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Conserved domains on  [gi|62822328|gb|AAY14877|]
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unknown, partial [Homo sapiens]

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;
24-84 4.19e-18

DNA-directed RNA-polymerase II subunit;


The actual alignment was detected with superfamily member smart00657:

Pssm-ID: 469853  Cd Length: 118  Bit Score: 72.00  E-value: 4.19e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62822328     24 KEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84
Cdd:smart00657   1 PEFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVR 61
 
Name Accession Description Interval E-value
RPOL4c smart00657
DNA-directed RNA-polymerase II subunit;
24-84 4.19e-18

DNA-directed RNA-polymerase II subunit;


Pssm-ID: 128904  Cd Length: 118  Bit Score: 72.00  E-value: 4.19e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62822328     24 KEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84
Cdd:smart00657   1 PEFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVR 61
RPB4 COG5250
RNA polymerase II, fourth largest subunit [Transcription];
14-84 2.03e-07

RNA polymerase II, fourth largest subunit [Transcription];


Pssm-ID: 227575  Cd Length: 138  Bit Score: 45.36  E-value: 2.03e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62822328  14 EEDASQLIFPKEFETAETLLNSEVHMLLE----HRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84
Cdd:COG5250   7 EEDAAQLKLGPEFENEDMLMLSEARYLIEgqleRRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALR 81
RNA_pol_Rpb4 pfam03874
RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka ...
 31-84 6.22e-07

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: 43.33  E-value: 6.22e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62822328    31 TLLNSEVHMLLEHRKQQNESAEDE-------QELSEVFMKTLNYTARFSRFKNRETIASVR 84
Cdd:pfam03874   1 FLSNSEVLLLLKKELEERRNWDFKeekedvpPNLNTILRKTLDYLNRFSRLKNEEAFKELV 61
 
Name Accession Description Interval E-value
RPOL4c smart00657
DNA-directed RNA-polymerase II subunit;
24-84 4.19e-18

DNA-directed RNA-polymerase II subunit;


Pssm-ID: 128904  Cd Length: 118  Bit Score: 72.00  E-value: 4.19e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62822328     24 KEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84
Cdd:smart00657   1 PEFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVR 61
RPB4 COG5250
RNA polymerase II, fourth largest subunit [Transcription];
14-84 2.03e-07

RNA polymerase II, fourth largest subunit [Transcription];


Pssm-ID: 227575  Cd Length: 138  Bit Score: 45.36  E-value: 2.03e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62822328  14 EEDASQLIFPKEFETAETLLNSEVHMLLE----HRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 84
Cdd:COG5250   7 EEDAAQLKLGPEFENEDMLMLSEARYLIEgqleRRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALR 81
RNA_pol_Rpb4 pfam03874
RNA polymerase Rpb4; This family includes the Rpb4 protein. This family also includes C17 (aka ...
 31-84 6.22e-07

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: 43.33  E-value: 6.22e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 62822328    31 TLLNSEVHMLLEHRKQQNESAEDE-------QELSEVFMKTLNYTARFSRFKNRETIASVR 84
Cdd:pfam03874   1 FLSNSEVLLLLKKELEERRNWDFKeekedvpPNLNTILRKTLDYLNRFSRLKNEEAFKELV 61
 
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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