bit Score: 53.73  E-value: 1.67e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063742909  10 ALTNFEVLDFLN-----SRGASKDTTRVIAPIARSE--YKVYDYLvETAASTQTRESINKFADKCKDFKLAKAEILNIIN 82
Cdd:pfam03874   1 FLSNSEVLLLLKkeleeRRNWDFKEEKEDVPPNLNTilRKTLDYL-NRFSRLKNEEAFKELVELLNEFELTKAEKLQIVN 79


                  ....*....
gi 1063742909  83 LRPSSIVEL 91
Cdd:pfam03874  80 LLPEDAVEL 88
 
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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